diff --git a/data/community/v-gen-lab/dengue/denv1/CHANGELOG.md b/data/community/v-gen-lab/dengue/denv1/CHANGELOG.md index 4cd318f9..8761db28 100644 --- a/data/community/v-gen-lab/dengue/denv1/CHANGELOG.md +++ b/data/community/v-gen-lab/dengue/denv1/CHANGELOG.md @@ -1,3 +1,7 @@ +## Unreleased + +- Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages. + ## 2024-08-31T20:44:06Z Initial release of a DENV-1 dataset for Lineage classification! diff --git a/data/community/v-gen-lab/dengue/denv1/README.md b/data/community/v-gen-lab/dengue/denv1/README.md index e91d2091..4f1f0e29 100644 --- a/data/community/v-gen-lab/dengue/denv1/README.md +++ b/data/community/v-gen-lab/dengue/denv1/README.md @@ -20,7 +20,7 @@ Broadly speaking, we define major and minor lineages within each genotype. These The source code is available at [V-GEN-Lab/dengue-lineages-workflow](https://github.com/V-GEN-Lab/dengue-lineages-workflow). -For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-workflow/issues). +For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-workflow/issues) ## Maintainers and Contacts: diff --git a/data/community/v-gen-lab/dengue/denv1/tree.json b/data/community/v-gen-lab/dengue/denv1/tree.json index cecc7751..3a998725 100644 --- a/data/community/v-gen-lab/dengue/denv1/tree.json +++ b/data/community/v-gen-lab/dengue/denv1/tree.json @@ -2,7 +2,7 @@ "version": "v2", "meta": { "title": "Dengue Lineages of DENV-1", - "updated": "2024-08-16", + "updated": "2024-09-10", "build_url": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade", "data_provenance": [ { @@ -24,86 +24,8 @@ "color_by": "country" }, "genome_annotations": { - "2K": { - "end": 6826, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 6758, - "strand": "+", - "type": "CDS" - }, - "C": { - "end": 436, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 95, - "strand": "+", - "type": "CDS" - }, - "E": { - "end": 2419, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 935, - "strand": "+", - "type": "CDS" - }, - "M": { - "end": 934, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 437, - "strand": "+", - "type": "CDS" - }, - "NS1": { - "end": 3475, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 2420, - "strand": "+", - "type": "CDS" - }, - "NS2A": { - "end": 4129, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 3476, - "strand": "+", - "type": "CDS" - }, - "NS2B": { - "end": 4519, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 4130, - "strand": "+", - "type": "CDS" - }, - "NS3": { - "end": 6376, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 4520, - "strand": "+", - "type": "CDS" - }, - "NS4A": { - "end": 6757, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 6377, - "strand": "+", - "type": "CDS" - }, - "NS4B": { - "end": 7573, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 6827, - "strand": "+", - "type": "CDS" - }, - "NS5": { - "end": 10270, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", - "start": 7574, - "strand": "+", - "type": "CDS" - }, "nuc": { "end": 10735, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv1.gb", "start": 1, "strand": "+", "type": "source" @@ -136,209 +58,173 @@ { "key": "country", "demes": { - "Brazil": { - "latitude": -10.3333332, - "longitude": -53.1999999 - }, - "Fiji": { - "latitude": -18.1239695, - "longitude": 179.0122737 - }, - "Taiwan": { - "latitude": 23.6978, - "longitude": 120.9605 - }, - "Peru": { - "latitude": -10.0, - "longitude": -75.25 - }, - "Paraguay": { - "latitude": -23.33333, - "longitude": -58.0 - }, - "Malaysia": { - "latitude": 2.3923759, - "longitude": 112.8471939 - }, - "Bolivia": { - "latitude": -17.0, - "longitude": -65.0 - }, - "Australia": { - "latitude": -24.7761085, - "longitude": 134.755 - }, - "Sri Lanka": { - "latitude": 7.75, - "longitude": 80.75 - }, - "Gabon": { - "latitude": -0.8999694, - "longitude": 11.6899699 - }, - "Vietnam": { - "latitude": 16.16667, - "longitude": 107.83333 - }, "Pakistan": { "latitude": 30.0, "longitude": 70.0 }, - "Reunion": { - "latitude": -21.1151, - "longitude": 55.5364 - }, - "Puerto Rico": { - "latitude": 18.2459121, - "longitude": -66.4164147 - }, - "Nigeria": { - "latitude": 10.0, - "longitude": 8.0 - }, - "Cameroon": { - "latitude": 6.0, - "longitude": 12.5 + "Colombia": { + "latitude": 2.893108, + "longitude": -73.7845142 }, - "Democratic Republic of the Congo": { - "latitude": -3.394559, - "longitude": 23.306004 + "Singapore": { + "latitude": 1.344189, + "longitude": 103.867546 }, - "India": { - "latitude": 22.3511148, - "longitude": 78.6677428 + "Costa Rica": { + "latitude": 10.0379, + "longitude": -83.818759 }, - "Singapore": { - "latitude": 1.2904527, - "longitude": 103.852038 + "Papua New Guinea": { + "latitude": -5.6816069, + "longitude": 144.2489081 }, "Myanmar": { - "latitude": 21.0, - "longitude": 96.0 + "latitude": 20.600856, + "longitude": 96.287616 }, - "Jamaica": { - "latitude": 18.16667, - "longitude": -77.25 + "Bolivia": { + "latitude": -17.0568696, + "longitude": -64.9912286 }, "Venezuela": { - "latitude": 8.0, - "longitude": -66.0 + "latitude": 7.838891, + "longitude": -65.916409 }, - "British Virgin Islands": { - "latitude": 18.437033, - "longitude": -64.616732 + "Cambodia": { + "latitude": 13.0, + "longitude": 105.0 }, - "Laos": { - "latitude": 20.0171109, - "longitude": 103.378253 + "Nicaragua": { + "latitude": 12.6090157, + "longitude": -85.2936911 }, - "New Caledonia": { - "latitude": -20.9043, - "longitude": 165.618 + "China": { + "latitude": 33.394333, + "longitude": 104.689839 }, - "Nicaragua": { - "latitude": 13.0, - "longitude": -85.0 + "Sri Lanka": { + "latitude": 7.8731, + "longitude": 80.7718 }, - "Ecuador": { - "latitude": -1.3397667, - "longitude": -79.3666964 + "Democratic Republic of the Congo": { + "latitude": -4.0383, + "longitude": 21.7587 }, - "Saudi Arabia": { - "latitude": 25.0, - "longitude": 45.0 + "Indonesia": { + "latitude": -0.897599, + "longitude": 114.181602 + }, + "Brunei": { + "latitude": 4.5353, + "longitude": 114.7277 }, "South Korea": { - "latitude": 35.3985008, - "longitude": 127.937111 + "latitude": 36.609249, + "longitude": 127.917932 }, - "Costa Rica": { - "latitude": 10.0, - "longitude": -84.0 + "Fiji": { + "latitude": -18.1239696, + "longitude": 179.0122737 }, - "Indonesia": { - "latitude": -5.0, - "longitude": 120.0 + "Thailand": { + "latitude": 14.8971921, + "longitude": 100.83273 }, - "China": { - "latitude": 35.000074, - "longitude": 104.999927 + "Gabon": { + "latitude": -0.8999695, + "longitude": 11.6899699 }, - "Nauru": { - "latitude": -0.517, - "longitude": 166.933 + "Cuba": { + "latitude": 23.0131338, + "longitude": -80.8328748 }, - "Italy": { - "latitude": 42.6384261, - "longitude": 12.674297 + "Brazil": { + "latitude": -10.3333332, + "longitude": -53.1999999 }, - "USA": { - "latitude": 39.7837304, - "longitude": -100.4458824 + "Paraguay": { + "latitude": -23.3165935, + "longitude": -58.1693445 }, - "Angola": { - "latitude": -11.8775767, - "longitude": 17.5691241 + "India": { + "latitude": 21.077353, + "longitude": 78.723951 }, - "Eritrea": { - "latitude": 15.9500319, - "longitude": 37.9999668 + "Cameroon": { + "latitude": 4.6125522, + "longitude": 13.1535811 }, - "Haiti": { - "latitude": 19.1399952, - "longitude": -72.3570971 + "Ecuador": { + "latitude": -1.0541, + "longitude": -78.1489 }, - "Colombia": { - "latitude": 2.893108, - "longitude": -73.7845142 + "Angola": { + "latitude": -11.8775768, + "longitude": 17.5691241 + }, + "Jamaica": { + "latitude": 18.1096, + "longitude": -77.2975 }, "Somalia": { "latitude": 8.3676771, "longitude": 49.083416 }, - "Philippines": { - "latitude": 12.8797, - "longitude": 121.774 + "Puerto Rico": { + "latitude": 18.2247706, + "longitude": -66.4858295 }, - "Mayotte": { - "latitude": -12.821908, - "longitude": 45.143906 + "Mexico": { + "latitude": 19.4325301, + "longitude": -99.1332101 }, "Argentina": { - "latitude": -34.0, - "longitude": -64.0 + "latitude": -37.052315, + "longitude": -64.869142 }, - "Bangladesh": { - "latitude": 24.4768783, - "longitude": 90.2932426 + "Peru": { + "latitude": -9.650468, + "longitude": -75.328211 }, "French Polynesia": { - "latitude": -17.6797, - "longitude": -149.4068 + "latitude": -16.03442485, + "longitude": -146.0490931059517 }, - "Mexico": { - "latitude": 19.4325301, - "longitude": -99.1332101 + "Philippines": { + "latitude": 11.383086, + "longitude": 123.521862 }, - "Cambodia": { - "latitude": 13.0, - "longitude": 105.0 + "Nigeria": { + "latitude": 10.0, + "longitude": 8.0 }, - "Papua New Guinea": { - "latitude": -6.0, - "longitude": 147.0 + "Republic of the Congo": { + "latitude": -0.516362, + "longitude": 15.877811 }, - "Brunei": { - "latitude": 4.5, - "longitude": 114.66667 + "Saudi Arabia": { + "latitude": 25.0, + "longitude": 45.0 }, - "Thailand": { - "latitude": 14.8971921, - "longitude": 100.83273 + "Australia": { + "latitude": -24.7761085, + "longitude": 134.755 }, - "Cuba": { - "latitude": 22.0, - "longitude": -79.5 + "Italy": { + "latitude": 43.382775, + "longitude": 12.183629 + }, + "Malaysia": { + "latitude": 4.264153, + "longitude": 102.222436 + }, + "USA": { + "latitude": 38.916963, + "longitude": -98.891372 + }, + "Laos": { + "latitude": 20.0171109, + "longitude": 103.378253 } } } @@ -364,8 +250,10 @@ "T208C", "T244C", "T274C", + "C328T", "G349A", "A355G", + "G388A", "T397C", "C412T", "C451A", @@ -511,6 +399,7 @@ "T3950C", "C3961T", "A3986G", + "C4024T", "T4030C", "T4058C", "C4061T", @@ -675,6 +564,7 @@ "A8296G", "A8371G", "G8383A", + "C8434T", "A8437G", "T8539C", "C8549T", @@ -742,73 +632,16 @@ "T10215A", "A10240G", "C10243T" - ], - "E": [ - "D37N", - "T88A", - "K203E", - "I293T", - "S339T", - "I436V" - ], - "M": [ - "T59A", - "E72D" - ], - "NS1": [ - "N146D", - "T307I", - "K347R" - ], - "NS2A": [ - "T44I", - "K67R", - "R82K", - "V106I", - "V155I", - "F159L", - "I171V", - "L199F" - ], - "NS2B": [ - "I106V" - ], - "NS3": [ - "A91T", - "A112T", - "V221I", - "V384I" - ], - "NS4A": [ - "I89M", - "A93V" - ], - "NS4B": [ - "A18V", - "A27T" - ], - "NS5": [ - "I34M", - "Y127H", - "K647E", - "T651V", - "F881Y" ] - }, - "labels": { - "aa": "E: D37N, T88A, K203E, I293T, S339T, I436V; M: T59A, E72D; NS1: N146D, T307I, K347R; NS2A: T44I, K67R, R82K, V106I, V155I, F159L, I171V, L199F; NS2B: I106V; NS3: A91T, A112T, V221I, V384I; NS4A: I89M, A93V; NS4B: A18V, A27T; NS5: I34M, Y127H, K647E, T651V, F881Y" } }, "children": [ { "name": "EF457905.1|1972", "node_attrs": { - "div": 0.0164867, - "country": { - "value": "Malaysia" - }, + "div": 0.0165, "clade_membership": { - "value": "Outgroup" + "value": "Outgoup" } }, "branch_attrs": { @@ -816,10 +649,8 @@ "nuc": [ "G109A", "C208T", - "C328T", "G340A", "G370A", - "G388A", "T395A", "A427G", "C448T", @@ -927,7 +758,6 @@ "A4000G", "T4003C", "T4013C", - "C4024T", "T4051C", "T4061C", "C4111T", @@ -1060,6 +890,7 @@ "G8317A", "A8344G", "C8389T", + "T8434C", "T8449C", "C8578T", "T8635C", @@ -1116,65 +947,17 @@ "C10208T", "T10213C", "A10264G" - ], - "C": [ - "S101T" - ], - "E": [ - "I6V", - "K120E", - "E157G", - "V345I" - ], - "M": [ - "S15N", - "T107A" - ], - "NS1": [ - "M103V", - "D146S", - "I224T" - ], - "NS2A": [ - "A38V", - "N51S", - "E115D" - ], - "NS2B": [ - "V120L" - ], - "NS3": [ - "F85L", - "G103R", - "T112M", - "S158G", - "A170T", - "S368A" - ], - "NS4B": [ - "M53L", - "T109I" - ], - "NS5": [ - "M34V", - "Q195R", - "A245T", - "T399I", - "D414N", - "I552V", - "S631N" ] }, "labels": { - "aa": "C: S101T; E: I6V, K120E, E157G, V345I; M: S15N, T107A; NS1: M103V, D146S, I224T; NS2A: A38V, N51S, E115D; NS2B: V120L; NS3: F85L, G103R, T112M, S158G, A170T, S368A; NS4B: M53L, T109I; NS5: M34V, Q195R, A245T, T399I, D414N, I552V, S631N", - "lineage": "Outgroup" + "lineage": "Outgoup" } } }, { "name": "NODE_0000001", "node_attrs": { - "div": 0.0149543, + "div": 0.015, "clade_membership": { "value": "unassigned" } @@ -1186,7 +969,7 @@ { "name": "NODE_0000002", "node_attrs": { - "div": 0.0350091, + "div": 0.035, "clade_membership": { "value": "unassigned" } @@ -1197,6 +980,7 @@ "T171G", "C253T", "G302A", + "T328C", "A363G", "C443T", "G466A", @@ -1204,12 +988,12 @@ "T634C", "G649A", "T784C", + "T817C", "C928A", "G970T", "T1021C", "C1055T", "A1087G", - "C1174T", "C1240T", "T1267A", "A1274C", @@ -1392,56 +1176,14 @@ "T10048C", "G10060A", "C10085T" - ], - "C": [ - "V26G", - "G70S", - "N90S" - ], - "E": [ - "I114L", - "T161I", - "A369T", - "I439V" - ], - "NS1": [ - "S94N", - "V128I", - "N139D", - "V178M" - ], - "NS2A": [ - "I15V", - "A147T", - "H162D" - ], - "NS3": [ - "E43D", - "K255R", - "I474V" - ], - "NS4A": [ - "Q19L", - "R76K" - ], - "NS5": [ - "K364R", - "R378K", - "N585S", - "A616V", - "S629L", - "I669T" ] - }, - "labels": { - "aa": "C: V26G, G70S, N90S; E: I114L, T161I, A369T, I439V; NS1: S94N, V128I, N139D, V178M; NS2A: I15V, A147T, H162D; NS3: E43D, K255R, I474V; NS4A: Q19L, R76K; NS5: K364R, R378K, N585S, A616V, S629L, I669T" } }, "children": [ { "name": "NODE_0000003", "node_attrs": { - "div": 0.036671260000000004, + "div": 0.0367, "clade_membership": { "value": "1VII" } @@ -1449,17 +1191,14 @@ "branch_attrs": { "mutations": { "nuc": [ + "A1549G", "G1759A", "C1895T", "C1950T", - "A2615G", - "A2716G", - "A2722G", "T3982C", "T4096C", "C4195A", "C4648T", - "C5569T", "C5977T", "G6190A", "C6199T", @@ -1467,20 +1206,12 @@ "C7202T", "G8296A", "T8549C", - "A10129G" - ], - "E": [ - "T339I" - ], - "NS1": [ - "I66V" - ], - "NS4A": [ - "R20K" + "T9772C", + "A10129G", + "C10153T" ] }, "labels": { - "aa": "E: T339I; NS1: I66V; NS4A: R20K", "lineage": "1VII" } }, @@ -1488,12 +1219,12 @@ { "name": "JQ922546.1|1971", "node_attrs": { - "div": 0.05604296, - "country": { - "value": "India" - }, + "div": 0.056, "clade_membership": { "value": "1VII" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -1504,11 +1235,11 @@ "A245C", "A269T", "C364T", - "G388A", "A401G", "C595G", "T685C", "G805A", + "C817T", "T895C", "A925G", "C943T", @@ -1516,9 +1247,9 @@ "T1045C", "T1093C", "C1109T", + "C1174T", "G1276C", "C1422T", - "A1549G", "T1606C", "T1640C", "T1729G", @@ -1528,10 +1259,13 @@ "C2197T", "G2239A", "G2545A", + "A2615G", "C2677T", "A2689G", "T2708C", + "A2716G", "G2719A", + "A2722G", "A2749G", "C2812T", "C2821T", @@ -1554,6 +1288,7 @@ "C3736T", "C3868T", "T4008C", + "T4024C", "C4078T", "C4258T", "T4279C", @@ -1576,6 +1311,7 @@ "A5413G", "T5461C", "T5497C", + "C5569T", "T5590C", "T5635C", "C5680T", @@ -1657,7 +1393,6 @@ "T8218C", "C8347T", "T8419C", - "C8434T", "T8488C", "T8580C", "A8620G", @@ -1681,7 +1416,6 @@ "A9625G", "T9642C", "C9694T", - "T9772C", "A9796C", "A9847G", "C9970T", @@ -1689,90 +1423,15 @@ "C10118A", "G10120T", "C10144T", - "C10153T", "T10192C" - ], - "C": [ - "K35R", - "I51L", - "I59L", - "T103A" - ], - "E": [ - "T163I" - ], - "M": [ - "C53W" - ], - "NS1": [ - "M178V", - "I224T" - ], - "NS2A": [ - "L41F", - "I54F", - "F178S" - ], - "NS2B": [ - "T102S" - ], - "NS3": [ - "V40I", - "T115I", - "A127T", - "I213M", - "D437E", - "N498H", - "S559T", - "T584M", - "K585E", - "R589K", - "L592I", - "D598E", - "A599I", - "R600E", - "T601K", - "A615S", - "G617K", - "R619K" - ], - "NS4A": [ - "S3L", - "I7K", - "L19I", - "Q22R", - "L57R", - "A59G", - "L64M", - "I83N" - ], - "NS4B": [ - "A19V", - "A140P", - "G141Q", - "P146Q", - "T147I", - "I154V" - ], - "NS5": [ - "M336T", - "R364K", - "K378N", - "D644N", - "I690T", - "Q741H", - "L849I" ] - }, - "labels": { - "aa": "C: K35R, I51L, I59L, T103A; E: T163I; M: C53W; NS1: M178V, I224T; NS2A: L41F, I54F, F178S; NS2B: T102S; NS3: V40I, T115I, A127T, I213M, D437E, N498H, S559T, T584M, K585E, R589K, L592I, D598E, A599I, R600E, T601K, A615S, G617K, R619K; NS4A: S3L, I7K, L19I, Q22R, L57R, A59G, L64M, I83N; NS4B: A19V, A140P, G141Q, P146Q, T147I, I154V; NS5: M336T, R364K, K378N, D644N, I690T, Q741H, L849I" } } }, { "name": "NODE_0000004", "node_attrs": { - "div": 0.058382460000000004, + "div": 0.0474, "clade_membership": { "value": "1VII" } @@ -1780,161 +1439,73 @@ "branch_attrs": { "mutations": { "nuc": [ - "T253C", "C304T", - "G436T", - "A493G", - "C544T", - "A568G", - "G610A", - "C612T", - "C634T", "T667C", - "C703A", - "C715A", - "C743T", - "C757T", "C835T", - "T850C", "C880T", - "A919G", - "G1009A", "A1039G", "A1042G", "C1069T", - "T1174C", - "C1178T", "T1337C", - "T1360C", "C1363T", - "A1618G", "C1780T", - "G1810A", "C1894T", - "C1971T", - "A2074G", - "T2083C", "G2090A", "G2113A", - "G2131A", "G2179A", - "T2206C", - "G2224A", - "T2254C", - "T2287C", "T2317C", - "G2368T", - "A2416G", - "C2440T", "T2590A", - "C2650T", "T2905C", "C2938T", - "A2968G", - "C3067A", - "C3118T", - "T3171C", "T3259C", "T3274A", - "T3319C", "C3358T", - "C3385T", - "C3388T", "A3394G", - "T3433C", - "T3496C", "C3517T", - "C3595T", + "A3535G", "C3637T", "C3661T", - "T3715C", - "C3757T", "C3761T", - "T3778C", "T3829C", "T3833C", - "G3847A", - "T3889C", "T3908C", - "T3916C", - "T3928C", "A3938G", "A3988G", "C3989T", - "C3997A", "C4085T", "T4099C", "A4129G", "T4144C", "C4216T", - "T4231C", "A4285T", - "T4286C", - "T4336C", "A4351C", - "T4369C", "T4557C", - "T4582A", "C4585T", - "A4624G", - "T4639C", - "C4782T", - "A4839G", "G4855A", "G4858A", - "G4939A", - "A4960G", "T4966C", "C5005T", - "A5110G", - "T5131C", "T5200C", - "G5268C", - "A5338G", - "T5374C", - "A5377G", "G5407A", - "C5419T", - "A5467G", - "C5536T", - "C5563T", - "T5581C", - "A5812G", "C5842T", "G5935A", - "T5962C", "T5965C", "A5995G", "C6043T", - "A6169G", - "A6295G", "T6508C", - "C6529T", "C6547T", "C6707T", - "G6712A", - "A6763G", "T6796C", "A6880G", - "A6890G", - "C6898A", "A6927G", "A6958G", "T7039C", - "T7048C", "A7078G", "C7093T", - "A7099G", "G7120A", "C7129T", - "G7144A", - "T7216C", - "C7246T", "T7267C", "T7282C", - "G7313A", - "A7318G", - "T7376C", "G7507A", "A7582G", "A7597G", @@ -1945,641 +1516,1029 @@ "G7675T", "C7690T", "A7711G", - "T7768C", 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"nuc": [ + "T1804C", + "T2731C", + "C4190T", + "A7615G", + "A8323G" + ] + } + } + }, + { + "name": "NODE_0000015", + "node_attrs": { + "div": 0.0736, + "clade_membership": { + "value": "1VII_A" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "MZ130534.1|2019-05-28", + "node_attrs": { + "div": 0.0758, + "clade_membership": { + "value": "1VII_A" + }, + "country": { + "value": "Democratic Republic of the Congo" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C724T", + "C1109T", + "C1271T", + "C2188T", + "T2476C", + "G4456A", + "G5059A", + "C5305T", + "C5398T", + "T5419C", + "T5443C", + "A6967T", + "T7018C", + "T7177C", + "G8056A", + "G8416A", + "C8578T", + "T8926C", + "C9247T", + "A9324G", + "G9664A" + ] + } + } + }, + { + "name": "MN577472.1|2019-07", + "node_attrs": { + "div": 0.0759, + "clade_membership": { + "value": "1VII_A" + }, + "country": { + "value": "Italy" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C908T", + "T1663A", + "G1732A", + "C2083T", + "C2254T", + "A2740G", + "C2966T", + "A3622G", + "T3754C", + "T3895C", + "T4963C", + "T5536C", + "A5992G", + "G6169A", + "C6518T", + "A6823G", + "T6952C", + "G7225A", + "G7384C", + "A7894G", + "G8056A", + "A8563G", + "T9470C", + "C10055T" + ] + } + } + } + ] + } ] - }, - "labels": { - "aa": "C: G26S; NS3: Y349H; NS5: E281K, G382S, I627V" } - } - } - ] - }, - { - "name": "NODE_0000012", - "node_attrs": { - "div": 0.07188245, - "clade_membership": { - "value": "1VII_B" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1769C", - "T2368C", - "A3730T", - "T5011C", - "A5721G" - ], - "E": [ - "F279L" - ], - "NS3": [ - "N401S" ] - }, - "labels": { - "aa": "E: F279L; NS3: N401S" - } - }, - "children": [ - { - "name": "OQ593392.1|2017-04-13", - "node_attrs": { - "div": 0.07345799, - "country": { - "value": "Cameroon" - }, - "clade_membership": { - "value": "1VII_B" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1069C", - "G1097A", - "C1195T", - "T1873C", - "C2983T", - "T3832C", - "A4028G", - "G4552A", - "T6654C", - "C6874T", - "C7018T", - "T8926C", - "A8980G", - "A9196T", - "C9479T", - "A10030G" - ], - "E": [ - "V55I" - ], - "NS2A": [ - "T185A" - ], - "NS4A": [ - "I93T" - ], - "NS5": [ - "P636S" - ] - }, - "labels": { - "aa": "E: V55I; NS2A: T185A; NS4A: I93T; NS5: P636S" - } - } - }, - { - "name": "LC707382.1|2021-06-30", - "node_attrs": { - "div": 0.07612785, - "country": { - "value": "Gabon" - }, - "clade_membership": { - "value": "1VII_B" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C595T", - "C810T", - "T904C", - "T1345C", - "T1441C", - "C1574T", - "C2083T", - "A2629G", - "T3175C", - "A3288G", - "T3754A", - "T4003C", - "A4113G", - "G4229T", - "C4306T", - "C4621T", - "C4657T", - "G4804A", - "A5116G", - "C5173T", - "G5236A", - "T5386C", - "C5962T", - "G6235A", - "G6310A", - "A6481G", - "G6556A", - "T7015C", - "C7030T", - "G7303A", - "A8047G", - "C8107T", - "C8584T", - "G8664A", - "A8665T", - "C8809T", - "C8916G", - "G8945A", - "A8949G", - "C9463T", - "C9526T", - "A9751G", - "A9886G" - ], - "M": [ - "T125I" - ], - "NS1": [ - "H290R" - ], - "NS2A": [ - "F93L", - "K213R" - ], - "NS2B": [ - "A34S" - ], - "NS3": [ - "M239I" - ], - "NS5": [ - "R364N", - "T448R", - "E458K", - "K459R" - ] - }, - "labels": { - "aa": "M: T125I; NS1: H290R; NS2A: F93L, K213R; NS2B: A34S; NS3: M239I; NS5: R364N, T448R, E458K, K459R" - } - } } ] } @@ -3259,9 +2947,9 @@ ] }, { - "name": "NODE_0000013", + "name": "NODE_0000016", "node_attrs": { - "div": 0.03639706, + "div": 0.0364, "clade_membership": { "value": "unassigned" } @@ -3275,25 +2963,18 @@ "C2237T", "T2697C", "C3884T", - "C4024T", "C7471T", "C7576T", "G9892A", "G10105A" - ], - "NS1": [ - "V93A" ] - }, - "labels": { - "aa": "NS1: V93A" } }, "children": [ { - "name": "NODE_0000014", + "name": "NODE_0000017", "node_attrs": { - "div": 0.047564260000000004, + "div": 0.0476, "clade_membership": { "value": "1III" } @@ -3307,10 +2988,10 @@ "C703T", "C712T", "A789G", - "T817C", "T898C", "A919G", "T1156C", + "C1174T", "G1219A", "A1261G", "C1271T", @@ -3395,7 +3076,6 @@ "A7945G", "C8212T", "A8344G", - "C8434T", "G8653A", "G8666C", "A8713G", @@ -3415,39 +3095,9 @@ "T10213C", "G10261A", "A10264C" - ], - "E": [ - "T272M", - "M297V", - "V380I" - ], - "M": [ - "K118R" - ], - "NS1": [ - "A98T", - "K227R" - ], - "NS2A": [ - "L41F", - "A64V", - "M168I" - ], - "NS3": [ - "V474I" - ], - "NS4B": [ - "A19V", - "V31I" - ], - "NS5": [ - "A365P", - "L629S", - "P636S" ] }, "labels": { - "aa": "E: T272M, M297V, V380I; M: K118R; NS1: A98T, K227R; NS2A: L41F, A64V, M168I; NS3: V474I; NS4B: A19V, V31I; NS5: A365P, L629S, P636S", "lineage": "1III" } }, @@ -3455,7 +3105,7 @@ { "name": "OA01|1973", "node_attrs": { - "div": 0.051157110000000006, + "div": 0.0512, "clade_membership": { "value": "1III" } @@ -3463,6 +3113,7 @@ "branch_attrs": { "mutations": { "nuc": [ + "A388G", "A745G", "C964T", "C1027T", @@ -3502,31 +3153,14 @@ "T9005C", "G9151A", "T9904C" - ], - "E": [ - "E203K" - ], - "NS3": [ - "F85L", - "N105S" - ], - "NS4B": [ - "I90M", - "L113S" - ], - "NS5": [ - "H127Y" ] - }, - "labels": { - "aa": "E: E203K; NS3: F85L, N105S; NS4B: I90M, L113S; NS5: H127Y" } } }, { - "name": "NODE_0000015", + "name": "NODE_0000018", "node_attrs": { - "div": 0.056217510000000005, + "div": 0.0562, "clade_membership": { "value": "1III" } @@ -3536,7 +3170,6 @@ "nuc": [ "A112G", "T253C", - "G388A", "G610A", "C631T", "A700G", @@ -3617,30 +3250,14 @@ "A9631G", "G9715A", "C10208T" - ], - "M": [ - "A143T" - ], - "NS3": [ - "R185K" - ], - "NS5": [ - "V270I", - "T635N" ] - }, - "labels": { - "aa": "M: A143T; NS3: R185K; NS5: V270I, T635N" } }, "children": [ { "name": "JQ922545.1|1982", "node_attrs": { - "div": 0.06284831, - "country": { - "value": "India" - }, + "div": 0.0628, "clade_membership": { "value": "1III" } @@ -3720,77 +3337,14 @@ "G9368A", "T9470A", "T9898C" - ], - "E": [ - "T19P", - "V31L", - "T32S", - "T33N", - "E44D", - "L45F", - "L46F" - ], - "M": [ - "L160T", - "V161G", - "T162A", - "S164I" - ], - "NS1": [ - "R62C" - ], - "NS2B": [ - "E66Q" - ], - "NS3": [ - "N370S", - "N374X", - "L376F", - "N379S", - "G380R", - "K381E", - "R382P", - "L435P" - ], - "NS4A": [ - "G11E", - "F114I" - ], - "NS5": [ - "N285I", - "E286G", - "L380M", - "S385F", - "K388R", - "K389P", - "E396D", - "T399A", - "N405S", - "A406T", - "I408N", - "Q547X", - "T553I", - "D554E", - "I555L", - "E557R", - "Y572F", - "N574I", - "K575S", - "V591X", - "R598K", - "G599R", - "L633M" ] - }, - "labels": { - "aa": "E: T19P, V31L, T32S, T33N, E44D, L45F, L46F; M: L160T, V161G, T162A, S164I; NS1: R62C; NS2B: E66Q; NS3: N370S, N374X, L376F, N379S, G380R, K381E, R382P, L435P; NS4A: G11E, F114I; NS5: N285I, E286G, L380M, S385F, K388R, K389P, E396D, T399A, N405S, A406T, I408N, Q547X, T553I, D554E, I555L, E557R, Y572F, N574I, K575S, V591X, R598K, G599R, L633M" } } }, { - "name": "NODE_0000016", + "name": "NODE_0000019", "node_attrs": { - "div": 0.05651003, + "div": 0.0565, "clade_membership": { "value": "1III" } @@ -3804,20 +3358,14 @@ "C7309T", "C7648T", "C8734T" - ], - "NS1": [ - "I128T" ] - }, - "labels": { - "aa": "NS1: I128T" } }, "children": [ { - "name": "NODE_0000017", + "name": "NODE_0000020", "node_attrs": { - "div": 0.06948573, + "div": 0.0695, "clade_membership": { "value": "1III_B" } @@ -3953,19 +3501,9 @@ "T10066C", "A10135G", "T10207C" - ], - "E": [ - "T339I", - "V358A" - ], - "NS5": [ - "K72R", - "H127Y", - "R429K" ] }, "labels": { - "aa": "E: T339I, V358A; NS5: K72R, H127Y, R429K", "lineage": "1III_B" } }, @@ -3973,12 +3511,12 @@ { "name": "KP406801.1|2004", "node_attrs": { - "div": 0.07284889, - "country": { - "value": "South Korea" - }, + "div": 0.0728, "clade_membership": { "value": "1III_B" + }, + "country": { + "value": "South Korea" } }, "branch_attrs": { @@ -4017,23 +3555,14 @@ "G9781A", "G9886A", "A9991G" - ], - "E": [ - "T265A" - ], - "NS2A": [ - "K218R" ] - }, - "labels": { - "aa": "E: T265A; NS2A: K218R" } } }, { - "name": "NODE_0000018", + "name": "NODE_0000021", "node_attrs": { - "div": 0.07097350999999999, + "div": 0.071, "clade_membership": { "value": "1III_B" } @@ -4060,9 +3589,9 @@ }, "children": [ { - "name": "NODE_0000019", + "name": "NODE_0000022", "node_attrs": { - "div": 0.07417155999999998, + "div": 0.0742, "clade_membership": { "value": "1III_B" } @@ -4103,28 +3632,19 @@ "C9757T", "C9860T", "T10204C" - ], - "NS3": [ - "F355Y" - ], - "NS5": [ - "M491I" ] - }, - "labels": { - "aa": "NS3: F355Y; NS5: M491I" } }, "children": [ { "name": "MK858130.1|2016-10-25", "node_attrs": { - "div": 0.07969663999999999, - "country": { - "value": "India" - }, + "div": 0.0797, "clade_membership": { "value": "1III_B" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -4183,35 +3703,19 @@ "C9716T", "G10058A", "A10177G" - ], - "C": [ - "S90I" - ], - "NS1": [ - "P296A" - ], - "NS2A": [ - "R67K" - ], - "NS5": [ - "K513R", - "V829I" ] - }, - "labels": { - "aa": "C: S90I; NS1: P296A; NS2A: R67K; NS5: K513R, V829I" } } }, { "name": "KJ806950.2|2013", "node_attrs": { - "div": 0.07911029999999998, - "country": { - "value": "Singapore" - }, + "div": 0.0791, "clade_membership": { "value": "1III_B" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -4269,37 +3773,16 @@ "C9606T", "C9619T", "C10216T" - ], - "E": [ - "A358V" - ], - "NS1": [ - "A60V", - "G95R" - ], - "NS2A": [ - "M68I", - "V175I" - ], - "NS3": [ - "V452A" - ], - "NS5": [ - "Y127H", - "T678I" ] - }, - "labels": { - "aa": "E: A358V; NS1: A60V, G95R; NS2A: M68I, V175I; NS3: V452A; NS5: Y127H, T678I" } } } ] }, { - "name": "NODE_0000020", + "name": "NODE_0000023", "node_attrs": { - "div": 0.0794877, + "div": 0.0795, "clade_membership": { "value": "1III_B" } @@ -4392,37 +3875,19 @@ "T9910C", "C10048T", "C10168T" - ], - "C": [ - "A19V" - ], - "E": [ - "T329A" - ], - "NS2B": [ - "S60L" - ], - "NS3": [ - "F85L" - ], - "NS5": [ - "Y127C" ] - }, - "labels": { - "aa": "C: A19V; E: T329A; NS2B: S60L; NS3: F85L; NS5: Y127C" } }, "children": [ { "name": "KX618706.1|2014", "node_attrs": { - "div": 0.08090216, - "country": { - "value": "India" - }, + "div": 0.0809, "clade_membership": { "value": "1III_B" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -4442,37 +3907,19 @@ "T5359C", "G5910A", "T7015C" - ], - "C": [ - "L54V" - ], - "E": [ - "D98G", - "Q248R" - ], - "NS1": [ - "T27A", - "A186V" - ], - "NS3": [ - "A168T", - "R464K" ] - }, - "labels": { - "aa": "C: L54V; E: D98G, Q248R; NS1: T27A, A186V; NS3: A168T, R464K" } } }, { "name": "KX618705.1|2014", "node_attrs": { - "div": 0.08053358999999999, - "country": { - "value": "India" - }, + "div": 0.0805, "clade_membership": { "value": "1III_B" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -4489,19 +3936,7 @@ "G5927C", "C6424T", "T7124A" - ], - "C": [ - "Q28R" - ], - "NS3": [ - "G470R" - ], - "NS4B": [ - "Y100N" ] - }, - "labels": { - "aa": "C: Q28R; NS3: G470R; NS4B: Y100N" } } } @@ -4512,9 +3947,9 @@ ] }, { - "name": "NODE_0000021", + "name": "NODE_0000024", "node_attrs": { - "div": 0.05893029, + "div": 0.0589, "clade_membership": { "value": "1III" } @@ -4544,35 +3979,14 @@ "G9926A", "C9973T", "G10138A" - ], - "E": [ - "M272T" - ], - "NS2A": [ - "V64A" - ], - "NS2B": [ - "K55R" - ], - "NS3": [ - "V452A" - ], - "NS5": [ - "D785N" ] - }, - "labels": { - "aa": "E: M272T; NS2A: V64A; NS2B: K55R; NS3: V452A; NS5: D785N" } }, "children": [ { "name": "OQ061315.1|1997", "node_attrs": { - "div": 0.06694098000000001, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0669, "clade_membership": { "value": "1III" } @@ -4659,41 +4073,14 @@ "G9613A", "C9868T", "C9916T" - ], - "C": [ - "T103I" - ], - "E": [ - "T230A" - ], - "NS1": [ - "Y175S", - "K324R" - ], - "NS3": [ - "E178D", - "V332I", - "T393A" - ], - "NS4A": [ - "M45V" - ], - "NS4B": [ - "V19D" - ], - "NS5": [ - "I541V" ] - }, - "labels": { - "aa": "C: T103I; E: T230A; NS1: Y175S, K324R; NS3: E178D, V332I, T393A; NS4A: M45V; NS4B: V19D; NS5: I541V" } } }, { - "name": "NODE_0000022", + "name": "NODE_0000025", "node_attrs": { - "div": 0.06227354, + "div": 0.0623, "clade_membership": { "value": "1III_A" } @@ -4735,13 +4122,9 @@ "C9952T", "G10006A", "T10066C" - ], - "NS1": [ - "D278N" ] }, "labels": { - "aa": "NS1: D278N", "lineage": "1III_A" } }, @@ -4749,12 +4132,12 @@ { "name": "JQ922548.1|2005", "node_attrs": { - "div": 0.07527584, - "country": { - "value": "India" - }, + "div": 0.0753, "clade_membership": { "value": "1III_A" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -4893,74 +4276,14 @@ "A10169T", "A10234G", "T10249C" - ], - "E": [ - "K36R", - "T170M", - "H244Q", - "I278M", - "V297A", - "S305P", - "V428A" - ], - "NS1": [ - "T128A", - "A213T", - "I224T", - "R294G", - "P296A", - "R299G", - "K324L", - "V346F" - ], - "NS2A": [ - "M68I", - "C201S" - ], - "NS2B": [ - "L22P", - "T83N", - "T94S" - ], - "NS3": [ - "E14V", - "T265N", - "F418S", - "A420T" - ], - "NS4A": [ - "M116K", - "V117E", - "E122D", - "P123A", - "R125G" - ], - "NS4B": [ - "D12N", - "W83R", - "I142L", - "V152A" - ], - "NS5": [ - "G223A", - "S307T", - "K378R", - "V642A", - "W693C", - "E833A", - "T853A", - "I866L" ] - }, - "labels": { - "aa": "E: K36R, T170M, H244Q, I278M, V297A, S305P, V428A; NS1: T128A, A213T, I224T, R294G, P296A, R299G, K324L, V346F; NS2A: M68I, C201S; NS2B: L22P, T83N, T94S; NS3: E14V, T265N, F418S, A420T; NS4A: M116K, V117E, E122D, P123A, R125G; NS4B: D12N, W83R, I142L, V152A; NS5: G223A, S307T, K378R, V642A, W693C, E833A, T853A, I866L" } } }, { - "name": "NODE_0000023", + "name": "NODE_0000026", "node_attrs": { - "div": 0.06477217, + "div": 0.0648, "clade_membership": { "value": "1III_A" } @@ -4988,31 +4311,19 @@ "T9169C", "C10117T", "C10189T" - ], - "C": [ - "L46M" - ], - "M": [ - "T143A" - ], - "NS5": [ - "L123I" ] - }, - "labels": { - "aa": "C: L46M; M: T143A; NS5: L123I" } }, "children": [ { "name": "EU179860.1|2005", "node_attrs": { - "div": 0.07809637, - "country": { - "value": "Brunei" - }, + "div": 0.0781, "clade_membership": { "value": "1III_A" + }, + "country": { + "value": "Brunei" } }, "branch_attrs": { @@ -5174,65 +4485,14 @@ "C9994T", "A10029-", "T10209C" - ], - "E": [ - "Q77P", - "F96L", - "V312M", - "G349-", - "P364S" - ], - "M": [ - "C53-", - "P54-", - "R55-", - "I56-", - "T57-", - "E58-", - "A59-", - "E60-", - "P61X" - ], - "NS1": [ - "G10A", - "R11T", - "E12Q", - "N293I", - "R347K" - ], - "NS2A": [ - "V15I", - "F41L", - "I44T", - "R67K", - "K82R", - "R95K", - "V114A", - "M170I", - "V171I" - ], - "NS2B": [ - "G30W" - ], - "NS5": [ - "A4X", - "Q19L", - "I408X", - "V434L", - "H441P", - "E819X", - "L879S" ] - }, - "labels": { - "aa": "E: Q77P, F96L, V312M, G349-, P364S; M: C53-, P54-, R55-, I56-, T57-, E58-, A59-, E60-, P61X; NS1: G10A, R11T, E12Q, N293I, R347K; NS2A: V15I, F41L, I44T, R67K, K82R, R95K, V114A, M170I, V171I; NS2B: G30W; NS5: A4X, Q19L, I408X, V434L, H441P, E819X, L879S" } } }, { - "name": "NODE_0000024", + "name": "NODE_0000027", "node_attrs": { - "div": 0.06898570000000001, + "div": 0.069, "clade_membership": { "value": "1III_A" } @@ -5292,37 +4552,14 @@ "A9628G", "T9706C", "A10000G" - ], - "E": [ - "F337I" - ], - "NS1": [ - "I162V", - "K324R" - ], - "NS2A": [ - "A64V", - "I168M" - ], - "NS3": [ - "R255K" - ], - "NS4B": [ - "K212R" - ], - "NS5": [ - "K130R" ] - }, - "labels": { - "aa": "E: F337I; NS1: I162V, K324R; NS2A: A64V, I168M; NS3: R255K; NS4B: K212R; NS5: K130R" } }, "children": [ { - "name": "NODE_0000025", + "name": "NODE_0000028", "node_attrs": { - "div": 0.06969095000000002, + "div": 0.0697, "clade_membership": { "value": "1III_A" } @@ -5343,10 +4580,7 @@ { "name": "JF960211.2|2009", "node_attrs": { - "div": 0.07176789000000001, - "country": { - "value": "Singapore" - }, + "div": 0.0718, "clade_membership": { "value": "1III_A" } @@ -5375,23 +4609,14 @@ "C8914T", "C9830T", "C9994T" - ], - "NS1": [ - "G125R" - ], - "NS4B": [ - "V18A" ] - }, - "labels": { - "aa": "NS1: G125R; NS4B: V18A" } } }, { - "name": "NODE_0000026", + "name": "NODE_0000029", "node_attrs": { - "div": 0.07429663000000002, + "div": 0.0743, "clade_membership": { "value": "1III_A" } @@ -5447,10 +4672,7 @@ { "name": "LC436668.1|2017-11", "node_attrs": { - "div": 0.07559194000000001, - "country": { - "value": "Bangladesh" - }, + "div": 0.0756, "clade_membership": { "value": "1III_A" } @@ -5471,27 +4693,14 @@ "C6196T", "A6775G", "A9513G" - ], - "NS2B": [ - "V59I" - ], - "NS3": [ - "F85L", - "M239I" - ], - "NS5": [ - "E647G" ] - }, - "labels": { - "aa": "NS2B: V59I; NS3: F85L, M239I; NS5: E647G" } } }, { - "name": "NODE_0000027", + "name": "NODE_0000030", "node_attrs": { - "div": 0.07977707000000002, + "div": 0.0798, "clade_membership": { "value": "1III_A.1" } @@ -5554,40 +4763,17 @@ "G9923A", "T9973C", "A10258G" - ], - "C": [ - "R10Q" - ], - "NS1": [ - "H77Y" - ], - "NS2A": [ - "F199L" - ], - "NS3": [ - "K185R" - ], - "NS4A": [ - "V2I" - ], - "NS5": [ - "T27I", - "H127Y", - "H435N", - "V642A", - "V784I" ] }, "labels": { - "aa": "C: R10Q; NS1: H77Y; NS2A: F199L; NS3: K185R; NS4A: V2I; NS5: T27I, H127Y, H435N, V642A, V784I", "lineage": "1III_A.1" } }, "children": [ { - "name": "NODE_0000028", + "name": "NODE_0000031", "node_attrs": { - "div": 0.08095722000000002, + "div": 0.081, "clade_membership": { "value": "1III_A.1" } @@ -5607,31 +4793,19 @@ "C8749A", "C9478T", "G9805A" - ], - "E": [ - "L468M" - ], - "NS2A": [ - "N63S" - ], - "NS4A": [ - "P102L" ] - }, - "labels": { - "aa": "E: L468M; NS2A: N63S; NS4A: P102L" } }, "children": [ { "name": "OP898557.1|2022-04", "node_attrs": { - "div": 0.08095965000000002, - "country": { - "value": "Pakistan" - }, + "div": 0.081, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5641,12 +4815,12 @@ { "name": "OP898558.1|2022-10", "node_attrs": { - "div": 0.08095929000000003, - "country": { - "value": "Pakistan" - }, + "div": 0.081, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5656,9 +4830,9 @@ ] }, { - "name": "NODE_0000029", + "name": "NODE_0000032", "node_attrs": { - "div": 0.07977918000000002, + "div": 0.0798, "clade_membership": { "value": "1III_A.1" } @@ -5668,9 +4842,9 @@ }, "children": [ { - "name": "NODE_0000030", + "name": "NODE_0000033", "node_attrs": { - "div": 0.08091598000000001, + "div": 0.0809, "clade_membership": { "value": "1III_A.1" } @@ -5690,28 +4864,19 @@ "C5356T", "C7843T", "T8728C" - ], - "E": [ - "V297M" - ], - "NS3": [ - "K117R" ] - }, - "labels": { - "aa": "E: V297M; NS3: K117R" } }, "children": [ { "name": "OR936755.1|2023-09-04", "node_attrs": { - "div": 0.08139324, - "country": { - "value": "Pakistan" - }, + "div": 0.0814, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5722,25 +4887,19 @@ "C3797T", "A3799G", "T9223C" - ], - "NS2A": [ - "I106V" ] - }, - "labels": { - "aa": "NS2A: I106V" } } }, { "name": "OR936761.1|2023-09-13", "node_attrs": { - "div": 0.08175861000000001, - "country": { - "value": "Pakistan" - }, + "div": 0.0818, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5754,22 +4913,16 @@ "G7771A", "C8677G", "G9532A" - ], - "NS3": [ - "S347L" ] - }, - "labels": { - "aa": "NS3: S347L" } } } ] }, { - "name": "NODE_0000031", + "name": "NODE_0000034", "node_attrs": { - "div": 0.08146799000000002, + "div": 0.0815, "clade_membership": { "value": "1III_A.1" } @@ -5801,12 +4954,12 @@ { "name": "OR936764.1|2023-09-12", "node_attrs": { - "div": 0.08146899000000002, - "country": { - "value": "Pakistan" - }, + "div": 0.0815, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5816,12 +4969,12 @@ { "name": "OR936768.1|2023-09-12", "node_attrs": { - "div": 0.08147055000000002, - "country": { - "value": "Pakistan" - }, + "div": 0.0815, "clade_membership": { "value": "1III_A.1" + }, + "country": { + "value": "Pakistan" } }, "branch_attrs": { @@ -5839,9 +4992,9 @@ ] }, { - "name": "NODE_0000032", + "name": "NODE_0000035", "node_attrs": { - "div": 0.06914893000000001, + "div": 0.0691, "clade_membership": { "value": "1III_A" } @@ -5855,9 +5008,9 @@ }, "children": [ { - "name": "NODE_0000033", + "name": "NODE_0000036", "node_attrs": { - "div": 0.07084266000000002, + "div": 0.0708, "clade_membership": { "value": "1III_A" } @@ -5884,27 +5037,14 @@ "T9498C", "C9712T", "C9799T" - ], - "M": [ - "S15T" - ], - "NS5": [ - "H127Y", - "V642A" ] - }, - "labels": { - "aa": "M: S15T; NS5: H127Y, V642A" } }, "children": [ { "name": "MK858117.2|2016-08-26", "node_attrs": { - "div": 0.07793577000000002, - "country": { - "value": "India" - }, + "div": 0.0779, "clade_membership": { "value": "1III_A" } @@ -5982,35 +5122,14 @@ "C10174T", "G10231A", "T10252C" - ], - "C": [ - "N3D", - "S90N" - ], - "E": [ - "A180T" - ], - "NS1": [ - "M103T", - "A213V", - "T264I" - ], - "NS3": [ - "A310T" - ], - "NS5": [ - "P630S" ] - }, - "labels": { - "aa": "C: N3D, S90N; E: A180T; NS1: M103T, A213V, T264I; NS3: A310T; NS5: P630S" } } }, { - "name": "NODE_0000034", + "name": "NODE_0000037", "node_attrs": { - "div": 0.07613629000000001, + "div": 0.0761, "clade_membership": { "value": "1III_A.2" } @@ -6018,10 +5137,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "A59T", - "G60A", - "T61G", - "T62A", "G340A", "T709C", "G1198A", @@ -6077,29 +5192,17 @@ "A9319G", "C9553T", "A9926G" - ], - "E": [ - "V428M" - ], - "NS3": [ - "Y349H" - ], - "NS5": [ - "I181V", - "E559Q", - "N785D" ] }, "labels": { - "aa": "E: V428M; NS3: Y349H; NS5: I181V, E559Q, N785D", "lineage": "1III_A.2" } }, "children": [ { - "name": "NODE_0000035", + "name": "NODE_0000038", "node_attrs": { - "div": 0.07679174000000001, + "div": 0.0768, "clade_membership": { "value": "1III_A.2" } @@ -6121,12 +5224,12 @@ { "name": "OR259175.1|2021-09", "node_attrs": { - "div": 0.07915226000000002, - "country": { - "value": "Nigeria" - }, + "div": 0.0791, "clade_membership": { "value": "1III_A.2" + }, + "country": { + "value": "Nigeria" } }, "branch_attrs": { @@ -6153,25 +5256,19 @@ "G9202A", "T9265C", "C9334T" - ], - "E": [ - "P169S" ] - }, - "labels": { - "aa": "E: P169S" } } }, { "name": "OR259174.1|2021-07", "node_attrs": { - "div": 0.07867722, - "country": { - "value": "Nigeria" - }, + "div": 0.0787, "clade_membership": { "value": "1III_A.2" + }, + "country": { + "value": "Nigeria" } }, "branch_attrs": { @@ -6193,28 +5290,16 @@ "T8233C", "G8509A", "A9111G" - ], - "C": [ - "A112V" - ], - "E": [ - "K295R" - ], - "NS5": [ - "K513R" ] - }, - "labels": { - "aa": "C: A112V; E: K295R; NS5: K513R" } } } ] }, { - "name": "NODE_0000036", + "name": "NODE_0000039", "node_attrs": { - "div": 0.07727553000000001, + "div": 0.0773, "clade_membership": { "value": "1III_A.2" } @@ -6233,12 +5318,12 @@ { "name": "OR235645.1|2021-06", "node_attrs": { - "div": 0.08086095000000001, - "country": { - "value": "Reunion" - }, + "div": 0.0809, "clade_membership": { "value": "1III_A.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -6269,23 +5354,14 @@ "A8396G", "T9388C", "T9904C" - ], - "E": [ - "A386T" - ], - "NS5": [ - "I275V" ] - }, - "labels": { - "aa": "E: A386T; NS5: I275V" } } }, { - "name": "NODE_0000037", + "name": "NODE_0000040", "node_attrs": { - "div": 0.07755049000000001, + "div": 0.0775, "clade_membership": { "value": "1III_A.2" } @@ -6308,12 +5384,12 @@ { "name": "OR235532.1|2022-04", "node_attrs": { - "div": 0.08021970000000002, - "country": { - "value": "Reunion" - }, + "div": 0.0802, "clade_membership": { "value": "1III_A.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -6344,28 +5420,19 @@ "C8788T", "A10090G", "T10243C" - ], - "M": [ - "M33V" - ], - "NS2A": [ - "F41L" ] - }, - "labels": { - "aa": "M: M33V; NS2A: F41L" } } }, { "name": "OR235733.1|2019-12", "node_attrs": { - "div": 0.07962318000000002, - "country": { - "value": "Mayotte" - }, + "div": 0.0796, "clade_membership": { "value": "1III_A.2" + }, + "country": { + "value": "Mayotte" } }, "branch_attrs": { @@ -6384,13 +5451,7 @@ "A7495G", "C8347T", "G9244A" - ], - "NS3": [ - "K185R" ] - }, - "labels": { - "aa": "NS3: K185R" } } } @@ -6403,9 +5464,9 @@ ] }, { - "name": "NODE_0000038", + "name": "NODE_0000041", "node_attrs": { - "div": 0.07087695000000001, + "div": 0.0709, "clade_membership": { "value": "1III_A" } @@ -6431,25 +5492,14 @@ "C9592T", "A9926G", "C10253T" - ], - "NS3": [ - "E122A" - ], - "NS5": [ - "A245T", - "N785D", - "P894S" ] - }, - "labels": { - "aa": "NS3: E122A; NS5: A245T, N785D, P894S" } }, "children": [ { - "name": "NODE_0000039", + "name": "NODE_0000042", "node_attrs": { - "div": 0.07167049, + "div": 0.0717, "clade_membership": { "value": "1III_A" } @@ -6465,23 +5515,14 @@ "T4061C", "C6553T", "T9898C" - ], - "E": [ - "I461V" ] - }, - "labels": { - "aa": "E: I461V" } }, "children": [ { "name": "MH822959.2|2012", "node_attrs": { - "div": 0.07285054, - "country": { - "value": "India" - }, + "div": 0.0728, "clade_membership": { "value": "1III_A" } @@ -6505,9 +5546,9 @@ } }, { - "name": "NODE_0000040", + "name": "NODE_0000043", "node_attrs": { - "div": 0.07406356, + "div": 0.0741, "clade_membership": { "value": "1III_A.4" } @@ -6539,13 +5580,9 @@ "G9298A", "T9358A", "C9874T" - ], - "NS3": [ - "K117M" ] }, "labels": { - "aa": "NS3: K117M", "lineage": "1III_A.4" } }, @@ -6553,12 +5590,12 @@ { "name": "ON123661.1|2018", "node_attrs": { - "div": 0.0784209, - "country": { - "value": "India" - }, + "div": 0.0784, "clade_membership": { "value": "1III_A.4" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -6608,34 +5645,14 @@ "A9424G", "T9952C", "C10084T" - ], - "E": [ - "N37D", - "V432L" - ], - "NS2A": [ - "F93L", - "T147I" - ], - "NS3": [ - "G144R" - ], - "NS4A": [ - "K76R" - ], - "NS5": [ - "F383L" ] - }, - "labels": { - "aa": "E: N37D, V432L; NS2A: F93L, T147I; NS3: G144R; NS4A: K76R; NS5: F383L" } } }, { - "name": "NODE_0000041", + "name": "NODE_0000044", "node_attrs": { - "div": 0.07668149, + "div": 0.0767, "clade_membership": { "value": "1III_A.4" } @@ -6662,23 +5679,14 @@ "A8845G", "T10012C", "A10105G" - ], - "M": [ - "V31I" - ], - "NS3": [ - "S88L" ] - }, - "labels": { - "aa": "M: V31I; NS3: S88L" } }, "children": [ { - "name": "NODE_0000042", + "name": "NODE_0000045", "node_attrs": { - "div": 0.07796464, + "div": 0.078, "clade_membership": { "value": "1III_A.4" } @@ -6698,25 +5706,19 @@ "G7507A", "C7882T", "A8719T" - ], - "NS4A": [ - "M97T" ] - }, - "labels": { - "aa": "NS4A: M97T" } }, "children": [ { "name": "OR394016.1|2019-10-30", "node_attrs": { - "div": 0.07953801, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0795, "clade_membership": { "value": "1III_A.4" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -6736,33 +5738,19 @@ "C8722T", "C9232T", "A10273G" - ], - "C": [ - "N93S" - ], - "E": [ - "S474P", - "V491A" - ], - "NS5": [ - "E374K", - "G382D" ] - }, - "labels": { - "aa": "C: N93S; E: S474P, V491A; NS5: E374K, G382D" } } }, { "name": "PP234949.1|2019-07-01", "node_attrs": { - "div": 0.07975736, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0798, "clade_membership": { "value": "1III_A.4" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -6785,23 +5773,16 @@ "C9133T", "T10207C", "C10216T" - ], - "NS2A": [ - "I44V", - "I54T" ] - }, - "labels": { - "aa": "NS2A: I44V, I54T" } } } ] }, { - "name": "NODE_0000043", + "name": "NODE_0000046", "node_attrs": { - "div": 0.078763, + "div": 0.0788, "clade_membership": { "value": "1III_A.4" } @@ -6825,28 +5806,19 @@ "T8212C", "G8772A", "G9958A" - ], - "E": [ - "A382V" - ], - "NS5": [ - "R400K" ] - }, - "labels": { - "aa": "E: A382V; NS5: R400K" } }, "children": [ { "name": "OR394051.1|2020-01-06", "node_attrs": { - "div": 0.07994556, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0799, "clade_membership": { "value": "1III_A.4" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -6862,25 +5834,19 @@ "C6082T", "C7246T", "A10273G" - ], - "NS2A": [ - "F93L" ] - }, - "labels": { - "aa": "NS2A: F93L" } } }, { "name": "ON680908.1|2020-08-24", "node_attrs": { - "div": 0.08083117, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0808, "clade_membership": { "value": "1III_A.4" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -6909,22 +5875,7 @@ "A9326G", "T9388C", "T9479C" - ], - "NS1": [ - "D92N" - ], - "NS3": [ - "Q172L", - "P356L" - ], - "NS5": [ - "V402I", - "S585G", - "S636P" ] - }, - "labels": { - "aa": "NS1: D92N; NS3: Q172L, P356L; NS5: V402I, S585G, S636P" } } } @@ -6937,9 +5888,9 @@ ] }, { - "name": "NODE_0000044", + "name": "NODE_0000047", "node_attrs": { - "div": 0.07361481, + "div": 0.0736, "clade_membership": { "value": "1III_A.3" } @@ -6977,22 +5928,9 @@ "A9331G", "A9661T", "A10190G" - ], - "NS1": [ - "D127E" - ], - "NS3": [ - "T91M" - ], - "NS4A": [ - "R20K" - ], - "NS5": [ - "I873V" ] }, "labels": { - "aa": "NS1: D127E; NS3: T91M; NS4A: R20K; NS5: I873V", "lineage": "1III_A.3" } }, @@ -7000,12 +5938,12 @@ { "name": "MF033212.1|2013-12", "node_attrs": { - "div": 0.07509399, - "country": { - "value": "Singapore" - }, + "div": 0.0751, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -7026,29 +5964,14 @@ "C8299T", "T9265C", "A9537G" - ], - "E": [ - "T430A" - ], - "NS2A": [ - "I174V" - ], - "NS4B": [ - "A26S" - ], - "NS5": [ - "K655R" ] - }, - "labels": { - "aa": "E: T430A; NS2A: I174V; NS4B: A26S; NS5: K655R" } } }, { - "name": "NODE_0000045", + "name": "NODE_0000048", "node_attrs": { - "div": 0.07370487, + "div": 0.0737, "clade_membership": { "value": "1III_A.3" } @@ -7064,12 +5987,12 @@ { "name": "MH891771.1|2017-10-22", "node_attrs": { - "div": 0.07853516, - "country": { - "value": "India" - }, + "div": 0.0785, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -7124,26 +6047,14 @@ "T9766C", "C9943T", "C10063T" - ], - "M": [ - "T125I" - ], - "NS3": [ - "N467T" - ], - "NS5": [ - "S585N" ] - }, - "labels": { - "aa": "M: T125I; NS3: N467T; NS5: S585N" } } }, { - "name": "NODE_0000046", + "name": "NODE_0000049", "node_attrs": { - "div": 0.07464595, + "div": 0.0746, "clade_membership": { "value": "1III_A.3" } @@ -7163,31 +6074,19 @@ "C7977T", "C8821T", "C9934G" - ], - "E": [ - "V297M" - ], - "NS3": [ - "R215G" - ], - "NS5": [ - "T135I" ] - }, - "labels": { - "aa": "E: V297M; NS3: R215G; NS5: T135I" } }, "children": [ { "name": "ON123650.1|2020", "node_attrs": { - "div": 0.07987235000000001, - "country": { - "value": "India" - }, + "div": 0.0799, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -7246,40 +6145,14 @@ "T9420C", "A9685G", "T10054C" - ], - "E": [ - "L114I", - "E203K", - "I337F" - ], - "M": [ - "A59V" - ], - "NS2A": [ - "K82R", - "I106V" - ], - "NS3": [ - "E394D" - ], - "NS4A": [ - "L19Q" - ], - "NS5": [ - "I181V", - "K422P", - "V616A" ] - }, - "labels": { - "aa": "E: L114I, E203K, I337F; M: A59V; NS2A: K82R, I106V; NS3: E394D; NS4A: L19Q; NS5: I181V, K422P, V616A" } } }, { - "name": "NODE_0000047", + "name": "NODE_0000050", "node_attrs": { - "div": 0.07474131, + "div": 0.0747, "clade_membership": { "value": "1III_A.3" } @@ -7297,12 +6170,12 @@ { "name": "MK588397.1|2017-04-22", "node_attrs": { - "div": 0.08072363, - "country": { - "value": "India" - }, + "div": 0.0807, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -7368,59 +6241,14 @@ "T9403C", "T9470C", "G9503A" - ], - "C": [ - "L38X", - "S39X", - "F50S", - "A67S", - "S71L", - "L106F" - ], - "E": [ - "P169H", - "T182P", - "L207F", - "T346I", - "S452X", - "A481V" - ], - "M": [ - "L23P", - "V31A", - "S113P" - ], - "NS1": [ - "A49V", - "M184S", - "T222I", - "I246M" - ], - "NS2A": [ - "V60I" - ], - "NS3": [ - "T111I", - "T225I", - "P320Q" - ], - "NS5": [ - "K46E", - "V132A", - "V220L", - "L433P", - "D644N" ] - }, - "labels": { - "aa": "C: L38X, S39X, F50S, A67S, S71L, L106F; E: P169H, T182P, L207F, T346I, S452X, A481V; M: L23P, V31A, S113P; NS1: A49V, M184S, T222I, I246M; NS2A: V60I; NS3: T111I, T225I, P320Q; NS5: K46E, V132A, V220L, L433P, D644N" } } }, { - "name": "NODE_0000048", + "name": "NODE_0000051", "node_attrs": { - "div": 0.08682011, + "div": 0.0868, "clade_membership": { "value": "1III_A.3" } @@ -7514,47 +6342,19 @@ "A10006G", "A10135G", "G10201A" - ], - "C": [ - "R10Q" - ], - "E": [ - "I161T", - "E203K", - "T293I", - "I337F", - "T339S", - "T369A" - ], - "NS3": [ - "M91I", - "T112M" - ], - "NS4A": [ - "V93A", - "M97I" - ], - "NS4B": [ - "H17Q" - ], - "NS5": [ - "P365A" ] - }, - "labels": { - "aa": "C: R10Q; E: I161T, E203K, T293I, I337F, T339S, T369A; NS3: M91I, T112M; NS4A: V93A, M97I; NS4B: H17Q; NS5: P365A" } }, "children": [ { "name": "ON109597.1|2021", "node_attrs": { - "div": 0.09240098000000001, - "country": { - "value": "India" - }, + "div": 0.0924, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -7608,32 +6408,19 @@ "A8719T", "T8734C", "C9884T" - ], - "NS1": [ - "N278D" - ], - "NS3": [ - "D392E" - ], - "NS5": [ - "R364K", - "K378R" ] - }, - "labels": { - "aa": "NS1: N278D; NS3: D392E; NS5: R364K, K378R" } } }, { "name": "ON123656.1|2019", "node_attrs": { - "div": 0.09619074000000001, - "country": { - "value": "India" - }, + "div": 0.0962, "clade_membership": { "value": "1III_A.3" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -7737,31 +6524,7 @@ "G8179A", "T8605C", "G9934C" - ], - "NS1": [ - "R347K" - ], - "NS2A": [ - "F41L", - "I44T", - "V64A", - "R67K", - "K82R", - "I106V", - "T147A", - "I155V", - "L159F", - "F199L" - ], - "NS3": [ - "N90S" - ], - "NS4B": [ - "A223T" ] - }, - "labels": { - "aa": "NS1: R347K; NS2A: F41L, I44T, V64A, R67K, K82R, I106V, T147A, I155V, L159F, F199L; NS3: N90S; NS4B: A223T" } } } @@ -7794,9 +6557,9 @@ ] }, { - "name": "NODE_0000049", + "name": "NODE_0000052", "node_attrs": { - "div": 0.038730940000000005, + "div": 0.0387, "clade_membership": { "value": "1V" } @@ -7819,20 +6582,14 @@ "T7198A", "A7213G", "T7291C", + "T8434C", "C9172T", "C9550T", "T9919C", "T10192C" - ], - "NS4A": [ - "V93A" - ], - "NS4B": [ - "H34R" ] }, "labels": { - "aa": "NS4A: V93A; NS4B: H34R", "lineage": "1V" } }, @@ -7840,24 +6597,21 @@ { "name": "KF289073.1|1956", "node_attrs": { - "div": 0.046357350000000005, - "country": { - "value": "India" - }, + "div": 0.0464, "clade_membership": { "value": "1V" + }, + "country": { + "value": "India" } }, "branch_attrs": { "mutations": { "nuc": [ - "G388A", "C410T", - "T817C", "T1055C", "T1070C", "C1135A", - "T1174C", "G1318A", "T1360C", "G1387A", @@ -7932,41 +6686,14 @@ "C9890T", "A10000G", "G10006A" - ], - "C": [ - "L106F" - ], - "E": [ - "N67K", - "F337I", - "V380I", - "I461V" - ], - "NS1": [ - "Q147H" - ], - "NS3": [ - "T91M", - "E515K" - ], - "NS4A": [ - "N23K" - ], - "NS5": [ - "A245T", - "A535T", - "V734M" ] - }, - "labels": { - "aa": "C: L106F; E: N67K, F337I, V380I, I461V; NS1: Q147H; NS3: T91M, E515K; NS4A: N23K; NS5: A245T, A535T, V734M" } } }, { - "name": "NODE_0000050", + "name": "NODE_0000053", "node_attrs": { - "div": 0.044806030000000004, + "div": 0.0448, "clade_membership": { "value": "1V" } @@ -7975,10 +6702,13 @@ "mutations": { "nuc": [ "C208T", + "A388G", "C532T", + "C817T", "C883T", "T1000C", "C1007T", + "C1174T", "T1249C", "G1528A", "C1597T", @@ -8030,27 +6760,14 @@ "C9579T", "C9784T", "A10135G" - ], - "NS2B": [ - "A70T" - ], - "NS5": [ - "V651A", - "T669I" ] - }, - "labels": { - "aa": "NS2B: A70T; NS5: V651A, T669I" } }, "children": [ { "name": "JQ922544.1|1963", "node_attrs": { - "div": 0.049667430000000005, - "country": { - "value": "India" - }, + "div": 0.0497, "clade_membership": { "value": "1V" } @@ -8112,57 +6829,14 @@ "T9766C", "G9767A", "G10014A" - ], - "C": [ - "Q4H", - "K45T" - ], - "E": [ - "D10E", - "V31L", - "T32H", - "K36Q", - "E157T", - "T369A", - "T454I" - ], - "M": [ - "S113C", - "T125I" - ], - "NS1": [ - "D288E" - ], - "NS2B": [ - "A40S", - "C41F", - "Y42F" - ], - "NS3": [ - "Y475N", - "E515K", - "I520V", - "G587R" - ], - "NS4B": [ - "K87L" - ], - "NS5": [ - "T27I", - "I408M", - "E732K", - "R814K" ] - }, - "labels": { - "aa": "C: Q4H, K45T; E: D10E, V31L, T32H, K36Q, E157T, T369A, T454I; M: S113C, T125I; NS1: D288E; NS2B: A40S, C41F, Y42F; NS3: Y475N, E515K, I520V, G587R; NS4B: K87L; NS5: T27I, I408M, E732K, R814K" } } }, { - "name": "NODE_0000051", + "name": "NODE_0000054", "node_attrs": { - "div": 0.049936860000000007, + "div": 0.0499, "clade_membership": { "value": "1V" } @@ -8219,33 +6893,14 @@ "T10085C", "A10090G", "A10129G" - ], - "NS1": [ - "K324R" - ], - "NS2A": [ - "L12I", - "S142P" - ], - "NS3": [ - "R185K" - ], - "NS4B": [ - "I48V" - ], - "NS5": [ - "D834E" ] - }, - "labels": { - "aa": "NS1: K324R; NS2A: L12I, S142P; NS3: R185K; NS4B: I48V; NS5: D834E" } }, "children": [ { - "name": "NODE_0000052", + "name": "NODE_0000055", "node_attrs": { - "div": 0.056213490000000005, + "div": 0.0562, "clade_membership": { "value": "1V_A" } @@ -8315,37 +6970,17 @@ "C9619T", "T9706C", "G9727A" - ], - "E": [ - "V436I" - ], - "M": [ - "A29V" - ], - "NS1": [ - "H77Y" - ], - "NS2A": [ - "M18L", - "V171A" - ], - "NS2B": [ - "L4I" - ], - "NS5": [ - "E640K" ] }, "labels": { - "aa": "E: V436I; M: A29V; NS1: H77Y; NS2A: M18L, V171A; NS2B: L4I; NS5: E640K", "lineage": "1V_A" } }, "children": [ { - "name": "NODE_0000053", + "name": "NODE_0000056", "node_attrs": { - "div": 0.06491459000000001, + "div": 0.0649, "clade_membership": { "value": "1V_A" } @@ -8437,41 +7072,19 @@ "C10126T", "C10153T", "C10216T" - ], - "E": [ - "S338L", - "V428L" - ], - "NS1": [ - "N293Y" - ], - "NS2A": [ - "K156R" - ], - "NS3": [ - "V474I" - ], - "NS4B": [ - "A153T" - ], - "NS5": [ - "L629S" ] - }, - "labels": { - "aa": "E: S338L, V428L; NS1: N293Y; NS2A: K156R; NS3: V474I; NS4B: A153T; NS5: L629S" } }, "children": [ { "name": "GQ868601.1|1985", "node_attrs": { - "div": 0.06572414000000001, - "country": { - "value": "British Virgin Islands" - }, + "div": 0.0657, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "British Virgin Islands" } }, "branch_attrs": { @@ -8488,29 +7101,14 @@ "T6842C", "T9520A", "C9949T" - ], - "C": [ - "M95R" - ], - "E": [ - "K124R" - ], - "NS2A": [ - "K30R" - ], - "NS5": [ - "H649Q" ] - }, - "labels": { - "aa": "C: M95R; E: K124R; NS2A: K30R; NS5: H649Q" } } }, { - "name": "NODE_0000054", + "name": "NODE_0000057", "node_attrs": { - "div": 0.07322256, + "div": 0.0732, "clade_membership": { "value": "1V_A" } @@ -8582,44 +7180,19 @@ "G10135A", "C10156T", "A10165G" - ], - "C": [ - "M95I" - ], - "NS1": [ - "Y175H", - "I242V" - ], - "NS2A": [ - "I106V", - "T158S" - ], - "NS3": [ - "S171T", - "D437E" - ], - "NS4B": [ - "A20V" - ], - "NS5": [ - "R30K", - "R641K" ] - }, - "labels": { - "aa": "C: M95I; NS1: Y175H, I242V; NS2A: I106V, T158S; NS3: S171T, D437E; NS4B: A20V; NS5: R30K, R641K" } }, "children": [ { "name": "OQ605987.1|2022-03-31", "node_attrs": { - "div": 0.08776496, - "country": { - "value": "Brazil" - }, + "div": 0.0878, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -8771,68 +7344,19 @@ "A9790G", "A9880G", "T9910C" - ], - "C": [ - "A114T" - ], - "E": [ - "A180T", - "E342D", - "V365I" - ], - "M": [ - "L138F" - ], - "NS1": [ - "Y77H", - "A93V", - "I246T" - ], - "NS2A": [ - "V5M", - "L41F", - "S160T" - ], - "NS2B": [ - "I39L", - "Y42S" - ], - "NS3": [ - "D43E", - "G44D", - "V45Y", - "F46V", - "H47V", - "M49T", - "W50*", - "V52F", - "T53R", - "R54K", - "V332A" - ], - "NS4A": [ - "M97V" - ], - "NS5": [ - "Q602H", - "V603K", - "G604P" ] - }, - "labels": { - "aa": "C: A114T; E: A180T, E342D, V365I; M: L138F; NS1: Y77H, A93V, I246T; NS2A: V5M, L41F, S160T; NS2B: I39L, Y42S; NS3: D43E, G44D, V45Y, F46V, H47V, M49T, W50*, V52F, T53R, R54K, V332A; NS4A: M97V; NS5: Q602H, V603K, G604P" } } }, { "name": "MT929552.1|2018-04-12", "node_attrs": { - "div": 0.08370876000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0837, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -8929,46 +7453,7 @@ "G9599T", "C9934T", "G10138A" - ], - "C": [ - "R82Q" - ], - "E": [ - "T51M", - "F392L" - ], - "NS1": [ - "T131A", - "Y293N" - ], - "NS2A": [ - "V60A" - ], - "NS3": [ - "I77F", - "P320Q", - "K590R", - "K591R", - "R595H", - "W596I", - "L597Q" - ], - "NS4A": [ - "M45I", - "M89T" - ], - "NS5": [ - "S39A", - "A370V", - "I473R", - "W474C", - "Y475C", - "M476L", - "A676S" ] - }, - "labels": { - "aa": "C: R82Q; E: T51M, F392L; NS1: T131A, Y293N; NS2A: V60A; NS3: I77F, P320Q, K590R, K591R, R595H, W596I, L597Q; NS4A: M45I, M89T; NS5: S39A, A370V, I473R, W474C, Y475C, M476L, A676S" } } } @@ -8977,9 +7462,9 @@ ] }, { - "name": "NODE_0000055", + "name": "NODE_0000058", "node_attrs": { - "div": 0.05984632000000001, + "div": 0.0598, "clade_membership": { "value": "1V_A" } @@ -9019,28 +7504,19 @@ "G9268A", "A10177G", "A10264G" - ], - "NS3": [ - "R338K" - ], - "NS5": [ - "T135I" ] - }, - "labels": { - "aa": "NS3: R338K; NS5: T135I" } }, "children": [ { "name": "DQ285559.1|2004", "node_attrs": { - "div": 0.07199152, - "country": { - "value": "Reunion" - }, + "div": 0.072, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -9171,42 +7647,14 @@ "A10220G", "A10225G", "A10273G" - ], - "C": [ - "A114T" - ], - "E": [ - "T176I", - "E203G", - "I436T" - ], - "NS1": [ - "R41K" - ], - "NS2A": [ - "R26K", - "I54T", - "M133I", - "A171T" - ], - "NS5": [ - "R173K", - "S566A", - "V616A", - "H649Y", - "T675K", - "T883A" ] - }, - "labels": { - "aa": "C: A114T; E: T176I, E203G, I436T; NS1: R41K; NS2A: R26K, I54T, M133I, A171T; NS5: R173K, S566A, V616A, H649Y, T675K, T883A" } } }, { - "name": "NODE_0000056", + "name": "NODE_0000059", "node_attrs": { - "div": 0.06233707000000001, + "div": 0.0623, "clade_membership": { "value": "1V_A" } @@ -9239,30 +7687,19 @@ "A8803T", "C9463T", "C9526T" - ], - "E": [ - "I129V", - "T339I", - "A481T" - ], - "M": [ - "K122R" ] - }, - "labels": { - "aa": "E: I129V, T339I, A481T; M: K122R" } }, "children": [ { "name": "JN903578.1|2007-07-26", "node_attrs": { - "div": 0.07641067000000001, - "country": { - "value": "India" - }, + "div": 0.0764, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -9408,55 +7845,19 @@ "T10066C", "C10150T", "T10223A" - ], - "E": [ - "S338L", - "W391R" - ], - "NS1": [ - "Y77H", - "V220I", - "Y256H", - "L279V" - ], - "NS2A": [ - "I12L", - "L18M", - "L41F", - "A64V", - "V114A", - "P142S", - "M168I", - "A169T", - "A171I" - ], - "NS2B": [ - "I4L" - ], - "NS3": [ - "E484G" - ], - "NS4B": [ - "G247S" - ], - "NS5": [ - "S884T" ] - }, - "labels": { - "aa": "E: S338L, W391R; NS1: Y77H, V220I, Y256H, L279V; NS2A: I12L, L18M, L41F, A64V, V114A, P142S, M168I, A169T, A171I; NS2B: I4L; NS3: E484G; NS4B: G247S; NS5: S884T" } } }, { "name": "EU081258.1|2005", "node_attrs": { - "div": 0.06985941000000001, - "country": { - "value": "Singapore" - }, + "div": 0.0699, "clade_membership": { "value": "1V_A" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -9538,24 +7939,7 @@ "A10165G", "C10237T", "C10255T" - ], - "E": [ - "F96L", - "L475F" - ], - "NS1": [ - "M84I", - "K101R" - ], - "NS2A": [ - "F87L" - ], - "NS5": [ - "N26D" ] - }, - "labels": { - "aa": "E: F96L, L475F; NS1: M84I, K101R; NS2A: F87L; NS5: N26D" } } } @@ -9566,9 +7950,9 @@ ] }, { - "name": "NODE_0000057", + "name": "NODE_0000060", "node_attrs": { - "div": 0.05426219000000001, + "div": 0.0543, "clade_membership": { "value": "1V" } @@ -9614,27 +7998,14 @@ "C9606T", "C9949A", "G9958A" - ], - "NS2A": [ - "D139E" - ], - "NS2B": [ - "V11I" - ], - "NS5": [ - "S585N", - "T678I" ] - }, - "labels": { - "aa": "NS2A: D139E; NS2B: V11I; NS5: S585N, T678I" } }, "children": [ { - "name": "NODE_0000058", + "name": "NODE_0000061", "node_attrs": { - "div": 0.05434735000000001, + "div": 0.0543, "clade_membership": { "value": "1V" } @@ -9652,7 +8023,7 @@ { "name": "OA04|1981", "node_attrs": { - "div": 0.05879805000000001, + "div": 0.0588, "clade_membership": { "value": "1V" } @@ -9707,37 +8078,14 @@ "C9754T", "C10192T", "A10202G" - ], - "NS1": [ - "I57V", - "D139N", - "I251T" - ], - "NS2A": [ - "I44V", - "N63S" - ], - "NS2B": [ - "A56V", - "V59A", - "V106I" - ], - "NS5": [ - "R247K", - "A583G", - "E647K", - "N877D" ] - }, - "labels": { - "aa": "NS1: I57V, D139N, I251T; NS2A: I44V, N63S; NS2B: A56V, V59A, V106I; NS5: R247K, A583G, E647K, N877D" } } }, { - "name": "NODE_0000059", + "name": "NODE_0000062", "node_attrs": { - "div": 0.06143550000000001, + "div": 0.0614, "clade_membership": { "value": "1V_J" } @@ -9815,28 +8163,9 @@ "T10066C", "C10144T", "C10153T" - ], - "E": [ - "N37D", - "T339A" - ], - "M": [ - "V31I" - ], - "NS1": [ - "K112R" - ], - "NS3": [ - "A170T" - ], - "NS5": [ - "L503F", - "A651T", - "I669V" ] }, "labels": { - "aa": "E: N37D, T339A; M: V31I; NS1: K112R; NS3: A170T; NS5: L503F, A651T, I669V", "lineage": "1V_J" } }, @@ -9844,12 +8173,12 @@ { "name": "FJ410184.1|1993", "node_attrs": { - "div": 0.06827720000000001, - "country": { - "value": "USA" - }, + "div": 0.0683, "clade_membership": { "value": "1V_J" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -9923,32 +8252,14 @@ "C10063T", "G10090A", "A10165G" - ], - "NS1": [ - "K341R", - "R347K" - ], - "NS2A": [ - "S2L", - "F199L" - ], - "NS3": [ - "S88A", - "P175S" - ], - "NS4B": [ - "H17Y" ] - }, - "labels": { - "aa": "NS1: K341R, R347K; NS2A: S2L, F199L; NS3: S88A, P175S; NS4B: H17Y" } } }, { - "name": "NODE_0000060", + "name": "NODE_0000063", "node_attrs": { - "div": 0.06358253000000001, + "div": 0.0636, "clade_membership": { "value": "1V_J" } @@ -9979,31 +8290,19 @@ "C9592T", "C9973T", "C10085T" - ], - "NS2A": [ - "K166R" - ], - "NS4A": [ - "S99N" - ], - "NS5": [ - "H127Y" ] - }, - "labels": { - "aa": "NS2A: K166R; NS4A: S99N; NS5: H127Y" } }, "children": [ { "name": "FJ205875.1|1995", "node_attrs": { - "div": 0.07087821000000001, - "country": { - "value": "USA" - }, + "div": 0.0709, "clade_membership": { "value": "1V_J" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -10085,37 +8384,14 @@ "A10234G", "C10237T", "T10243C" - ], - "E": [ - "V55I", - "A339T" - ], - "NS1": [ - "R112K" - ], - "NS2A": [ - "R29K" - ], - "NS3": [ - "N90S" - ], - "NS5": [ - "F65L", - "A245V", - "E509D", - "V616A", - "I678T" ] - }, - "labels": { - "aa": "E: V55I, A339T; NS1: R112K; NS2A: R29K; NS3: N90S; NS5: F65L, A245V, E509D, V616A, I678T" } } }, { - "name": "NODE_0000061", + "name": "NODE_0000064", "node_attrs": { - "div": 0.06663906000000001, + "div": 0.0666, "clade_membership": { "value": "1V_J" } @@ -10153,32 +8429,19 @@ "T9145C", "G9886A", "T10078C" - ], - "C": [ - "R100K" - ], - "E": [ - "A88S", - "T442A" - ], - "M": [ - "I136T" ] - }, - "labels": { - "aa": "C: R100K; E: A88S, T442A; M: I136T" } }, "children": [ { "name": "EU482567.1|1998", "node_attrs": { - "div": 0.07371759000000001, - "country": { - "value": "USA" - }, + "div": 0.0737, "clade_membership": { "value": "1V_J" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -10252,38 +8515,14 @@ "T9583C", "C9586G", "G10135T" - ], - "E": [ - "V432A", - "M492V" - ], - "M": [ - "M159I" - ], - "NS1": [ - "T131A" - ], - "NS2A": [ - "N51K", - "K156N", - "V175I" - ], - "NS5": [ - "K42R", - "T135I", - "D432N", - "D671E" ] - }, - "labels": { - "aa": "E: V432A, M492V; M: M159I; NS1: T131A; NS2A: N51K, K156N, V175I; NS5: K42R, T135I, D432N, D671E" } } }, { - "name": "NODE_0000062", + "name": "NODE_0000065", "node_attrs": { - "div": 0.07189224000000001, + "div": 0.0719, "clade_membership": { "value": "1V_J" } @@ -10340,36 +8579,19 @@ "C10048T", "C10118T", "G10195A" - ], - "NS1": [ - "T131S" - ], - "NS3": [ - "D181E", - "K399R" - ], - "NS4B": [ - "H23Q" - ], - "NS5": [ - "A245T", - "D644N" ] - }, - "labels": { - "aa": "NS1: T131S; NS3: D181E, K399R; NS4B: H23Q; NS5: A245T, D644N" } }, "children": [ { "name": "KF955437.1|1998", "node_attrs": { - "div": 0.07535393000000001, - "country": { - "value": "Puerto Rico" - }, + "div": 0.0754, "clade_membership": { "value": "1V_J" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -10407,34 +8629,19 @@ "G7702A", "T8395C", "T9373C" - ], - "E": [ - "V312M" - ], - "NS1": [ - "S72T" - ], - "NS3": [ - "G144E" - ], - "NS4B": [ - "H17Y" ] - }, - "labels": { - "aa": "E: V312M; NS1: S72T; NS3: G144E; NS4B: H17Y" } } }, { "name": "FJ390380.1|1998", "node_attrs": { - "div": 0.07474646000000001, - "country": { - "value": "USA" - }, + "div": 0.0747, "clade_membership": { "value": "1V_J" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -10464,20 +8671,7 @@ "C6769T", "C7336T", "C9676T" - ], - "NS1": [ - "D278E" - ], - "NS2A": [ - "A38V", - "L41F" - ], - "NS2B": [ - "L118F" ] - }, - "labels": { - "aa": "NS1: D278E; NS2A: A38V, L41F; NS2B: L118F" } } } @@ -10492,9 +8686,9 @@ ] }, { - "name": "NODE_0000063", + "name": "NODE_0000066", "node_attrs": { - "div": 0.05910179000000001, + "div": 0.0591, "clade_membership": { "value": "1V" } @@ -10548,32 +8742,14 @@ "C9409T", "T9550C", "C9676T" - ], - "E": [ - "M297T" - ], - "NS2A": [ - "M168T" - ], - "NS4A": [ - "M89T" - ], - "NS4B": [ - "H24Q" - ], - "NS5": [ - "T135M" ] - }, - "labels": { - "aa": "E: M297T; NS2A: M168T; NS4A: M89T; NS4B: H24Q; NS5: T135M" } }, "children": [ { - "name": "NODE_0000064", + "name": "NODE_0000067", "node_attrs": { - "div": 0.06037228000000001, + "div": 0.0604, "clade_membership": { "value": "1V" } @@ -10594,26 +8770,14 @@ "A8050T", "A8242G", "G9568A" - ], - "NS1": [ - "D146E" - ], - "NS2A": [ - "R67K" ] - }, - "labels": { - "aa": "NS1: D146E; NS2A: R67K" } }, "children": [ { "name": "OR389273.1|1986", "node_attrs": { - "div": 0.06074953000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0607, "clade_membership": { "value": "1V" } @@ -10630,9 +8794,9 @@ } }, { - "name": "NODE_0000065", + "name": "NODE_0000068", "node_attrs": { - "div": 0.06516878000000001, + "div": 0.0652, "clade_membership": { "value": "1V_H" } @@ -10690,28 +8854,9 @@ "C9477G", "G9493A", "G9589A" - ], - "NS1": [ - "K48R", - "M84I", - "D92N", - "I246M", - "N293S" - ], - "NS2A": [ - "K213E" - ], - "NS4B": [ - "R34H", - "I90L" - ], - "NS5": [ - "L629F", - "T635S" ] }, "labels": { - "aa": "NS1: K48R, M84I, D92N, I246M, N293S; NS2A: K213E; NS4B: R34H, I90L; NS5: L629F, T635S", "lineage": "1V_H" } }, @@ -10719,12 +8864,12 @@ { "name": "JX669469.1|1997", "node_attrs": { - "div": 0.06744078, - "country": { - "value": "Brazil" - }, + "div": 0.0674, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -10753,26 +8898,14 @@ "T9562C", "C9802T", "A10272G" - ], - "E": [ - "E62K" - ], - "NS2A": [ - "G46A" - ], - "NS4B": [ - "M28I" ] - }, - "labels": { - "aa": "E: E62K; NS2A: G46A; NS4B: M28I" } } }, { - "name": "NODE_0000066", + "name": "NODE_0000069", "node_attrs": { - "div": 0.06544627000000001, + "div": 0.0654, "clade_membership": { "value": "1V_H" } @@ -10790,12 +8923,12 @@ { "name": "OK605754.1|1997", "node_attrs": { - "div": 0.06929195000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0693, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -10840,27 +8973,14 @@ "G9512A", "T9673C", "A9739G" - ], - "NS1": [ - "I128T" - ], - "NS2B": [ - "I39M", - "E58G" - ], - "NS5": [ - "E647K" ] - }, - "labels": { - "aa": "NS1: I128T; NS2B: I39M, E58G; NS5: E647K" } } }, { - "name": "NODE_0000067", + "name": "NODE_0000070", "node_attrs": { - "div": 0.06621115000000001, + "div": 0.0662, "clade_membership": { "value": "1V_H" } @@ -10881,9 +9001,9 @@ }, "children": [ { - "name": "NODE_0000068", + "name": "NODE_0000071", "node_attrs": { - "div": 0.06661152000000001, + "div": 0.0666, "clade_membership": { "value": "1V_H" } @@ -10895,25 +9015,19 @@ "C5755T", "C6923T", "C7598T" - ], - "NS1": [ - "R105K" ] - }, - "labels": { - "aa": "NS1: R105K" } }, "children": [ { "name": "OR389007.1|2000", "node_attrs": { - "div": 0.07145746, - "country": { - "value": "Brazil" - }, + "div": 0.0715, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -10969,39 +9083,19 @@ "C9830T", "T9904C", "G9926A" - ], - "NS1": [ - "V5A", - "A98T", - "K192M" - ], - "NS2A": [ - "V171I" - ], - "NS3": [ - "K117R" - ], - "NS5": [ - "T399I", - "E559Q", - "S635N", - "D785N" ] - }, - "labels": { - "aa": "NS1: V5A, A98T, K192M; NS2A: V171I; NS3: K117R; NS5: T399I, E559Q, S635N, D785N" } } }, { "name": "AB519681.1|2001", "node_attrs": { - "div": 0.07142704000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0714, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -11056,39 +9150,16 @@ "A9589G", "C9754T", "A9892G" - ], - "E": [ - "A180T" - ], - "NS1": [ - "I84M", - "T131A" - ], - "NS2A": [ - "N212Y" - ], - "NS3": [ - "G174E" - ], - "NS4A": [ - "T89M" - ], - "NS5": [ - "F629L", - "S635T" ] - }, - "labels": { - "aa": "E: A180T; NS1: I84M, T131A; NS2A: N212Y; NS3: G174E; NS4A: T89M; NS5: F629L, S635T" } } } ] }, { - "name": "NODE_0000069", + "name": "NODE_0000072", "node_attrs": { - "div": 0.06660853000000001, + "div": 0.0666, "clade_membership": { "value": "1V_H" } @@ -11107,12 +9178,12 @@ { "name": "KF672764.1|2001", "node_attrs": { - "div": 0.07107211000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0711, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -11161,32 +9232,19 @@ "C10048T", "A10114G", "C10255T" - ], - "NS1": [ - "A98T", - "R347K" - ], - "NS2A": [ - "E213K" - ], - "NS5": [ - "S39T" ] - }, - "labels": { - "aa": "NS1: A98T, R347K; NS2A: E213K; NS5: S39T" } } }, { "name": "FJ850073.1|2001", "node_attrs": { - "div": 0.07172928, - "country": { - "value": "Brazil" - }, + "div": 0.0717, "clade_membership": { "value": "1V_H" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -11244,30 +9302,7 @@ "T9766C", "C9916T", "A10200G" - ], - "NS1": [ - "N94D", - "P141L", - "I251V" - ], - "NS2A": [ - "I12V" - ], - "NS2B": [ - "A65V" - ], - "NS4A": [ - "I61M", - "T89M" - ], - "NS5": [ - "Q547R", - "P630S", - "E876G" ] - }, - "labels": { - "aa": "NS1: N94D, P141L, I251V; NS2A: I12V; NS2B: A65V; NS4A: I61M, T89M; NS5: Q547R, P630S, E876G" } } } @@ -11282,9 +9317,9 @@ ] }, { - "name": "NODE_0000070", + "name": "NODE_0000073", "node_attrs": { - "div": 0.061487740000000006, + "div": 0.0615, "clade_membership": { "value": "1V" } @@ -11316,33 +9351,14 @@ "T9583C", "T9606C", "T9901C" - ], - "M": [ - "K122R" - ], - "NS1": [ - "I224T" - ], - "NS2B": [ - "E63Q" - ], - "NS5": [ - "A370T", - "I678T" ] - }, - "labels": { - "aa": "M: K122R; NS1: I224T; NS2B: E63Q; NS5: A370T, I678T" } }, "children": [ { "name": "GU131835.1|2004", "node_attrs": { - "div": 0.06950361000000001, - "country": { - "value": "Venezuela" - }, + "div": 0.0695, "clade_membership": { "value": "1V" } @@ -11430,42 +9446,14 @@ "A9985T", "T10102C", "C10254T" - ], - "E": [ - "V83A" - ], - "M": [ - "A127V", - "L138F" - ], - "NS3": [ - "I213M", - "D350E" - ], - "NS4A": [ - "T69M", - "I110V" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "S23P", - "S188T", - "K523R", - "A676S", - "P894L" ] - }, - "labels": { - "aa": "E: V83A; M: A127V, L138F; NS3: I213M, D350E; NS4A: T69M, I110V; NS4B: V18A; NS5: S23P, S188T, K523R, A676S, P894L" } } }, { - "name": "NODE_0000071", + "name": "NODE_0000074", "node_attrs": { - "div": 0.061788130000000004, + "div": 0.0618, "clade_membership": { "value": "1V" } @@ -11480,9 +9468,9 @@ }, "children": [ { - "name": "NODE_0000072", + "name": "NODE_0000075", "node_attrs": { - "div": 0.062367780000000005, + "div": 0.0624, "clade_membership": { "value": "1V" } @@ -11500,9 +9488,9 @@ }, "children": [ { - "name": "NODE_0000073", + "name": "NODE_0000076", "node_attrs": { - "div": 0.06424931, + "div": 0.0642, "clade_membership": { "value": "1V_C" } @@ -11540,12 +9528,12 @@ { "name": "GU056032.1|1998", "node_attrs": { - "div": 0.06709124000000001, - "country": { - "value": "Venezuela" - }, + "div": 0.0671, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -11581,28 +9569,14 @@ "G9629A", "C9812T", "C10253A" - ], - "C": [ - "T103A" - ], - "NS2B": [ - "I11V", - "I16M" - ], - "NS5": [ - "V686I", - "P894T" ] - }, - "labels": { - "aa": "C: T103A; NS2B: I11V, I16M; NS5: V686I, P894T" } } }, { - "name": "NODE_0000074", + "name": "NODE_0000077", "node_attrs": { - "div": 0.06812033, + "div": 0.0681, "clade_membership": { "value": "1V_C" } @@ -11647,29 +9621,14 @@ "A9892G", "C10216T", "A10272G" - ], - "E": [ - "V55I" - ], - "M": [ - "R55Q" - ], - "NS1": [ - "D146N" - ], - "NS2A": [ - "V171A" ] - }, - "labels": { - "aa": "E: V55I; M: R55Q; NS1: D146N; NS2A: V171A" } }, "children": [ { - "name": "NODE_0000075", + "name": "NODE_0000078", "node_attrs": { - "div": 0.07147496, + "div": 0.0715, "clade_membership": { "value": "1V_C" } @@ -11709,32 +9668,19 @@ "T9346C", "T9412C", "G10090A" - ], - "NS2A": [ - "V15A" - ], - "NS4B": [ - "A163T" - ], - "NS5": [ - "T27I", - "H200Y" ] - }, - "labels": { - "aa": "NS2A: V15A; NS4B: A163T; NS5: T27I, H200Y" } }, "children": [ { "name": "MZ008453.1|2013", "node_attrs": { - "div": 0.07836868000000001, - "country": { - "value": "Nicaragua" - }, + "div": 0.0784, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Nicaragua" } }, "branch_attrs": { @@ -11799,31 +9745,19 @@ "C9610T", "G9775A", "G10186A" - ], - "NS2A": [ - "V175I" - ], - "NS2B": [ - "L4I" - ], - "NS4B": [ - "V148I" ] - }, - "labels": { - "aa": "NS2A: V175I; NS2B: L4I; NS4B: V148I" } } }, { "name": "OQ821332.1|2016-03-15", "node_attrs": { - "div": 0.07810091000000001, - "country": { - "value": "Costa Rica" - }, + "div": 0.0781, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Costa Rica" } }, "branch_attrs": { @@ -11897,29 +9831,16 @@ "A10024C", "T10054C", "A10087G" - ], - "NS1": [ - "N94T", - "I128T" - ], - "NS3": [ - "V100I" - ], - "NS5": [ - "P335S" ] - }, - "labels": { - "aa": "NS1: N94T, I128T; NS3: V100I; NS5: P335S" } } } ] }, { - "name": "NODE_0000076", + "name": "NODE_0000079", "node_attrs": { - "div": 0.06841704000000001, + "div": 0.0684, "clade_membership": { "value": "1V_C" } @@ -11940,12 +9861,12 @@ { "name": "ON426292.1|2020-01-22", "node_attrs": { - "div": 0.08189914000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0819, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -12079,46 +10000,14 @@ "T10213C", "T10216C", "G10272A" - ], - "C": [ - "P11Q", - "S12A" - ], - "E": [ - "N52S" - ], - "M": [ - "D89E" - ], - "NS1": [ - "I6V" - ], - "NS2A": [ - "N51K", - "Q141H", - "A171T" - ], - "NS2B": [ - "V120L" - ], - "NS3": [ - "R15K" - ], - "NS5": [ - "I227V", - "V642A", - "R748K" ] - }, - "labels": { - "aa": "C: P11Q, S12A; E: N52S; M: D89E; NS1: I6V; NS2A: N51K, Q141H, A171T; NS2B: V120L; NS3: R15K; NS5: I227V, V642A, R748K" } } }, { - "name": "NODE_0000077", + "name": "NODE_0000080", "node_attrs": { - "div": 0.07038870000000001, + "div": 0.0704, "clade_membership": { "value": "1V_C" } @@ -12145,28 +10034,19 @@ "T7567C", "G9025A", "C9235A" - ], - "NS2A": [ - "I44V" - ], - "NS5": [ - "D554E" ] - }, - "labels": { - "aa": "NS2A: I44V; NS5: D554E" } }, "children": [ { "name": "KF955424.1|2007", "node_attrs": { - "div": 0.08072690000000002, - "country": { - "value": "Mexico" - }, + "div": 0.0807, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -12264,101 +10144,19 @@ "A9873C", "G9893C", "T9928-" - ], - "2K": [ - "V11G", - "L15V", - "V21G" - ], - "NS3": [ - "V274G", - "G477R", - "P479L", - "D497A", - "N500T", - "T501P", - "V545G" - ], - "NS4A": [ - "V2G", - "L95F", - "F113V", - "M116V", - "P123A" - ], - "NS4B": [ - "D80A", - "P84A", - "A96G", - "N104T", - "S221V", - "F238L", - "G245R" - ], - "NS5": [ - "G3A", - "Q5H", - "E112G", - "A117G", - "V132G", - "T192A", - "T243P", - "D254A", - "G258A", - "T261P", - "A265P", - "E267D", - "E286D", - "H287P", - "T290P", - "W291C", - "H292P", - "D296A", - "Y299S", - "V333G", - "Q351E", - "R352X", - "V353G", - "C446W", - "E486Q", - "A487G", - "F497V", - "S498R", - "S504R", - "T571P", - "N574T", - "T587P", - "R594S", - "D596A", - "T605P", - "T675P", - "D682A", - "E694D", - "H713P", - "C727S", - "G735A", - "T750P", - "G754A", - "W761C", - "H767P", - "A774P", - "D785X" ] - }, - "labels": { - "aa": "2K: V11G, L15V, V21G; NS3: V274G, G477R, P479L, D497A, N500T, T501P, V545G; NS4A: V2G, L95F, F113V, M116V, P123A; NS4B: D80A, P84A, A96G, N104T, S221V, F238L, G245R; NS5: G3A, Q5H, E112G, A117G, V132G, T192A, T243P, D254A, G258A, T261P, A265P, E267D, E286D, H287P, T290P, W291C, H292P, D296A, Y299S, V333G, Q351E, R352X, V353G, C446W, E486Q, A487G, F497V, S498R, S504R, T571P, N574T, T587P, R594S, D596A, T605P, T675P, D682A, E694D, H713P, C727S, G735A, T750P, G754A, W761C, H767P, A774P, D785X" } } }, { "name": "KJ189368.1|2012", "node_attrs": { - "div": 0.07531493000000002, - "country": { - "value": "Mexico" - }, + "div": 0.0753, "clade_membership": { "value": "1V_C" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -12411,23 +10209,7 @@ "C9916T", "T9928C", "C9952T" - ], - "E": [ - "S305P" - ], - "M": [ - "T83N" - ], - "NS4A": [ - "V2I" - ], - "NS5": [ - "I555F", - "L643F" ] - }, - "labels": { - "aa": "E: S305P; M: T83N; NS4A: V2I; NS5: I555F, L643F" } } } @@ -12440,9 +10222,9 @@ ] }, { - "name": "NODE_0000078", + "name": "NODE_0000081", "node_attrs": { - "div": 0.06589034, + "div": 0.0659, "clade_membership": { "value": "1V_B" } @@ -12486,27 +10268,17 @@ "G9148A", "C9352T", "C9961T" - ], - "NS2A": [ - "V171A" - ], - "NS2B": [ - "R91K" - ], - "NS4B": [ - "K11R" ] }, "labels": { - "aa": "NS2A: V171A; NS2B: R91K; NS4B: K11R", "lineage": "1V_B" } }, "children": [ { - "name": "NODE_0000079", + "name": "NODE_0000082", "node_attrs": { - "div": 0.06637793, + "div": 0.0664, "clade_membership": { "value": "1V_B" } @@ -12518,28 +10290,19 @@ "C955T", "C2824A", "G3251A" - ], - "M": [ - "I136T" - ], - "NS1": [ - "D278N" ] - }, - "labels": { - "aa": "M: I136T; NS1: D278N" } }, "children": [ { "name": "JN819415.1|2006", "node_attrs": { - "div": 0.06677107, - "country": { - "value": "Venezuela" - }, + "div": 0.0668, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -12555,12 +10318,12 @@ { "name": "FJ639735.1|1997", "node_attrs": { - "div": 0.06696779, - "country": { - "value": "Venezuela" - }, + "div": 0.067, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -12573,22 +10336,16 @@ "A5366G", "C6340T", "T8596C" - ], - "NS3": [ - "I283V" ] - }, - "labels": { - "aa": "NS3: I283V" } } } ] }, { - "name": "NODE_0000080", + "name": "NODE_0000083", "node_attrs": { - "div": 0.07060263, + "div": 0.0706, "clade_membership": { "value": "1V_B" } @@ -12643,34 +10400,19 @@ "C9295T", "G9775A", "C9860T" - ], - "M": [ - "Q17H" - ], - "NS2A": [ - "L91I" - ], - "NS2B": [ - "L4I" - ], - "NS5": [ - "S23P" ] - }, - "labels": { - "aa": "M: Q17H; NS2A: L91I; NS2B: L4I; NS5: S23P" } }, "children": [ { "name": "MZ008452.1|2014", "node_attrs": { - "div": 0.08233203, - "country": { - "value": "Nicaragua" - }, + "div": 0.0823, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "Nicaragua" } }, "branch_attrs": { @@ -12782,89 +10524,14 @@ "T9823C", "G10090A", "T10213G" - ], - "C": [ - "L109M" - ], - "E": [ - "L41M", - "T182A" - ], - "M": [ - "S22A", - "A29T" - ], - "NS1": [ - "F323V" - ], - "NS2A": [ - "M83L", - "T148N", - "L152M", - "T158S", - "W165G", - "T168K", - "A171E", - "L172M", - "I174S", - "V175G", - "S176A", - "F178Y", - "F207Y" - ], - "NS2B": [ - "I4V", - "E6K", - "I8N", - "M9K", - "A10V", - "I11T", - "G12R", - "I13K", - "K23T", - "Q63K", - "T83K", - "K85R", - "D88E" - ], - "NS3": [ - "P119S", - "L149I", - "A170T", - "P224H", - "A235E", - "I241R", - "F266L", - "L270H", - "T316K", - "V323G", - "F326V", - "Y602D" - ], - "NS4B": [ - "V48I", - "Q102K", - "P105T" - ], - "NS5": [ - "L62M", - "P73Q", - "T192I", - "V220G", - "R595L", - "A676D", - "D880E" ] - }, - "labels": { - "aa": "C: L109M; E: L41M, T182A; M: S22A, A29T; NS1: F323V; NS2A: M83L, T148N, L152M, T158S, W165G, T168K, A171E, L172M, I174S, V175G, S176A, F178Y, F207Y; NS2B: I4V, E6K, I8N, M9K, A10V, I11T, G12R, I13K, K23T, Q63K, T83K, K85R, D88E; NS3: P119S, L149I, A170T, P224H, A235E, I241R, F266L, L270H, T316K, V323G, F326V, Y602D; NS4B: V48I, Q102K, P105T; NS5: L62M, P73Q, T192I, V220G, R595L, A676D, D880E" } } }, { - "name": "NODE_0000081", + "name": "NODE_0000084", "node_attrs": { - "div": 0.07100153, + "div": 0.071, "clade_membership": { "value": "1V_B" } @@ -12883,12 +10550,12 @@ { "name": "MT929160.1|2019-10-07", "node_attrs": { - "div": 0.07973024, - "country": { - "value": "Mexico" - }, + "div": 0.0797, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -12979,36 +10646,14 @@ "C9994T", "A10165G", "A10273G" - ], - "C": [ - "N2K", - "K86R", - "T103A" - ], - "E": [ - "L475F" - ], - "NS1": [ - "A60V" - ], - "NS2A": [ - "L159F", - "K166R" - ], - "NS5": [ - "T98S", - "D644N" ] - }, - "labels": { - "aa": "C: N2K, K86R, T103A; E: L475F; NS1: A60V; NS2A: L159F, K166R; NS5: T98S, D644N" } } }, { - "name": "NODE_0000082", + "name": "NODE_0000085", "node_attrs": { - "div": 0.07173521, + "div": 0.0717, "clade_membership": { "value": "1V_B" } @@ -13031,12 +10676,12 @@ { "name": "OQ445882.1|2022-08-15", "node_attrs": { - "div": 0.08120013999999999, - "country": { - "value": "USA" - }, + "div": 0.0812, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -13138,40 +10783,19 @@ "G9886A", "A10000G", "A10234G" - ], - "E": [ - "T155S", - "S227P", - "K363R" - ], - "NS1": [ - "I128T" - ], - "NS3": [ - "P119S", - "R215K" - ], - "NS5": [ - "S39T", - "A245V", - "N387S", - "V642A" ] - }, - "labels": { - "aa": "E: T155S, S227P, K363R; NS1: I128T; NS3: P119S, R215K; NS5: S39T, A245V, N387S, V642A" } } }, { "name": "MZ343259.1|2015-11", "node_attrs": { - "div": 0.07716722999999999, - "country": { - "value": "Mexico" - }, + "div": 0.0772, "clade_membership": { "value": "1V_B" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -13232,30 +10856,7 @@ "C9934T", "T10213C", "C10255T" - ], - "NS1": [ - "D139E" - ], - "NS2A": [ - "L41F", - "K218R" - ], - "NS2B": [ - "K85R" - ], - "NS3": [ - "V332A", - "R338K" - ], - "NS4B": [ - "R11K" - ], - "NS5": [ - "P137A" ] - }, - "labels": { - "aa": "NS1: D139E; NS2A: L41F, K218R; NS2B: K85R; NS3: V332A, R338K; NS4B: R11K; NS5: P137A" } } } @@ -13270,9 +10871,9 @@ ] }, { - "name": "NODE_0000083", + "name": "NODE_0000086", "node_attrs": { - "div": 0.06657550000000001, + "div": 0.0666, "clade_membership": { "value": "1V" } @@ -13330,35 +10931,14 @@ "T9484C", "A9539C", "G10261A" - ], - "E": [ - "T297M" - ], - "NS1": [ - "D146G" - ], - "NS2A": [ - "I155V" - ], - "NS2B": [ - "T70A" - ], - "NS4B": [ - "H17Y" ] - }, - "labels": { - "aa": "E: T297M; NS1: D146G; NS2A: I155V; NS2B: T70A; NS4B: H17Y" } }, "children": [ { "name": "GU131948.1|2001", "node_attrs": { - "div": 0.07012161000000001, - "country": { - "value": "Colombia" - }, + "div": 0.0701, "clade_membership": { "value": "1V" } @@ -13403,29 +10983,14 @@ "T9642C", "C10168T", "C10216T" - ], - "NS2A": [ - "V101I" - ], - "NS3": [ - "T115I" - ], - "NS4A": [ - "V2I" - ], - "NS5": [ - "I690T" ] - }, - "labels": { - "aa": "NS2A: V101I; NS3: T115I; NS4A: V2I; NS5: I690T" } } }, { - "name": "NODE_0000084", + "name": "NODE_0000087", "node_attrs": { - "div": 0.06657650000000001, + "div": 0.0666, "clade_membership": { "value": "1V" } @@ -13435,9 +11000,9 @@ }, "children": [ { - "name": "NODE_0000085", + "name": "NODE_0000088", "node_attrs": { - "div": 0.06740804000000002, + "div": 0.0674, "clade_membership": { "value": "1V_E" } @@ -13457,28 +11022,17 @@ "T6622C", "G6927A", "G9511A" - ], - "E": [ - "K394R" - ], - "M": [ - "D89E", - "L138F" - ], - "NS4B": [ - "R34H" ] }, "labels": { - "aa": "E: K394R; M: D89E, L138F; NS4B: R34H", "lineage": "1V_E" } }, "children": [ { - "name": "NODE_0000086", + "name": "NODE_0000089", "node_attrs": { - "div": 0.07189506000000001, + "div": 0.0719, "clade_membership": { "value": "1V_E" } @@ -13526,28 +11080,19 @@ "T9157C", "A9451G", "C9883T" - ], - "NS2A": [ - "S7N" - ], - "NS3": [ - "S71C" ] - }, - "labels": { - "aa": "NS2A: S7N; NS3: S71C" } }, "children": [ { "name": "KU509252.1|2010", "node_attrs": { - "div": 0.07861145000000001, - "country": { - "value": "Venezuela" - }, + "div": 0.0786, "clade_membership": { "value": "1V_E" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -13620,45 +11165,19 @@ "G8875A", "T9049C", "T9498C" - ], - "E": [ - "K118E", - "E126Q" - ], - "M": [ - "P10Q", - "H11P", - "R87Q" - ], - "NS3": [ - "K73R", - "I179V", - "R255K" - ], - "NS4B": [ - "M88K", - "G245E", - "G246E" - ], - "NS5": [ - "G3E", - "V642A" ] - }, - "labels": { - "aa": "E: K118E, E126Q; M: P10Q, H11P, R87Q; NS3: K73R, I179V, R255K; NS4B: M88K, G245E, G246E; NS5: G3E, V642A" } } }, { "name": "FJ639819.1|2006", "node_attrs": { - "div": 0.07199321000000002, - "country": { - "value": "Venezuela" - }, + "div": 0.072, "clade_membership": { "value": "1V_E" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -13666,22 +11185,16 @@ "nuc": [ "T898C", "C4782T" - ], - "NS3": [ - "S88L" ] - }, - "labels": { - "aa": "NS3: S88L" } } } ] }, { - "name": "NODE_0000087", + "name": "NODE_0000090", "node_attrs": { - "div": 0.07168238000000002, + "div": 0.0717, "clade_membership": { "value": "1V_E" } @@ -13729,24 +11242,14 @@ "C9694T", "G10090A", "C10208T" - ], - "NS1": [ - "I162V" - ], - "NS5": [ - "Q195R", - "V642A" ] - }, - "labels": { - "aa": "NS1: I162V; NS5: Q195R, V642A" } }, "children": [ { - "name": "NODE_0000088", + "name": "NODE_0000091", "node_attrs": { - "div": 0.07538017000000002, + "div": 0.0754, "clade_membership": { "value": "1V_E" } @@ -13791,26 +11294,14 @@ "A9938G", "G10015A", "T10102C" - ], - "NS1": [ - "Y247F" - ], - "NS5": [ - "T789A" ] - }, - "labels": { - "aa": "NS1: Y247F; NS5: T789A" } }, "children": [ { "name": "MW946053.1|2010", "node_attrs": { - "div": 0.07626532000000003, - "country": { - "value": "Bolivia" - }, + "div": 0.0763, "clade_membership": { "value": "1V_E" } @@ -13828,23 +11319,14 @@ "G8157A", "T9445C", "C9485T" - ], - "NS1": [ - "I246T" - ], - "NS5": [ - "R195Q" ] - }, - "labels": { - "aa": "NS1: I246T; NS5: R195Q" } } }, { - "name": "NODE_0000089", + "name": "NODE_0000092", "node_attrs": { - "div": 0.07632389000000002, + "div": 0.0763, "clade_membership": { "value": "1V_E" } @@ -13865,9 +11347,9 @@ }, "children": [ { - "name": "NODE_0000090", + "name": "NODE_0000093", "node_attrs": { - "div": 0.07867662000000002, + "div": 0.0787, "clade_membership": { "value": "1V_E.4" } @@ -13900,16 +11382,9 @@ "A9094G", "A10165G", "G10201A" - ], - "E": [ - "R394K" - ], - "NS4B": [ - "A26V" ] }, "labels": { - "aa": "E: R394K; NS4B: A26V", "lineage": "1V_E.4" } }, @@ -13917,12 +11392,12 @@ { "name": "OQ567786.1|2016-01-29", "node_attrs": { - "div": 0.07950940000000002, - "country": { - "value": "Paraguay" - }, + "div": 0.0795, "clade_membership": { "value": "1V_E.4" + }, + "country": { + "value": "Paraguay" } }, "branch_attrs": { @@ -13936,20 +11411,14 @@ "C7148T", "T7306C", "G9661A" - ], - "NS1": [ - "I128M" ] - }, - "labels": { - "aa": "NS1: I128M" } } }, { - "name": "NODE_0000091", + "name": "NODE_0000094", "node_attrs": { - "div": 0.07908874000000002, + "div": 0.0791, "clade_membership": { "value": "1V_E.4" } @@ -13963,20 +11432,14 @@ "T9286G", "C9485T", "C9592T" - ], - "NS5": [ - "R195Q" ] - }, - "labels": { - "aa": "NS5: R195Q" } }, "children": [ { - "name": "NODE_0000092", + "name": "NODE_0000095", "node_attrs": { - "div": 0.07920517000000002, + "div": 0.0792, "clade_membership": { "value": "1V_E.4" } @@ -13988,12 +11451,12 @@ { "name": "OQ567798.1|2017-04-26", "node_attrs": { - "div": 0.08012354000000002, - "country": { - "value": "Paraguay" - }, + "div": 0.0801, "clade_membership": { "value": "1V_E.4" + }, + "country": { + "value": "Paraguay" } }, "branch_attrs": { @@ -14014,12 +11477,12 @@ { "name": "OQ567781.1|2015-12-18", "node_attrs": { - "div": 0.08019785000000001, - "country": { - "value": "Paraguay" - }, + "div": 0.0802, "clade_membership": { "value": "1V_E.4" + }, + "country": { + "value": "Paraguay" } }, "branch_attrs": { @@ -14034,22 +11497,16 @@ "A8167G", "A8785G", "C9830T" - ], - "C": [ - "A19P" ] - }, - "labels": { - "aa": "C: A19P" } } } ] }, { - "name": "NODE_0000093", + "name": "NODE_0000096", "node_attrs": { - "div": 0.07956552000000001, + "div": 0.0796, "clade_membership": { "value": "1V_E.4" } @@ -14067,12 +11524,12 @@ { "name": "OQ567778.1|2015-05-13", "node_attrs": { - "div": 0.08037691000000001, - "country": { - "value": "Paraguay" - }, + "div": 0.0804, "clade_membership": { "value": "1V_E.4" + }, + "country": { + "value": "Paraguay" } }, "branch_attrs": { @@ -14084,28 +11541,19 @@ "T5386C", "T8527C", "A8820G" - ], - "E": [ - "I378T" - ], - "NS5": [ - "N416S" ] - }, - "labels": { - "aa": "E: I378T; NS5: N416S" } } }, { "name": "OQ567790.1|2016-01-24", "node_attrs": { - "div": 0.08035914000000001, - "country": { - "value": "Paraguay" - }, + "div": 0.0804, "clade_membership": { "value": "1V_E.4" + }, + "country": { + "value": "Paraguay" } }, "branch_attrs": { @@ -14132,9 +11580,9 @@ ] }, { - "name": "NODE_0000094", + "name": "NODE_0000097", "node_attrs": { - "div": 0.07699089000000002, + "div": 0.077, "clade_membership": { "value": "1V_E" } @@ -14156,10 +11604,7 @@ { "name": "KF672760.1|2011", "node_attrs": { - "div": 0.07747444000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0775, "clade_membership": { "value": "1V_E" } @@ -14169,21 +11614,14 @@ "nuc": [ "A3526G", "C3813G" - ], - "NS2A": [ - "I17M", - "S113C" ] - }, - "labels": { - "aa": "NS2A: I17M, S113C" } } }, { - "name": "NODE_0000095", + "name": "NODE_0000098", "node_attrs": { - "div": 0.08082836000000002, + "div": 0.0808, "clade_membership": { "value": "1V_E.1" } @@ -14223,20 +11661,9 @@ "G9106A", "C9518T", "A10165G" - ], - "E": [ - "I480V" - ], - "M": [ - "F138L" - ], - "NS5": [ - "K311R", - "H649Y" ] }, "labels": { - "aa": "E: I480V; M: F138L; NS5: K311R, H649Y", "lineage": "1V_E.1" } }, @@ -14244,12 +11671,12 @@ { "name": "ON632053.1|2022-04-04", "node_attrs": { - "div": 0.08941639000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0894, "clade_membership": { "value": "1V_E.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -14332,51 +11759,14 @@ "T10208C", "C10216T", "A10261G" - ], - "E": [ - "R394K" - ], - "M": [ - "M39I" - ], - "NS1": [ - "A93V", - "I335V" - ], - "NS2A": [ - "G107R", - "S109K", - "L110R", - "V111L", - "S113Y", - "V114W", - "E115A", - "L116R", - "N118P" - ], - "NS3": [ - "K145V", - "I146E", - "V147L", - "G148S" - ], - "NS5": [ - "P363X", - "R364X", - "A365L", - "K366A", - "R367Q" ] - }, - "labels": { - "aa": "E: R394K; M: M39I; NS1: A93V, I335V; NS2A: G107R, S109K, L110R, V111L, S113Y, V114W, E115A, L116R, N118P; NS3: K145V, I146E, V147L, G148S; NS5: P363X, R364X, A365L, K366A, R367Q" } } }, { - "name": "NODE_0000096", + "name": "NODE_0000099", "node_attrs": { - "div": 0.08099775000000002, + "div": 0.081, "clade_membership": { "value": "1V_E.1" } @@ -14392,12 +11782,12 @@ { "name": "MT862857.1|2019-05-13", "node_attrs": { - "div": 0.08940017000000003, - "country": { - "value": "Brazil" - }, + "div": 0.0894, "clade_membership": { "value": "1V_E.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -14479,46 +11869,14 @@ "A10000G", "G10165A", "A10239G" - ], - "C": [ - "M95I" - ], - "E": [ - "F429L" - ], - "M": [ - "R55Q" - ], - "NS2A": [ - "T168M" - ], - "NS3": [ - "V183M" - ], - "NS4B": [ - "A19V", - "I218N" - ], - "NS5": [ - "R57I", - "A60G", - "K96R", - "A245T", - "P312T", - "R429G", - "Y649H", - "K889R" ] - }, - "labels": { - "aa": "C: M95I; E: F429L; M: R55Q; NS2A: T168M; NS3: V183M; NS4B: A19V, I218N; NS5: R57I, A60G, K96R, A245T, P312T, R429G, Y649H, K889R" } } }, { - "name": "NODE_0000097", + "name": "NODE_0000100", "node_attrs": { - "div": 0.08203426000000003, + "div": 0.082, "clade_membership": { "value": "1V_E.1" } @@ -14540,31 +11898,19 @@ "T8488C", "G9923A", "C10153T" - ], - "NS1": [ - "K227R" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "V784I" ] - }, - "labels": { - "aa": "NS1: K227R; NS4B: V18A; NS5: V784I" } }, "children": [ { "name": "ON632121.1|2022-03-17", "node_attrs": { - "div": 0.08940419000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0894, "clade_membership": { "value": "1V_E.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -14621,44 +11967,14 @@ "A8670C", "C8743T", "A8785G" - ], - "C": [ - "I94T" - ], - "E": [ - "R394K" - ], - "NS2A": [ - "S28N", - "S109K", - "L110R", - "V111L", - "S113Y", - "V114W", - "E115A", - "L116R", - "N118P" - ], - "NS3": [ - "K145V", - "I146V" - ], - "NS5": [ - "P363X", - "R364X", - "A365L", - "K366A" ] - }, - "labels": { - "aa": "C: I94T; E: R394K; NS2A: S28N, S109K, L110R, V111L, S113Y, V114W, E115A, L116R, N118P; NS3: K145V, I146V; NS5: P363X, R364X, A365L, K366A" } } }, { - "name": "NODE_0000098", + "name": "NODE_0000101", "node_attrs": { - "div": 0.08344404000000002, + "div": 0.0834, "clade_membership": { "value": "1V_E.1" } @@ -14680,12 +11996,12 @@ { "name": "OQ605977.1|2022-03-15", "node_attrs": { - "div": 0.08893466000000003, - "country": { - "value": "Brazil" - }, + "div": 0.0889, "clade_membership": { "value": "1V_E.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -14746,55 +12062,19 @@ "T10208C", "C10216T", "A10261G" - ], - "E": [ - "S227P", - "K288I", - "M289T", - "D290Y", - "K291D", - "L292I", - "T293P", - "T339I" - ], - "NS1": [ - "D83H" - ], - "NS2A": [ - "S28N" - ], - "NS4A": [ - "M45I" - ], - "NS5": [ - "A758G", - "Q759G", - "M760G", - "Q762R", - "L763F", - "M764X", - "Y765X", - "F766S", - "H767X", - "R768X", - "R769T", - "D770G" ] - }, - "labels": { - "aa": "E: S227P, K288I, M289T, D290Y, K291D, L292I, T293P, T339I; NS1: D83H; NS2A: S28N; NS4A: M45I; NS5: A758G, Q759G, M760G, Q762R, L763F, M764X, Y765X, F766S, H767X, R768X, R769T, D770G" } } }, { "name": "OR167255.1|2023-03-23", "node_attrs": { - "div": 0.08970240000000003, - "country": { - "value": "Brazil" - }, + "div": 0.0897, "clade_membership": { "value": "1V_E.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -14858,25 +12138,7 @@ "G8686A", "G8791A", "G9298A" - ], - "E": [ - "R394K" - ], - "NS3": [ - "P119S", - "V323M" - ], - "NS4A": [ - "F72L" - ], - "NS5": [ - "K199E", - "R311K", - "T370I" ] - }, - "labels": { - "aa": "E: R394K; NS3: P119S, V323M; NS4A: F72L; NS5: K199E, R311K, T370I" } } } @@ -14895,9 +12157,9 @@ ] }, { - "name": "NODE_0000099", + "name": "NODE_0000102", "node_attrs": { - "div": 0.07378449000000002, + "div": 0.0738, "clade_membership": { "value": "1V_E" } @@ -14926,29 +12188,14 @@ "A8557G", "G9715A", "C10253T" - ], - "NS2A": [ - "V171A" - ], - "NS2B": [ - "N73S" - ], - "NS3": [ - "D20N" - ], - "NS5": [ - "P894S" ] - }, - "labels": { - "aa": "NS2A: V171A; NS2B: N73S; NS3: D20N; NS5: P894S" } }, "children": [ { - "name": "NODE_0000100", + "name": "NODE_0000103", "node_attrs": { - "div": 0.07378693000000003, + "div": 0.0738, "clade_membership": { "value": "1V_E" } @@ -14960,10 +12207,7 @@ { "name": "MG877553.1|2012", "node_attrs": { - "div": 0.07911865000000003, - "country": { - "value": "Haiti" - }, + "div": 0.0791, "clade_membership": { "value": "1V_E" } @@ -15025,33 +12269,14 @@ "T10054C", "T10213C", "T10253C" - ], - "E": [ - "S171A", - "T478M" - ], - "M": [ - "S15T" - ], - "NS3": [ - "R15K" - ], - "NS4A": [ - "G4S" - ], - "NS5": [ - "S894P" ] - }, - "labels": { - "aa": "E: S171A, T478M; M: S15T; NS3: R15K; NS4A: G4S; NS5: S894P" } } }, { - "name": "NODE_0000101", + "name": "NODE_0000104", "node_attrs": { - "div": 0.07707369000000003, + "div": 0.0771, "clade_membership": { "value": "1V_E.2" } @@ -15094,22 +12319,9 @@ "A9397G", "A9631G", "T9928C" - ], - "E": [ - "V55I", - "T160I" - ], - "M": [ - "F138L" - ], - "NS3": [ - "I241V", - "V323M", - "R338K" ] }, "labels": { - "aa": "E: V55I, T160I; M: F138L; NS3: I241V, V323M, R338K", "lineage": "1V_E.2" } }, @@ -15117,12 +12329,12 @@ { "name": "OQ821377.1|2013-08-29", "node_attrs": { - "div": 0.07804299000000003, - "country": { - "value": "USA" - }, + "div": 0.078, "clade_membership": { "value": "1V_E.2" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -15137,20 +12349,14 @@ "T7102C", "A8059G", "T9580C" - ], - "NS2A": [ - "I17V" ] - }, - "labels": { - "aa": "NS2A: I17V" } } }, { - "name": "NODE_0000102", + "name": "NODE_0000105", "node_attrs": { - "div": 0.07923546000000002, + "div": 0.0792, "clade_membership": { "value": "1V_E.2" } @@ -15186,25 +12392,19 @@ "A9319G", "C9523T", "C9829T" - ], - "E": [ - "A180S" ] - }, - "labels": { - "aa": "E: A180S" } }, "children": [ { "name": "OM833055.1|2020-02-18", "node_attrs": { - "div": 0.08321540000000002, - "country": { - "value": "USA" - }, + "div": 0.0832, "clade_membership": { "value": "1V_E.2" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -15249,31 +12449,14 @@ "A9715G", "C9928T", "C10048T" - ], - "NS2B": [ - "K126R" - ], - "NS3": [ - "M323V", - "K338R", - "S517G" - ], - "NS5": [ - "T27I", - "S39F", - "T370A", - "D538I" ] - }, - "labels": { - "aa": "NS2B: K126R; NS3: M323V, K338R, S517G; NS5: T27I, S39F, T370A, D538I" } } }, { - "name": "NODE_0000103", + "name": "NODE_0000106", "node_attrs": { - "div": 0.08074155000000002, + "div": 0.0807, "clade_membership": { "value": "1V_E.2" } @@ -15296,12 +12479,12 @@ { "name": "OM833058.1|2020-06-27", "node_attrs": { - "div": 0.08415849000000002, - "country": { - "value": "USA" - }, + "div": 0.0842, "clade_membership": { "value": "1V_E.2" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -15342,29 +12525,14 @@ "A9513G", "A9700C", "C9716T" - ], - "E": [ - "V432M", - "V485I" - ], - "M": [ - "V31A" - ], - "NS5": [ - "K29R", - "V266M", - "E647G" ] - }, - "labels": { - "aa": "E: V432M, V485I; M: V31A; NS5: K29R, V266M, E647G" } } }, { - "name": "NODE_0000104", + "name": "NODE_0000107", "node_attrs": { - "div": 0.08099751000000002, + "div": 0.081, "clade_membership": { "value": "1V_E.2" } @@ -15380,12 +12548,12 @@ { "name": "OQ445884.1|2022-10-01", "node_attrs": { - "div": 0.08754610000000002, - "country": { - "value": "USA" - }, + "div": 0.0875, "clade_membership": { "value": "1V_E.2" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -15445,40 +12613,19 @@ "G9397A", "T9523C", "T9829C" - ], - "E": [ - "I160T", - "S180A" - ], - "NS1": [ - "N82K", - "G146S" - ], - "NS3": [ - "V241I" - ], - "NS4A": [ - "S99G" - ], - "NS5": [ - "K76R", - "W418C" ] - }, - "labels": { - "aa": "E: I160T, S180A; NS1: N82K, G146S; NS3: V241I; NS4A: S99G; NS5: K76R, W418C" } } }, { "name": "OQ821340.1|2021-11-16", "node_attrs": { - "div": 0.08498732000000002, - "country": { - "value": "Cuba" - }, + "div": 0.085, "clade_membership": { "value": "1V_E.2" + }, + "country": { + "value": "Cuba" } }, "branch_attrs": { @@ -15526,24 +12673,7 @@ "C9890T", "T9904C", "C9946T" - ], - "C": [ - "L106F" - ], - "NS2A": [ - "V111M" - ], - "NS3": [ - "M59T" - ], - "NS5": [ - "V190I", - "E647G", - "K648R" ] - }, - "labels": { - "aa": "C: L106F; NS2A: V111M; NS3: M59T; NS5: V190I, E647G, K648R" } } } @@ -15558,9 +12688,9 @@ ] }, { - "name": "NODE_0000105", + "name": "NODE_0000108", "node_attrs": { - "div": 0.07400753000000002, + "div": 0.074, "clade_membership": { "value": "1V_E" } @@ -15572,25 +12702,19 @@ "T5874C", "T7576C", "A7624G" - ], - "NS3": [ - "V452A" ] - }, - "labels": { - "aa": "NS3: V452A" } }, "children": [ { "name": "KU509249.1|2012", "node_attrs": { - "div": 0.08312356000000001, - "country": { - "value": "Jamaica" - }, + "div": 0.0831, "clade_membership": { "value": "1V_E" + }, + "country": { + "value": "Jamaica" } }, "branch_attrs": { @@ -15686,48 +12810,14 @@ "C9952T", "T10127C", "A10165G" - ], - "C": [ - "I65F" - ], - "E": [ - "K118Q", - "C121F", - "V139E", - "F279I", - "N348I" - ], - "M": [ - "T134M" - ], - "NS1": [ - "V89I" - ], - "NS3": [ - "R255K", - "E503K" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "G3R", - "T370R", - "T565K", - "Q580R", - "G607A", - "L629F" ] - }, - "labels": { - "aa": "C: I65F; E: K118Q, C121F, V139E, F279I, N348I; M: T134M; NS1: V89I; NS3: R255K, E503K; NS4B: V18A; NS5: G3R, T370R, T565K, Q580R, G607A, L629F" } } }, { - "name": "NODE_0000106", + "name": "NODE_0000109", "node_attrs": { - "div": 0.07612468000000001, + "div": 0.0761, "clade_membership": { "value": "1V_E.3" } @@ -15756,25 +12846,17 @@ "T8572C", "A9194G", "G10046A" - ], - "E": [ - "V439I" - ], - "NS5": [ - "I541V", - "D825N" ] }, "labels": { - "aa": "E: V439I; NS5: I541V, D825N", "lineage": "1V_E.3" } }, "children": [ { - "name": "NODE_0000107", + "name": "NODE_0000110", "node_attrs": { - "div": 0.07869568000000002, + "div": 0.0787, "clade_membership": { "value": "1V_E.3" } @@ -15815,12 +12897,12 @@ { "name": "OM833059.1|2013-07-24", "node_attrs": { - "div": 0.08115884000000002, - "country": { - "value": "USA" - }, + "div": 0.0812, "clade_membership": { "value": "1V_E.3" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -15848,34 +12930,19 @@ "G8776A", "C9829T", "A10046G" - ], - "C": [ - "L113M" - ], - "E": [ - "K110N" - ], - "M": [ - "F138L" - ], - "NS5": [ - "N825D" ] - }, - "labels": { - "aa": "C: L113M; E: K110N; M: F138L; NS5: N825D" } } }, { "name": "KJ189363.1|2010", "node_attrs": { - "div": 0.07997352000000002, - "country": { - "value": "Puerto Rico" - }, + "div": 0.08, "clade_membership": { "value": "1V_E.3" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -15893,22 +12960,16 @@ "T8419C", "C9028T", "C9235T" - ], - "M": [ - "T134M" ] - }, - "labels": { - "aa": "M: T134M" } } } ] }, { - "name": "NODE_0000108", + "name": "NODE_0000111", "node_attrs": { - "div": 0.07652515000000001, + "div": 0.0765, "clade_membership": { "value": "1V_E.3" } @@ -15926,12 +12987,12 @@ { "name": "KJ189366.1|2010", "node_attrs": { - "div": 0.08084734000000002, - "country": { - "value": "Puerto Rico" - }, + "div": 0.0808, "clade_membership": { "value": "1V_E.3" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -15981,31 +13042,14 @@ "G9535C", "G9682A", "C9871T" - ], - "M": [ - "T57A" - ], - "NS3": [ - "N401S" - ], - "NS4B": [ - "A26V", - "T60A" - ], - "NS5": [ - "I156V", - "I408V" ] - }, - "labels": { - "aa": "M: T57A; NS3: N401S; NS4B: A26V, T60A; NS5: I156V, I408V" } } }, { - "name": "NODE_0000109", + "name": "NODE_0000112", "node_attrs": { - "div": 0.07903999000000002, + "div": 0.079, "clade_membership": { "value": "1V_E.3" } @@ -16044,12 +13088,12 @@ { "name": "KJ189362.1|2010", "node_attrs": { - "div": 0.08061330000000001, - "country": { - "value": "Puerto Rico" - }, + "div": 0.0806, "clade_membership": { "value": "1V_E.3" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -16072,32 +13116,19 @@ "T8395C", "C9523T", "C10168T" - ], - "E": [ - "F96L", - "V345M" - ], - "NS2A": [ - "K156R" - ], - "NS4A": [ - "A93V" ] - }, - "labels": { - "aa": "E: F96L, V345M; NS2A: K156R; NS4A: A93V" } } }, { "name": "KJ189354.1|2012", "node_attrs": { - "div": 0.08041645000000001, - "country": { - "value": "Puerto Rico" - }, + "div": 0.0804, "clade_membership": { "value": "1V_E.3" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -16116,13 +13147,7 @@ "T8689C", "G8859A", "C10216T" - ], - "NS5": [ - "R429K" ] - }, - "labels": { - "aa": "NS5: R429K" } } } @@ -16141,9 +13166,9 @@ ] }, { - "name": "NODE_0000110", + "name": "NODE_0000113", "node_attrs": { - "div": 0.06751319000000001, + "div": 0.0675, "clade_membership": { "value": "1V" } @@ -16166,9 +13191,9 @@ }, "children": [ { - "name": "NODE_0000111", + "name": "NODE_0000114", "node_attrs": { - "div": 0.06859950000000001, + "div": 0.0686, "clade_membership": { "value": "1V_G" } @@ -16186,24 +13211,17 @@ "A8713G", "T9085C", "T9928A" - ], - "NS2A": [ - "I54T" - ], - "NS5": [ - "D785E" ] }, "labels": { - "aa": "NS2A: I54T; NS5: D785E", "lineage": "1V_G" } }, "children": [ { - "name": "NODE_0000112", + "name": "NODE_0000115", "node_attrs": { - "div": 0.06957943000000001, + "div": 0.0696, "clade_membership": { "value": "1V_G" } @@ -16228,12 +13246,12 @@ { "name": "GQ868564.1|2006", "node_attrs": { - "div": 0.07319046000000001, - "country": { - "value": "Colombia" - }, + "div": 0.0732, "clade_membership": { "value": "1V_G" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -16275,30 +13293,14 @@ "C8278T", "A8494T", "C10267T" - ], - "M": [ - "S22A" - ], - "NS1": [ - "K341R" - ], - "NS2B": [ - "Q63H", - "T102A" - ], - "NS4B": [ - "Y17H" ] - }, - "labels": { - "aa": "M: S22A; NS1: K341R; NS2B: Q63H, T102A; NS4B: Y17H" } } }, { - "name": "NODE_0000113", + "name": "NODE_0000116", "node_attrs": { - "div": 0.07603426, + "div": 0.076, "clade_membership": { "value": "1V_G" } @@ -16370,40 +13372,14 @@ "A9790G", "T9904C", "C9970T" - ], - "C": [ - "G26V" - ], - "E": [ - "I173V" - ], - "NS1": [ - "T131A" - ], - "NS3": [ - "S88L", - "P439S" - ], - "NS4A": [ - "T89M" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "E439D", - "L629S" ] - }, - "labels": { - "aa": "C: G26V; E: I173V; NS1: T131A; NS3: S88L, P439S; NS4A: T89M; NS4B: V18A; NS5: E439D, L629S" } }, "children": [ { "name": "OA08|2011", "node_attrs": { - "div": 0.07652477, + "div": 0.0765, "clade_membership": { "value": "1V_G" } @@ -16416,20 +13392,14 @@ "T6424C", "T7957C", "C9500T" - ], - "NS5": [ - "L643F" ] - }, - "labels": { - "aa": "NS5: L643F" } } }, { "name": "OA10|2012", "node_attrs": { - "div": 0.07711722, + "div": 0.0771, "clade_membership": { "value": "1V_G" } @@ -16448,19 +13418,7 @@ "C5614T", "C6646T", "C7314T" - ], - "E": [ - "A331T" - ], - "M": [ - "A29V" - ], - "NS4B": [ - "A163V" ] - }, - "labels": { - "aa": "E: A331T; M: A29V; NS4B: A163V" } } } @@ -16469,9 +13427,9 @@ ] }, { - "name": "NODE_0000114", + "name": "NODE_0000117", "node_attrs": { - "div": 0.07205620000000001, + "div": 0.0721, "clade_membership": { "value": "1V_G" } @@ -16514,31 +13472,19 @@ "G8005A", "A8701G", "C9281T" - ], - "M": [ - "A143V" - ], - "NS1": [ - "I128T" - ], - "NS3": [ - "I520V" ] - }, - "labels": { - "aa": "M: A143V; NS1: I128T; NS3: I520V" } }, "children": [ { "name": "KJ189303.1|1998", "node_attrs": { - "div": 0.07205720000000002, - "country": { - "value": "Colombia" - }, + "div": 0.0721, "clade_membership": { "value": "1V_G" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -16546,9 +13492,9 @@ } }, { - "name": "NODE_0000115", + "name": "NODE_0000118", "node_attrs": { - "div": 0.07254719000000001, + "div": 0.0725, "clade_membership": { "value": "1V_G" } @@ -16568,12 +13514,12 @@ { "name": "KJ189304.1|2005", "node_attrs": { - "div": 0.07422079000000001, - "country": { - "value": "Colombia" - }, + "div": 0.0742, "clade_membership": { "value": "1V_G" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -16603,12 +13549,12 @@ { "name": "GQ868568.1|2007", "node_attrs": { - "div": 0.07392515000000001, - "country": { - "value": "Colombia" - }, + "div": 0.0739, "clade_membership": { "value": "1V_G" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -16628,13 +13574,7 @@ "T8572C", "T9898C", "T10066C" - ], - "E": [ - "T454I" ] - }, - "labels": { - "aa": "E: T454I" } } } @@ -16645,9 +13585,9 @@ ] }, { - "name": "NODE_0000116", + "name": "NODE_0000119", "node_attrs": { - "div": 0.06761600000000001, + "div": 0.0676, "clade_membership": { "value": "1V" } @@ -16661,9 +13601,9 @@ }, "children": [ { - "name": "NODE_0000117", + "name": "NODE_0000120", "node_attrs": { - "div": 0.06945274000000001, + "div": 0.0695, "clade_membership": { "value": "1V_F" } @@ -16698,9 +13638,9 @@ }, "children": [ { - "name": "NODE_0000118", + "name": "NODE_0000121", "node_attrs": { - "div": 0.07195099, + "div": 0.072, "clade_membership": { "value": "1V_F" } @@ -16733,25 +13673,19 @@ "T9265C", "C9967T", "C10153T" - ], - "NS3": [ - "E12K" ] - }, - "labels": { - "aa": "NS3: E12K" } }, "children": [ { "name": "KY474306.1|2014", "node_attrs": { - "div": 0.07851430000000001, - "country": { - "value": "Ecuador" - }, + "div": 0.0785, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Ecuador" } }, "branch_attrs": { @@ -16824,49 +13758,19 @@ "A9625G", "A10056G", "A10272G" - ], - "E": [ - "V379M" - ], - "M": [ - "V31I" - ], - "NS1": [ - "A93V", - "N94Y" - ], - "NS2A": [ - "I209V" - ], - "NS2B": [ - "K126R" - ], - "NS3": [ - "R215K" - ], - "NS4B": [ - "H23Q" - ], - "NS5": [ - "I156V", - "L629S", - "H828R" ] - }, - "labels": { - "aa": "E: V379M; M: V31I; NS1: A93V, N94Y; NS2A: I209V; NS2B: K126R; NS3: R215K; NS4B: H23Q; NS5: I156V, L629S, H828R" } } }, { "name": "KC692517.1|2010-12-29", "node_attrs": { - "div": 0.07708829, - "country": { - "value": "Argentina" - }, + "div": 0.0771, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Argentina" } }, "branch_attrs": { @@ -16923,32 +13827,16 @@ "A10114G", "C10141T", "C10150T" - ], - "E": [ - "T156I", - "S227P", - "P364S", - "A382V" - ], - "NS2A": [ - "K202N" - ], - "NS5": [ - "I619V", - "A651V" ] - }, - "labels": { - "aa": "E: T156I, S227P, P364S, A382V; NS2A: K202N; NS5: I619V, A651V" } } } ] }, { - "name": "NODE_0000119", + "name": "NODE_0000122", "node_attrs": { - "div": 0.07053675000000001, + "div": 0.0705, "clade_membership": { "value": "1V_F" } @@ -16968,25 +13856,19 @@ "G8091A", "C9478T", "T9784C" - ], - "NS5": [ - "R173K" ] - }, - "labels": { - "aa": "NS5: R173K" } }, "children": [ { "name": "FJ639794.1|2004", "node_attrs": { - "div": 0.07132301, - "country": { - "value": "Venezuela" - }, + "div": 0.0713, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -17000,27 +13882,14 @@ "C8307T", "A9154G", "A9719G" - ], - "E": [ - "A481V" - ], - "NS3": [ - "S347L" - ], - "NS5": [ - "A245V", - "I716V" ] - }, - "labels": { - "aa": "E: A481V; NS3: S347L; NS5: A245V, I716V" } } }, { - "name": "NODE_0000120", + "name": "NODE_0000123", "node_attrs": { - "div": 0.07401961000000001, + "div": 0.074, "clade_membership": { "value": "1V_F" } @@ -17059,30 +13928,19 @@ "T8869C", "C9760T", "T9904C" - ], - "NS2A": [ - "V111M", - "V114M", - "V171I" - ], - "NS5": [ - "K96R" ] - }, - "labels": { - "aa": "NS2A: V111M, V114M, V171I; NS5: K96R" } }, "children": [ { "name": "KU509254.1|2011", "node_attrs": { - "div": 0.08123629000000002, - "country": { - "value": "Venezuela" - }, + "div": 0.0812, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Venezuela" } }, "branch_attrs": { @@ -17162,50 +14020,14 @@ "T9277C", "T9286C", "T9400C" - ], - "E": [ - "V439D" - ], - "M": [ - "H11P" - ], - "NS1": [ - "A93V", - "N94A", - "I128V" - ], - "NS2A": [ - "Y74H" - ], - "NS2B": [ - "P111L", - "M112L", - "W121S", - "K127N" - ], - "NS3": [ - "E12K", - "V13L", - "R255K" - ], - "NS4B": [ - "L94I" - ], - "NS5": [ - "R160K", - "S188N", - "D554E" ] - }, - "labels": { - "aa": "E: V439D; M: H11P; NS1: A93V, N94A, I128V; NS2A: Y74H; NS2B: P111L, M112L, W121S, K127N; NS3: E12K, V13L, R255K; NS4B: L94I; NS5: R160K, S188N, D554E" } } }, { - "name": "NODE_0000121", + "name": "NODE_0000124", "node_attrs": { - "div": 0.07829841000000001, + "div": 0.0783, "clade_membership": { "value": "1V_F" } @@ -17245,31 +14067,19 @@ "T9019C", "G9091T", "T9998C" - ], - "M": [ - "A29V" - ], - "NS1": [ - "I242V" - ], - "NS2A": [ - "I171T" ] - }, - "labels": { - "aa": "M: A29V; NS1: I242V; NS2A: I171T" } }, "children": [ { "name": "ON632090.1|2022-03-25", "node_attrs": { - "div": 0.09012201000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0901, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -17345,39 +14155,19 @@ "T10012C", "G10096A", "A10165G" - ], - "E": [ - "V83M", - "S390C", - "W391C", - "K393L" - ], - "M": [ - "I136V", - "L138F" - ], - "NS3": [ - "D350E", - "R377K" - ], - "NS5": [ - "G607S" ] - }, - "labels": { - "aa": "E: V83M, S390C, W391C, K393L; M: I136V, L138F; NS3: D350E, R377K; NS5: G607S" } } }, { "name": "MW377899.1|2014-12-10", "node_attrs": { - "div": 0.08671066000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0867, "clade_membership": { "value": "1V_F" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -17480,68 +14270,7 @@ "A9250G", "T9265C", "A9492G" - ], - "E": [ - "K204N", - "W212S", - "G223V", - "S227A", - "Q228P", - "E229V", - "T230A", - "A354D", - "E375G", - "A495V" - ], - "NS1": [ - "N76D", - "K85E", - "I104V", - "S117R", - "G119E", - "K120N", - "A121V", - "I123G", - "A126E" - ], - "NS2A": [ - "Y74H" - ], - "NS2B": [ - "G7K", - "I8-", - "M9L", - "I11N" - ], - "NS3": [ - "G62W", - "S68N", - "E101G", - "M232T", - "A233E", - "L236F", - "R242K", - "H252T", - "G463D", - "R464W" - ], - "NS5": [ - "E396W", - "N405T", - "D414N", - "R457S", - "E458L", - "K459R", - "K460P", - "E463R", - "K468M", - "S470K", - "Q547H", - "E640G" ] - }, - "labels": { - "aa": "E: K204N, W212S, G223V, S227A, Q228P, E229V, T230A, A354D, E375G, A495V; NS1: N76D, K85E, I104V, S117R, G119E, K120N, A121V, I123G, A126E; NS2A: Y74H; NS2B: G7K, I8-, M9L, I11N; NS3: G62W, S68N, E101G, M232T, A233E, L236F, R242K, H252T, G463D, R464W; NS5: E396W, N405T, D414N, R457S, E458L, K459R, K460P, E463R, K468M, S470K, Q547H, E640G" } } } @@ -17554,9 +14283,9 @@ ] }, { - "name": "NODE_0000122", + "name": "NODE_0000125", "node_attrs": { - "div": 0.06974455000000002, + "div": 0.0697, "clade_membership": { "value": "1V_D" } @@ -17586,21 +14315,17 @@ "C8830T", "C9526T", "T9928C" - ], - "NS5": [ - "T27I" ] }, "labels": { - "aa": "NS5: T27I", "lineage": "1V_D" } }, "children": [ { - "name": "NODE_0000123", + "name": "NODE_0000126", "node_attrs": { - "div": 0.07444613000000001, + "div": 0.0744, "clade_membership": { "value": "1V_D.2" } @@ -17612,7 +14337,7 @@ "C346T", "G436C", "T742C", - "A922T", + "A922C", "T1174A", "A1546G", "T1597C", @@ -17656,24 +14381,9 @@ "T9457C", "G9613T", "C9619T" - ], - "NS1": [ - "T131A", - "N293S" - ], - "NS3": [ - "Y349H", - "I520V" - ], - "NS4A": [ - "A93T" - ], - "NS5": [ - "R367Q" ] }, "labels": { - "aa": "NS1: T131A, N293S; NS3: Y349H, I520V; NS4A: A93T; NS5: R367Q", "lineage": "1V_D.2" } }, @@ -17681,12 +14391,12 @@ { "name": "OQ603261.1|2015-10-09", "node_attrs": { - "div": 0.07871304000000001, - "country": { - "value": "Colombia" - }, + "div": 0.0787, "clade_membership": { "value": "1V_D.2" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -17694,6 +14404,7 @@ "nuc": [ "C469T", "G805A", + "C922T", "T1015C", "G1118A", "T1147C", @@ -17732,27 +14443,14 @@ "T9706C", "T10012C", "A10072G" - ], - "E": [ - "E62K" - ], - "NS3": [ - "I462V" - ], - "NS5": [ - "I340T", - "A341D" ] - }, - "labels": { - "aa": "E: E62K; NS3: I462V; NS5: I340T, A341D" } } }, { - "name": "NODE_0000124", + "name": "NODE_0000127", "node_attrs": { - "div": 0.08066605000000002, + "div": 0.0777, "clade_membership": { "value": "1V_D.2" } @@ -17761,142 +14459,119 @@ "mutations": { "nuc": [ "G316A", - "A372G", - "A649T", - "T922C", "C943T", "C967T", "G1057A", - "C1393T", - "C1486T", - "C1951T", - "T2011C", - "C2149T", "A2164G", "T2458C", "G2572A", - "A2776G", "G2887A", "T3865A", "C3904T", - "C4019T", "A4128G", - "T4211C", - "G4303A", - "C4648T", - "C4723T", - "G4981A", "C5098T", - "T5248C", "T5326C", - "C5422T", "T5617C", - "C5656T", "C5689T", - "A5818G", "G6085A", - "G6343A", "T6508C", - "C6548T", "T6571C", "A6616G", "C6682T", "C7202T", - "G7906A", "G7948A", "C8335T", "T8398C", "T8455C", - "A8557G", - "T8572C", "T8635C", - "G8664A", - "T8719C", "T8725C", "T9019C", "A9148G", - "A9790G", "G9859A", "A9880G", - "T9904C", "T10066C", - "G10231A" - ], - "C": [ - "N93S" - ], - "NS2A": [ - "K218R" - ], - "NS5": [ - "R364K" + "C10237T" ] - }, - "labels": { - "aa": "C: N93S; NS2A: K218R; NS5: R364K" } }, "children": [ { - "name": "ON123596.1|2021-08-20", + "name": "OR654272.1|2023-05-20", "node_attrs": { - "div": 0.08361847000000001, - "country": { - "value": "Peru" - }, + "div": 0.083, "clade_membership": { "value": "1V_D.2" + }, + "country": { + "value": "USA" } }, "branch_attrs": { "mutations": { "nuc": [ - "A286G", - "C419T", - "G568A", - "C811T", - "A1327G", - "T1432C", - "A1618G", - "C1630T", - "C1744T", - "A2016G", - "C2399T", - "T2875C", - "T3385G", - "G4210A", - "A4828G", - "T5317C", - "C6346T", - "A6481G", - "T6566C", - "C6874T", - "G6884A", - "T6904C", - "A6925G", + "T346C", + "G673A", + "C784A", + "T862C", + "C1141T", + "C1624T", + "C2014T", + "A2167G", + "G2240C", + "T2336C", + "C2497T", + "C2521T", + "T2659C", + "A2719G", + "C2980T", + "T3121C", + "T3319C", + "A3433G", + "G3488A", + "C3646T", + "T3797C", + "C3814T", + "T3832C", + "C3923T", + "T3987C", + "T4024C", + "T4372C", + "T4378C", + "C4443T", + "C4678T", + "A5116G", + "C5564T", + "C5773T", + "G5971A", + "T6185C", + "T6398C", + "G6730A", + "C6776T", + "A7171G", "C7372T", - "C8288T", - "T9157C", - "A9166G", - "T9289C", - "A9631G" - ], - "E": [ - "K361R" - ], - "NS4B": [ - "A20T" + "A7459G", + "G7507A", + "G7621A", + "G7762A", + "A7885C", + "C8650T", + "A8657G", + "C8767T", + "T9395C", + "C9425T", + "G9917A", + "A9937G", + "A9988T", + "G10090A", + "T10252C" ] - }, - "labels": { - "aa": "E: K361R; NS4B: A20T" } } }, { - "name": "NODE_0000125", + "name": "NODE_0000128", "node_attrs": { - "div": 0.08076386000000002, + "div": 0.0806, "clade_membership": { "value": "1V_D.2" } @@ -17904,67 +14579,66 @@ "branch_attrs": { "mutations": { "nuc": [ - "T10102C" + "A372G", + "A649T", + "C1393T", + "C1486T", + "C1951T", + "T2011C", + "A2776G", + "C4019T", + "T4211C", + "G4303A", + "C4648T", + "C4723T", + "G4981A", + "T5248C", + "C5422T", + "C5656T", + "A5818G", + "G6343A", + "C6548T", + "G7906A", + "A8557G", + "T8572C", + "G8664A", + "T8719C", + "A9790G", + "T9904C", + "G10231A" ] } }, "children": [ { - "name": "ON426300.1|2021-03-26", + "name": "OQ821326.1|2020-03-15", "node_attrs": { - "div": 0.08263423000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0813, "clade_membership": { "value": "1V_D.2" + }, + "country": { + "value": "Bolivia" } }, "branch_attrs": { "mutations": { "nuc": [ - "C634T", - "A763C", - "C2083T", - "C2650T", - "G3297A", - "C3919T", - "T3929C", - "C3952T", - "A4238C", - "A4244T", - "C4248T", - "A4249G", - "A4748C", - "T4749C", - "A6493G", - "T8896C", - "C9721T", - "G9886A", - "A10165G", - "C10237T" - ], - "NS1": [ - "S293N" - ], - "NS2B": [ - "M37L", - "I39L", - "A40V" - ], - "NS3": [ - "I77P" + "G1087A", + "G1702A", + "T2557C", + "A8059G", + "G8880A", + "C9812T", + "G10090A" ] - }, - "labels": { - "aa": "NS1: S293N; NS2B: M37L, I39L, A40V; NS3: I77P" } } }, { - "name": "NODE_0000126", + "name": "NODE_0000129", "node_attrs": { - "div": 0.08204491000000003, + "div": 0.0807, "clade_membership": { "value": "1V_D.2" } @@ -17972,76 +14646,63 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1690T", - "G2965A", - "A3163G", - "G4060A", - "C4241T", - "T4378C", - "A5116G", - "T5149C", - "T7928C", - "G9244A", - "C9479T", - "T9823C" - ], - "NS5": [ - "Y119H", - "P636S" + "C2149T" ] - }, - "labels": { - "aa": "NS5: Y119H, P636S" } }, "children": [ { - "name": "OR025611.1|2023-04-08", + "name": "ON123596.1|2021-08-20", "node_attrs": { - "div": 0.08302905000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0836, "clade_membership": { "value": "1V_D.2" + }, + "country": { + "value": "Peru" } }, "branch_attrs": { "mutations": { "nuc": [ - "A316G", - "G421A", - "T898C", - "C1842T", - "T2686C", - "T3591C", - "C4594T", - "G5163A", - "T6467C", - "C7684T" - ], - "E": [ - "T303I" - ], - "NS2A": [ - "V39A" - ], - "NS3": [ - "R215K" + "A286G", + "C419T", + "G568A", + "C811T", + "A1327G", + "T1432C", + "A1618G", + "C1630T", + "C1744T", + "A2016G", + "C2399T", + "T2875C", + "T3385G", + "G4210A", + "A4828G", + "T5317C", + "C6346T", + "A6481G", + "T6566C", + "C6874T", + "G6884A", + "T6904C", + "A6925G", + "C7372T", + "C8288T", + "T9157C", + "A9166G", + "T9289C", + "A9631G", + "T10237C" ] - }, - "labels": { - "aa": "E: T303I; NS2A: V39A; NS3: R215K" } } }, { - "name": "OR025607.1|2023-03-29", + "name": "NODE_0000130", "node_attrs": { - "div": 0.08302965000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0808, "clade_membership": { "value": "1V_D.2" } @@ -18049,28 +14710,135 @@ "branch_attrs": { "mutations": { "nuc": [ - "T442C", - "G3297A", - "T3406C", - "A3811C", - "C5773T", - "T6548C", - "A6619T", - "T6797C", - "A9141G", - "T9253C" - ], - "NS1": [ - "S293N" - ], - "NS5": [ - "K523R" + "T10102C" ] + } + }, + "children": [ + { + "name": "ON426300.1|2021-03-26", + "node_attrs": { + "div": 0.0826, + "clade_membership": { + "value": "1V_D.2" + }, + "country": { + "value": "Brazil" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C634T", + "A763C", + "C2083T", + "C2650T", + "G3297A", + "C3919T", + "T3929C", + "C3952T", + "A4238C", + "A4244T", + "C4248T", + "A4249G", + "A4748C", + "T4749C", + "A6493G", + "T8896C", + "C9721T", + "G9886A", + "A10165G" + ] + } + } }, - "labels": { - "aa": "NS1: S293N; NS5: K523R" + { + "name": "NODE_0000131", + "node_attrs": { + "div": 0.082, + "clade_membership": { + "value": "1V_D.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1690T", + "G2965A", + "A3163G", + "G4060A", + "C4241T", + "T4378C", + "A5116G", + "T5149C", + "T7928C", + "G9244A", + "C9479T", + "T9823C", + "T10237C" + ] + } + }, + "children": [ + { + "name": "OR025611.1|2023-04-08", + "node_attrs": { + "div": 0.083, + "clade_membership": { + "value": "1V_D.2" + }, + "country": { + "value": "Brazil" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A316G", + "G421A", + "T898C", + "C1842T", + "T2686C", + "T3591C", + "C4594T", + "G5163A", + "T6467C", + "C7684T" + ] + } + } + }, + { + "name": "OR025607.1|2023-03-29", + "node_attrs": { + "div": 0.083, + "clade_membership": { + "value": "1V_D.2" + }, + "country": { + "value": "Brazil" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T442C", + "G3297A", + "T3406C", + "A3811C", + "C5773T", + "T6548C", + "A6619T", + "T6797C", + "A9141G", + "T9253C" + ] + } + } + } + ] } - } + ] } ] } @@ -18081,11 +14849,11 @@ ] }, { - "name": "NODE_0000127", + "name": "NODE_0000132", "node_attrs": { - "div": 0.07265268000000001, + "div": 0.0727, "clade_membership": { - "value": "1V_D" + "value": "1V_D.1" } }, "branch_attrs": { @@ -18121,32 +14889,22 @@ "T9400C", "A9596G", "G10201A" - ], - "NS1": [ - "A60V", - "I128T" - ], - "NS4B": [ - "A20T" - ], - "NS5": [ - "T675A" ] }, "labels": { - "aa": "NS1: A60V, I128T; NS4B: A20T; NS5: T675A" + "lineage": "1V_D.1" } }, "children": [ { "name": "OQ603259.1|2013-06-01", "node_attrs": { - "div": 0.07807180000000001, + "div": 0.0781, + "clade_membership": { + "value": "1V_D.1" + }, "country": { "value": "Colombia" - }, - "clade_membership": { - "value": "1V_D" } }, "branch_attrs": { @@ -18207,34 +14965,14 @@ "G10090A", "C10144T", "C10254T" - ], - "E": [ - "T454I" - ], - "M": [ - "A29V", - "G115S" - ], - "NS1": [ - "H77Y" - ], - "NS3": [ - "R15K" - ], - "NS5": [ - "H435R", - "P894L" ] - }, - "labels": { - "aa": "E: T454I; M: A29V, G115S; NS1: H77Y; NS3: R15K; NS5: H435R, P894L" } } }, { - "name": "NODE_0000128", + "name": "NODE_0000133", "node_attrs": { - "div": 0.07297370000000002, + "div": 0.073, "clade_membership": { "value": "1V_D.1" } @@ -18246,16 +14984,13 @@ "C2437T", "T7126C" ] - }, - "labels": { - "lineage": "1V_D.1" } }, "children": [ { - "name": "NODE_0000129", + "name": "NODE_0000134", "node_attrs": { - "div": 0.07612909000000001, + "div": 0.0761, "clade_membership": { "value": "1V_D.1.2" } @@ -18269,6 +15004,7 @@ "C1291T", "A1633G", "C1947T", + "T2317C", "C2836T", "G3178A", "C3367T", @@ -18295,213 +15031,17 @@ "T9904C", "T9910C", "T10018C" - ], - "E": [ - "S338L" - ], - "NS4A": [ - "S99G" ] }, "labels": { - "aa": "E: S338L; NS4A: S99G", "lineage": "1V_D.1.2" } }, "children": [ { - "name": "NODE_0000130", - "node_attrs": { - "div": 0.08116285000000001, - "clade_membership": { - "value": "1V_D.1.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1441C", - "T2413C", - "C2440T", - "C2821T", - "C3187T", - "A3301G", - "A3605G", - "C3736T", - "T3778C", - "T3850C", - "A4039G", - "C4058T", - "C4181T", - "C4447T", - "G4617A", - "T4654C", - "A4903G", - "T5473C", - "A5668G", - "T5842C", - "G6052A", - "C6091T", - "C6478T", - "C6548T", - "C6697T", - "A6958T", - "C7021T", - "G7069A", - "A8329G", - "T8536C", - "T8602C", - "G8761A", - "T8779C", - "C8923T", - "G8962A", - "A9118T", - "C9229T", - "T9265C", - "T9509C", - "A9625G", - "C9760T", - "C9860T" - ], - "NS2A": [ - "I44V" - ], - "NS3": [ - "R33K" - ] - }, - "labels": { - "aa": "NS2A: I44V; NS3: R33K" - } - }, - "children": [ - { - "name": "ON123575.1|2021-08-03", - "node_attrs": { - "div": 0.08589477000000001, - "clade_membership": { - "value": "1V_D.1.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T289C", - "C429T", - "C478T", - "C586T", - "C595T", - "C598T", - "A697G", - "C703T", - "C781T", - "G802A", - "C901T", - "G991A", - "G1054A", - "T1070C", - "A1123T", - "C1144T", - "T1204C", - "G1264A", - "T1291C", - "C1441A", - "A1528G", - "G1633A", - "A1684G", - "T1729A", - "C1846T", - "C1924T", - "T1947C", - "T1957C", - "C2176T", - "T2221C", - "A3241T", - "C3595T", - "C5275T", - "G6613A", - "T6842C", - "G7132A", - "G7294A", - "T8794A", - "C9890T", - "T10198C" - ], - "C": [ - "A112V" - ], - "E": [ - "L338S" - ], - "NS1": [ - "E274D" - ] - }, - "labels": { - "aa": "C: A112V; E: L338S; NS1: E274D" - } - } - }, - { - "name": "ON123586.1|2021-05-07", - "node_attrs": { - "div": 0.08263994000000001, - "country": { - "value": "Peru" - }, - "clade_membership": { - "value": "1V_D.1.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G109A", - "G123A", - "G385A", - "C877T", - "C880T", - "T883C", - "C905T", - "C1228T", - "A1367G", - "G1447A", - "C2140T", - "C2494T", - "C4594T", - "T4655C", - "A4777C", - "T6398C", - "T6622C", - "T7346C", - "C7757T", - "T8752C", - "C9295T", - "T9391C", - "T9403C" - ], - "C": [ - "R10Q" - ], - "E": [ - "T145A" - ], - "NS3": [ - "F46L", - "Q86H" - ] - }, - "labels": { - "aa": "C: R10Q; E: T145A; NS3: F46L, Q86H" - } - } - } - ] - }, - { - "name": "NODE_0000131", + "name": "NODE_0000135", "node_attrs": { - "div": 0.07642410000000001, + "div": 0.0764, "clade_membership": { "value": "1V_D.1.2" } @@ -18509,7 +15049,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "T2317C", "C2989T", "C4615T" ] @@ -18519,12 +15058,12 @@ { "name": "OQ603263.1|2016-06-24", "node_attrs": { - "div": 0.07925474, - "country": { - "value": "Colombia" - }, + "div": 0.0793, "clade_membership": { "value": "1V_D.1.2" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -18560,31 +15099,14 @@ "T9076C", "T9509C", "A9742T" - ], - "E": [ - "A117V", - "G445E" - ], - "NS1": [ - "G47E", - "F86L" - ], - "NS3": [ - "I520V" - ], - "NS4A": [ - "T89M" ] - }, - "labels": { - "aa": "E: A117V, G445E; NS1: G47E, F86L; NS3: I520V; NS4A: T89M" } } }, { - "name": "NODE_0000132", + "name": "NODE_0000136", "node_attrs": { - "div": 0.07734004000000001, + "div": 0.0773, "clade_membership": { "value": "1V_D.1.2" } @@ -18608,12 +15130,12 @@ { "name": "OQ821367.1|2022-12-07", "node_attrs": { - "div": 0.08358673000000001, - "country": { - "value": "Mexico" - }, + "div": 0.0836, "clade_membership": { "value": "1V_D.1.2" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -18678,37 +15200,19 @@ "G10090A", "C10153T", "C10156T" - ], - "E": [ - "V485I" - ], - "NS1": [ - "K227R" - ], - "NS2A": [ - "F93L" - ], - "NS3": [ - "T246A" - ], - "NS5": [ - "I283L" ] - }, - "labels": { - "aa": "E: V485I; NS1: K227R; NS2A: F93L; NS3: T246A; NS5: I283L" } } }, { "name": "MN556095.1|2017-04", "node_attrs": { - "div": 0.07947539, - "country": { - "value": "Ecuador" - }, + "div": 0.0795, "clade_membership": { "value": "1V_D.1.2" + }, + "country": { + "value": "Ecuador" } }, "branch_attrs": { @@ -18737,28 +15241,260 @@ "C9382T", "A9631G", "A9685G" - ], - "E": [ - "P364A" - ], - "NS1": [ - "I57V" - ], - "NS2B": [ - "N24D" - ], - "NS3": [ - "A293T" - ], - "NS5": [ - "K52R", - "Q195R" ] + } + } + } + ] + } + ] + }, + { + "name": "NODE_0000137", + "node_attrs": { + "div": 0.0767, + "clade_membership": { + "value": "1V_D.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C4181T", + "A5668G", + "C7021T", + "G7069A", + "A9625G", + "C9860T" + ] + } + }, + "children": [ + { + "name": "MN449014.1|2015-04-20", + "node_attrs": { + "div": 0.0792, + "clade_membership": { + "value": "1V_D.1.2" + }, + "country": { + "value": "Ecuador" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C538T", + "A794G", + "A940G", + "C967T", + "T1947C", + "A1970G", + "C2398T", + "C2944T", + "C3106T", + "A3297C", + "A3643G", + "T3793C", + "A4357G", + "C5104T", + "C5419T", + "A6373G", + "T6445C", + "C6592T", + "T6718C", + "C6826T", + "C7672T", + "C9043T", + "T9373C", + "C9709T", + "A10264T" + ] + } + } + }, + { + "name": "NODE_0000138", + "node_attrs": { + "div": 0.0782, + "clade_membership": { + "value": "1V_D.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G123A", + "C877T", + "C880T", + "C2821T", + "A3605G", + "G4617A", + "A4903G", + "T5473C", + "G6052A", + "C6478T", + "C6548T", + "C8923T", + "T9265C", + "T9509C", + "C9760T" + ] + } + }, + "children": [ + { + "name": "MN449016.1|2015-04-08", + "node_attrs": { + "div": 0.0782, + "clade_membership": { + "value": "1V_D.1.2" }, - "labels": { - "aa": "E: P364A; NS1: I57V; NS2B: N24D; NS3: A293T; NS5: K52R, Q195R" + "country": { + "value": "Ecuador" } + }, + "branch_attrs": { + "mutations": {} } + }, + { + "name": "NODE_0000139", + "node_attrs": { + "div": 0.0812, + "clade_membership": { + "value": "1V_D.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1441C", + "C2317T", + "T2413C", + "C2440T", + "C3187T", + "A3301G", + "C3736T", + "T3778C", + "T3850C", + "A4039G", + "C4058T", + "C4447T", + "T4654C", + "T5842C", + "C6091T", + "C6697T", + "A6958T", + "A8329G", + "T8536C", + "T8602C", + "G8761A", + "T8779C", + "G8962A", + "A9118T", + "C9229T" + ] + } + }, + "children": [ + { + "name": "ON123575.1|2021-08-03", + "node_attrs": { + "div": 0.0859, + "clade_membership": { + "value": "1V_D.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A123G", + "T289C", + "C429T", + "C478T", + "C586T", + "C595T", + "C598T", + "A697G", + "C703T", + "C781T", + "G802A", + "T877C", + "T880C", + "C901T", + "G991A", + "G1054A", + "T1070C", + "A1123T", + "C1144T", + "T1204C", + "G1264A", + "T1291C", + "C1441A", + "A1528G", + "G1633A", + "A1684G", + "T1729A", + "C1846T", + "C1924T", + "T1947C", + "T1957C", + "C2176T", + "T2221C", + "A3241T", + "C3595T", + "C5275T", + "G6613A", + "T6842C", + "G7132A", + "G7294A", + "T8794A", + "C9890T", + "T10198C" + ] + } + } + }, + { + "name": "ON123586.1|2021-05-07", + "node_attrs": { + "div": 0.0826, + "clade_membership": { + "value": "1V_D.1.2" + }, + "country": { + "value": "Peru" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G109A", + "G385A", + "T883C", + "C905T", + "C1228T", + "A1367G", + "G1447A", + "C2140T", + "C2494T", + "C4594T", + "T4655C", + "A4777C", + "T6398C", + "T6622C", + "T7346C", + "C7757T", + "T8752C", + "C9295T", + "T9391C", + "T9403C" + ] + } + } + } + ] } ] } @@ -18767,9 +15503,9 @@ ] }, { - "name": "NODE_0000133", + "name": "NODE_0000140", "node_attrs": { - "div": 0.07317307000000002, + "div": 0.0732, "clade_membership": { "value": "1V_D.1" } @@ -18779,23 +15515,14 @@ "nuc": [ "G6750A", "C8395T" - ], - "NS4A": [ - "R125K" ] - }, - "labels": { - "aa": "NS4A: R125K" } }, "children": [ { "name": "OQ603260.1|2013-06-18", "node_attrs": { - "div": 0.07911197000000002, - "country": { - "value": "Colombia" - }, + "div": 0.0791, "clade_membership": { "value": "1V_D.1" } @@ -18862,32 +15589,14 @@ "G9735A", "A9892G", "T9998C" - ], - "NS2A": [ - "L195M" - ], - "NS3": [ - "A166T", - "P356S" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "H53Y", - "T370I", - "R721K" ] - }, - "labels": { - "aa": "NS2A: L195M; NS3: A166T, P356S; NS4B: V18A; NS5: H53Y, T370I, R721K" } } }, { - "name": "NODE_0000134", + "name": "NODE_0000141", "node_attrs": { - "div": 0.07425049000000002, + "div": 0.0742, "clade_membership": { "value": "1V_D.1" } @@ -18905,25 +15614,19 @@ "T8173C", "T9260C", "T9826C" - ], - "E": [ - "I457V" ] - }, - "labels": { - "aa": "E: I457V" } }, "children": [ { "name": "GQ868570.1|2008", "node_attrs": { - "div": 0.07524621000000002, - "country": { - "value": "Colombia" - }, + "div": 0.0752, "clade_membership": { "value": "1V_D.1" + }, + "country": { + "value": "Colombia" } }, "branch_attrs": { @@ -18940,23 +15643,14 @@ "A6815G", "C7576T", "C9829T" - ], - "2K": [ - "T20A" - ], - "NS1": [ - "S2L" ] - }, - "labels": { - "aa": "2K: T20A; NS1: S2L" } } }, { - "name": "NODE_0000135", + "name": "NODE_0000142", "node_attrs": { - "div": 0.07444976000000002, + "div": 0.0744, "clade_membership": { "value": "1V_D.1" } @@ -18974,12 +15668,12 @@ { "name": "MT899083.1|2019-09-29", "node_attrs": { - "div": 0.08295599000000002, - "country": { - "value": "Mexico" - }, + "div": 0.083, "clade_membership": { "value": "1V_D.1" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -19073,34 +15767,14 @@ "G10090A", "G10120T", "A10165G" - ], - "E": [ - "T163I" - ], - "M": [ - "D89E" - ], - "NS3": [ - "T91M" - ], - "NS4A": [ - "A93V" - ], - "NS5": [ - "I27T", - "H200Y", - "E647G" ] - }, - "labels": { - "aa": "E: T163I; M: D89E; NS3: T91M; NS4A: A93V; NS5: I27T, H200Y, E647G" } } }, { - "name": "NODE_0000136", + "name": "NODE_0000143", "node_attrs": { - "div": 0.07773819000000001, + "div": 0.0777, "clade_membership": { "value": "1V_D.1" } @@ -19145,23 +15819,14 @@ "G10045A", "G10186A", "C10216T" - ], - "NS5": [ - "N637D" ] - }, - "labels": { - "aa": "NS5: N637D" } }, "children": [ { "name": "OQ821380.1|2019-10-23", "node_attrs": { - "div": 0.08262019000000001, - "country": { - "value": "Venezuela" - }, + "div": 0.0826, "clade_membership": { "value": "1V_D.1" } @@ -19210,27 +15875,14 @@ "G9745A", "T9823C", "C9830T" - ], - "NS2A": [ - "F199L" - ], - "NS3": [ - "S553A" - ], - "NS5": [ - "S39T", - "K248R" ] - }, - "labels": { - "aa": "NS2A: F199L; NS3: S553A; NS5: S39T, K248R" } } }, { - "name": "NODE_0000137", + "name": "NODE_0000144", "node_attrs": { - "div": 0.07978546000000002, + "div": 0.0798, "clade_membership": { "value": "1V_D.1.1" } @@ -19254,13 +15906,9 @@ "C9890T", "G10180A", "C10255T" - ], - "C": [ - "A112V" ] }, "labels": { - "aa": "C: A112V", "lineage": "1V_D.1.1" } }, @@ -19268,12 +15916,12 @@ { "name": "OR167130.1|2023-03-03", "node_attrs": { - "div": 0.08852567000000001, - "country": { - "value": "Brazil" - }, + "div": 0.0885, "clade_membership": { "value": "1V_D.1.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -19347,40 +15995,14 @@ "C9907T", "A10114G", "A10165G" - ], - "C": [ - "V102A" - ], - "E": [ - "K394R", - "V439I" - ], - "NS1": [ - "T128I", - "I246V" - ], - "NS2A": [ - "V60A" - ], - "NS3": [ - "T91M" - ], - "NS5": [ - "T370I", - "E426Q", - "L503F", - "D637N" ] - }, - "labels": { - "aa": "C: V102A; E: K394R, V439I; NS1: T128I, I246V; NS2A: V60A; NS3: T91M; NS5: T370I, E426Q, L503F, D637N" } } }, { - "name": "NODE_0000138", + "name": "NODE_0000145", "node_attrs": { - "div": 0.08072873000000001, + "div": 0.0807, "clade_membership": { "value": "1V_D.1.1" } @@ -19400,9 +16022,9 @@ }, "children": [ { - "name": "NODE_0000139", + "name": "NODE_0000146", "node_attrs": { - "div": 0.08209938000000001, + "div": 0.0821, "clade_membership": { "value": "1V_D.1.1" } @@ -19427,7 +16049,7 @@ { "name": "ON123574.1|2021-07-07", "node_attrs": { - "div": 0.08685535000000001, + "div": 0.0869, "clade_membership": { "value": "1V_D.1.1" } @@ -19475,32 +16097,19 @@ "C6862T", "T7471C", "C9553T" - ], - "C": [ - "R10Q", - "V112A" - ], - "E": [ - "S338L" - ], - "NS1": [ - "M178T" ] - }, - "labels": { - "aa": "C: R10Q, V112A; E: S338L; NS1: M178T" } } }, { "name": "ON632040.1|2022-04-12", "node_attrs": { - "div": 0.08812899000000002, - "country": { - "value": "Brazil" - }, + "div": 0.0881, "clade_membership": { "value": "1V_D.1.1" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -19567,46 +16176,16 @@ "T10216C", "G10246A", "T10255C" - ], - "E": [ - "V457I" - ], - "NS1": [ - "V60A", - "T128V" - ], - "NS2A": [ - "S109K", - "L110R", - "V111L", - "S113Y", - "V114W", - "E115A", - "L116R", - "N118P" - ], - "NS4A": [ - "T89M" - ], - "NS5": [ - "I27T", - "K311R", - "R364V", - "K366Q", - "A675T" ] - }, - "labels": { - "aa": "E: V457I; NS1: V60A, T128V; NS2A: S109K, L110R, V111L, S113Y, V114W, E115A, L116R, N118P; NS4A: T89M; NS5: I27T, K311R, R364V, K366Q, A675T" } } } ] }, { - "name": "NODE_0000140", + "name": "NODE_0000147", "node_attrs": { - "div": 0.08193388000000001, + "div": 0.0819, "clade_membership": { "value": "1V_D.1.1" } @@ -19625,25 +16204,19 @@ "T7108C", "T7849C", "C8728T" - ], - "NS1": [ - "S239G" ] - }, - "labels": { - "aa": "NS1: S239G" } }, "children": [ { "name": "OQ821348.1|2022-08-28", "node_attrs": { - "div": 0.08818384000000001, - "country": { - "value": "Cuba" - }, + "div": 0.0882, "clade_membership": { "value": "1V_D.1.1" + }, + "country": { + "value": "Cuba" } }, "branch_attrs": { @@ -19707,39 +16280,19 @@ "C9539A", "A10093G", "T10102C" - ], - "C": [ - "R10K", - "F13I", - "A19V", - "S39N", - "I65V", - "S70G" - ], - "NS2A": [ - "V111M" - ], - "NS3": [ - "I520V" - ], - "NS5": [ - "A230T" ] - }, - "labels": { - "aa": "C: R10K, F13I, A19V, S39N, I65V, S70G; NS2A: V111M; NS3: I520V; NS5: A230T" } } }, { "name": "OQ821349.1|2022-09-01", "node_attrs": { - "div": 0.08659263000000002, - "country": { - "value": "Cuba" - }, + "div": 0.0866, "clade_membership": { "value": "1V_D.1.1" + }, + "country": { + "value": "Cuba" } }, "branch_attrs": { @@ -19793,26 +16346,7 @@ "G9733A", "T10207C", "A10273G" - ], - "NS1": [ - "K211M" - ], - "NS3": [ - "G62E" - ], - "NS4A": [ - "A93V" - ], - "NS5": [ - "M135L", - "I372V", - "H512Q", - "D637Y", - "T678I" ] - }, - "labels": { - "aa": "NS1: K211M; NS3: G62E; NS4A: A93V; NS5: M135L, I372V, H512Q, D637Y, T678I" } } } @@ -19863,9 +16397,9 @@ ] }, { - "name": "NODE_0000141", + "name": "NODE_0000148", "node_attrs": { - "div": 0.02003695, + "div": 0.02, "clade_membership": { "value": "unassigned" } @@ -19875,6 +16409,7 @@ "nuc": [ "A349G", "G355A", + "A388G", "T1100C", "A1252G", "C1477T", @@ -19900,6 +16435,7 @@ "T3908C", "C3950T", "T3961C", + "T4024C", "A4063G", "T4070C", "T4286C", @@ -19916,7 +16452,6 @@ "G8179A", "C8278T", "G8290A", - "C8434T", "A8794T", "C8821T", "T8965C", @@ -19926,27 +16461,14 @@ "C9721T", "C9970T", "A10165G" - ], - "NS1": [ - "R347K" - ], - "NS2A": [ - "L159F", - "F199L" - ], - "NS3": [ - "T112A" ] - }, - "labels": { - "aa": "NS1: R347K; NS2A: L159F, F199L; NS3: T112A" } }, "children": [ { - "name": "NODE_0000142", + "name": "NODE_0000149", "node_attrs": { - "div": 0.03877635, + "div": 0.0388, "clade_membership": { "value": "1II" } @@ -19957,7 +16479,6 @@ "A99T", "G109A", "C254T", - "C328T", "T368C", "G370A", "C448G", @@ -20146,46 +16667,9 @@ "A10051G", "C10153T", "C10156T" - ], - "C": [ - "N2I" - ], - "E": [ - "V345A", - "V432M", - "I439V", - "S472N", - "T478M" - ], - "M": [ - "T107A" - ], - "NS1": [ - "D146N", - "L279F", - "E340D" - ], - "NS2A": [ - "R29K", - "N51S", - "N118S", - "M129I", - "T205P" - ], - "NS3": [ - "M239V", - "V332I" - ], - "NS5": [ - "T135I", - "K523R", - "S629L", - "E640G", - "H649Y" ] }, "labels": { - "aa": "C: N2I; E: V345A, V432M, I439V, S472N, T478M; M: T107A; NS1: D146N, L279F, E340D; NS2A: R29K, N51S, N118S, M129I, T205P; NS3: M239V, V332I; NS5: T135I, K523R, S629L, E640G, H649Y", "lineage": "1II" } }, @@ -20193,12 +16677,12 @@ { "name": "MW945844.1|1964", "node_attrs": { - "div": 0.04665785, - "country": { - "value": "Thailand" - }, + "div": 0.0467, "clade_membership": { "value": "1II" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -20283,46 +16767,19 @@ "C9907T", "T10075A", "A10093G" - ], - "C": [ - "K86R" - ], - "E": [ - "A180T", - "K204R" - ], - "NS2A": [ - "R67K" - ], - "NS3": [ - "A112T", - "F510Y" - ], - "NS4A": [ - "V93A" - ], - "NS4B": [ - "T109I" - ], - "NS5": [ - "D432E", - "D834E" ] - }, - "labels": { - "aa": "C: K86R; E: A180T, K204R; NS2A: R67K; NS3: A112T, F510Y; NS4A: V93A; NS4B: T109I; NS5: D432E, D834E" } } }, { "name": "JQ922547.1|1960", "node_attrs": { - "div": 0.05114545, - "country": { - "value": "Thailand" - }, + "div": 0.0511, "clade_membership": { "value": "1II" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -20455,93 +16912,16 @@ "T9904C", "A10090G", "C10118T" - ], - "C": [ - "F13S", - "N14Q", - "M15G", - "L16G", - "K31R" - ], - "E": [ - "T19P", - "F90C", - "E157T", - "F402L" - ], - "NS1": [ - "K14L", - "S17T", - "E30D", - "Q31P", - "S38P", - "P39S", - "K40N", - "A44P", - "A45I", - "W50C", - "E51V", - "E52I", - "G53R", - "K101E", - "I224T" - ], - "NS2A": [ - "T34V", - "R94P", - "R95K", - "I129K" - ], - "NS2B": [ - "I39V", - "M84R", - "K128N" - ], - "NS3": [ - "V3X", - "L4-", - "W5L", - "K104R", - "A127P", - "Q167R", - "P320T", - "R377K", - "L480S", - "M578K", - "P594T", - "R595C" - ], - "NS4A": [ - "R20K", - "N23K" - ], - "NS4B": [ - "H34R", - "K212R" - ], - "NS5": [ - "M453K", - "V591A", - "T612L", - "N613H", - "M614K", - "S624F", - "K648Q", - "N700G", - "G720V" ] - }, - "labels": { - "aa": "C: F13S, N14Q, M15G, L16G, K31R; E: T19P, F90C, E157T, F402L; NS1: K14L, S17T, E30D, Q31P, S38P, P39S, K40N, A44P, A45I, W50C, E51V, E52I, G53R, K101E, I224T; NS2A: T34V, R94P, R95K, I129K; NS2B: I39V, M84R, K128N; NS3: V3X, L4-, W5L, K104R, A127P, Q167R, P320T, R377K, L480S, M578K, P594T, R595C; NS4A: R20K, N23K; NS4B: H34R, K212R; NS5: M453K, V591A, T612L, N613H, M614K, S624F, K648Q, N700G, G720V" } } } ] }, { - "name": "NODE_0000143", + "name": "NODE_0000150", "node_attrs": { - "div": 0.02348843, + "div": 0.0235, "clade_membership": { "value": "unassigned" } @@ -20580,23 +16960,14 @@ "G9892A", "A10000G", "T10243C" - ], - "E": [ - "N37D" - ], - "NS5": [ - "H127Y" ] - }, - "labels": { - "aa": "E: N37D; NS5: H127Y" } }, "children": [ { - "name": "NODE_0000144", + "name": "NODE_0000151", "node_attrs": { - "div": 0.039294430000000005, + "div": 0.0393, "clade_membership": { "value": "1IV" } @@ -20628,6 +16999,7 @@ "A1963G", "A2041G", "A2044G", + "C2068T", "A2116G", "C2125T", "A2155T", @@ -20747,35 +17119,9 @@ "G10105A", "T10213C", "G10240A" - ], - "E": [ - "A88T", - "T339S" - ], - "M": [ - "A59T" - ], - "NS2A": [ - "I44T", - "R67K", - "K82R", - "I106V", - "I155V", - "V171I" - ], - "NS4A": [ - "V93A" - ], - "NS4B": [ - "T27A" - ], - "NS5": [ - "M34I", - "V651I" ] }, "labels": { - "aa": "E: A88T, T339S; M: A59T; NS2A: I44T, R67K, K82R, I106V, I155V, V171I; NS4A: V93A; NS4B: T27A; NS5: M34I, V651I", "lineage": "1IV" } }, @@ -20783,18 +17129,19 @@ { "name": "MW582813.1|2019-06-21", "node_attrs": { - "div": 0.06920973, - "country": { - "value": "China" - }, + "div": 0.0692, "clade_membership": { "value": "1IV" + }, + "country": { + "value": "China" } }, "branch_attrs": { "mutations": { "nuc": [ "A318G", + "T328C", "A331G", "T335C", "T368C", @@ -20858,7 +17205,6 @@ "C1812T", "C1846G", "G2038A", - "C2068T", "A2215G", "G2240A", "A2257G", @@ -21072,63 +17418,14 @@ "C10085T", "T10102C", "A10215T" - ], - "C": [ - "N75S", - "L109M" - ], - "E": [ - "N8S", - "N52D", - "E203K", - "T293I", - "V436I" - ], - "M": [ - "K122R", - "I136M" - ], - "NS1": [ - "S94A", - "I307T" - ], - "NS2B": [ - "M112L" - ], - "NS3": [ - "F85L", - "A293S", - "Y349H", - "D350E", - "Q466H" - ], - "NS4A": [ - "M89I" - ], - "NS4B": [ - "A20V" - ], - "NS5": [ - "H200Y", - "N285H", - "R325K", - "E647K", - "I651T", - "V787I", - "V829I", - "E833G", - "Y881F" ] - }, - "labels": { - "aa": "C: N75S, L109M; E: N8S, N52D, E203K, T293I, V436I; M: K122R, I136M; NS1: S94A, I307T; NS2B: M112L; NS3: F85L, A293S, Y349H, D350E, Q466H; NS4A: M89I; NS4B: A20V; NS5: H200Y, N285H, R325K, E647K, I651T, V787I, V829I, E833G, Y881F" } } }, { - "name": "NODE_0000145", + "name": "NODE_0000152", "node_attrs": { - "div": 0.04629540000000001, + "div": 0.0463, "clade_membership": { "value": "1IV" } @@ -21162,6 +17459,7 @@ "C2989T", "C3046T", "C3227T", + "A4015G", "G4210A", "A4273G", "T4352C", @@ -21220,33 +17518,14 @@ "G10120A", "A10136C", "G10138A" - ], - "M": [ - "D72E" - ], - "NS2B": [ - "V106I" - ], - "NS3": [ - "I221V", - "I384V" - ], - "NS4B": [ - "V18A" ] - }, - "labels": { - "aa": "M: D72E; NS2B: V106I; NS3: I221V, I384V; NS4B: V18A" } }, "children": [ { "name": "OK469342.1|1997", "node_attrs": { - "div": 0.0668611, - "country": { - "value": "Malaysia" - }, + "div": 0.0669, "clade_membership": { "value": "1IV" } @@ -21255,7 +17534,6 @@ "mutations": { "nuc": [ "T244C", - "C328T", "A352G", "C382T", "C407A", @@ -21298,7 +17576,6 @@ "T1957C", "G1963A", "G2044A", - "C2068T", "C2296T", "C2330T", "T2359C", @@ -21330,7 +17607,6 @@ "C3915T", "T3956G", "T3982C", - "A4015G", "G4060C", "C4061T", "C4078T", @@ -21462,53 +17738,14 @@ "A10210T", "C10213T", "C10243T" - ], - "C": [ - "L105I" - ], - "E": [ - "E157D", - "S225T" - ], - "M": [ - "A29V", - "T107A" - ], - "NS1": [ - "A60T", - "K206R", - "R214K" - ], - "NS2A": [ - "F93I", - "A147V", - "L161V" - ], - "NS3": [ - "K216R", - "Y549H" - ], - "NS4B": [ - "A19V", - "V116L", - "I172V" - ], - "NS5": [ - "I34M", - "N528S", - "S629L", - "H828Y" ] - }, - "labels": { - "aa": "C: L105I; E: E157D, S225T; M: A29V, T107A; NS1: A60T, K206R, R214K; NS2A: F93I, A147V, L161V; NS3: K216R, Y549H; NS4B: A19V, V116L, I172V; NS5: I34M, N528S, S629L, H828Y" } } }, { - "name": "NODE_0000146", + "name": "NODE_0000153", "node_attrs": { - "div": 0.047870010000000005, + "div": 0.0479, "clade_membership": { "value": "1IV" } @@ -21524,6 +17761,7 @@ "A4474G", "T4570C", "C4621T", + "C4861T", "C5320T", "C7183T" ] @@ -21531,9 +17769,9 @@ }, "children": [ { - "name": "NODE_0000147", + "name": "NODE_0000154", "node_attrs": { - "div": 0.05519327, + "div": 0.0552, "clade_membership": { "value": "1IV_A" } @@ -21541,55 +17779,60 @@ "branch_attrs": { "mutations": { "nuc": [ + "G349A", "G434A", + "T556C", "T557C", "C811A", "C955A", - "T1123C", - "C1135T", "C1144T", + "A1159G", "G1252A", "C1307T", "A1354C", + "C1357T", "C1416T", + "T1495C", "G1600A", + "G1822A", "G1825A", + "T1847C", + "G1900A", "T2188C", "T2413C", - "T2809C", + "C2812T", "G2965A", + "C3184T", "C3512T", "C3698T", "T3787C", + "G3877A", "G3898A", - "T4007C", + "A4042G", "T4099C", "C4223T", "C4412A", "T4420C", "C4480T", "G4654A", - "C4837A", - "C4861T", "C4874T", "C5002T", + "C5011T", "G5669A", "C5773T", "A5824G", "G6058A", "C6163T", "G6190A", - "A6535G", + "C6463T", + "C6496T", "T6584C", "T6607C", - "A6613G", "G6644T", "T6800C", "T6901C", - "T6952C", "A6967G", - "C7066T", - "T7216C", + "G7174A", "G7294A", "C7309T", "A7366T", @@ -21602,56 +17845,28 @@ "A8035G", "C8335T", "G8371A", - "T8395C", "A8467G", - "G8706A", + "T8722C", "C8788T", "T9019C", "T9040C", + "T9260C", "A9301T", "A9355G", "A9492G", - "T9697C", - "G9739A", "C9829T", "A10090G" - ], - "C": [ - "A114T" - ], - "E": [ - "T161I", - "M297I" - ], - "NS2A": [ - "F178L" - ], - "NS2B": [ - "L95I" - ], - "NS3": [ - "P119S", - "V384I" - ], - "NS4A": [ - "A90S" - ], - "NS5": [ - "T135I", - "R378K", - "E640G" ] }, "labels": { - "aa": "C: A114T; E: T161I, M297I; NS2A: F178L; NS2B: L95I; NS3: P119S, V384I; NS4A: A90S; NS5: T135I, R378K, E640G", "lineage": "1IV_A" } }, "children": [ { - "name": "NODE_0000148", + "name": "NODE_0000155", "node_attrs": { - "div": 0.07893297, + "div": 0.0557, "clade_membership": { "value": "1IV_A" } @@ -21659,636 +17874,147 @@ "branch_attrs": { "mutations": { "nuc": [ - "G302A", - "A361G", - "G388A", - "C429T", - "C598T", - "G610A", - "C694T", - "G721A", - "G892A", - "A1006G", - "A1054G", - "C1069T", - "G1072A", - "G1078A", - "C1109T", - "C1141T", - "G1180A", - "C1240G", - "T1267C", - "C1270T", "T1282C", - "C1284T", - "T1285C", - "T1337C", - "C1357A", - "C1375T", - "G1447A", - "T1489C", - "T1495C", - "G1675A", - "C1717T", - "C1780T", "C1789T", - "A1792G", - "C1793T", "T1824C", - "T1847C", - "T1906C", - "C1971T", - "G1981A", - "G2027A", - "G2167A", - "C2176T", - "G2228A", - "A2257G", - "G2263T", - "G2275A", - "T2336C", - "A2338G", - "T2380A", "C2440T", - "C2497T", - "C2608T", - "G2683A", - "A2689T", - "A2704G", - "A2719G", - "C2812T", - "C2849T", - "T2905C", - "T2930C", - "C2959T", - "A2994G", - 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"G574T", + "A580G", + "C715T", + "A789G", + "G1003A", + "T1123C", + "C1135T", + "G1456A", + "A1777C", + "T1804C", + "T1814C", + "A1988G", + "A2332G", + "T2727C", + "A2791T", + "A2803T", + "T2809C", + "C2962T", + "T3079C", + "A3562G", + "T3628C", + "T3646C", + "G3676T", + "A3790G", + "G3874A", + "T3916C", + "T3929C", + "T4007C", + "G4015A", + "G4060T", + "T4153C", + "T4186C", + "G4361A", + "A4411G", + "T4435C", + "T4642C", + "C4690T", + "C4837A", + "C5045T", + "A5047G", + "T5104C", + "C5182T", + "T5206C", + "T5365A", + "G5532A", + "C5962T", + "T6034C", + "A6073T", + "C6121T", + "C6518T", + "A6520G", + "A6535G", + "A6613G", + "C6776T", + "T6904C", + "T6952C", + "C7066T", + "T7163C", + "T7198A", + "T7216C", + "A7510G", + "C7576G", + "A7609G", + "A7699G", + "G8077A", + "C8269T", + "A8344G", + "A8356G", + "T8395C", + "G8626A", + "C8656T", + "G8706A", + "C8858A", + "A8877G", + "C9388T", + "C9485T", + "C9502T", + "A9537G", + "T9610C", + "T9697C", + "T9706C", + "G9739A", + "T9772G", + "A9841G", + "C9943T", + "T10066C" + ] + } + }, + "children": [ + { + "name": "JN697056.1|2005-01-01", + "node_attrs": { + "div": 0.0791, + "clade_membership": { + "value": "1IV_A" + }, + "country": { + "value": "Malaysia" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G484A", + "T505C", + "G649A", + "A655G", + "T685C", + "G731A", + "A745G", + "T817C", + "C883T", + "T1345C", + "A1477G", + "C1481T", + "T1486C", + "C1574T", + "T1580C", + "C1717T", + "G1735T", + "C1777T", + "C1780T", + "A1993G", + "T2068C", + "T2083A", + "T2125C", + "T2266C", + "C2281T", + "T2287C", "C2356T", "G2387A", "C2515T", @@ -22332,6 +18594,7 @@ "A2716G", "A2726T", "C2752T", + "T2812C", "C2815T", "C2890T", "C2959T", @@ -22346,7 +18609,6 @@ "A3487G", "G3561A", "C3787T", - "G3877A", "G3886A", "A3931G", "T3949C", @@ -22397,6 +18659,7 @@ "C6923T", "T7015C", "T7030C", + "A7174G", "T7453C", "C7465T", "G7591A", @@ -22438,43 +18701,14 @@ "C9916T", "T10057C", "C10075T" - ], - "E": [ - "S305P", - "V485I" - ], - "M": [ - "V99I" - ], - "NS1": [ - "T103S" - ], - "NS2A": [ - "R29K" - ], - "NS2B": [ - "K127R" - ], - "NS3": [ - "K255R", - "Q334L" - ], - "NS5": [ - "T27I", - "I34V", - "E615G", - "S629L" ] - }, - "labels": { - "aa": "E: S305P, V485I; M: V99I; NS1: T103S; NS2A: R29K; NS2B: K127R; NS3: K255R, Q334L; NS5: T27I, I34V, E615G, S629L" } } }, { - "name": "NODE_0000150", + "name": "NODE_0000158", "node_attrs": { - "div": 0.06847745, + "div": 0.0685, "clade_membership": { "value": "1IV_A" } @@ -22484,18 +18718,20 @@ "nuc": [ "G466T", "T1070C", + "C1495T", "T1606C", "G1810A", + "C1847T", "G2038A", "T2050C", "C2527T", - "C2812T", "C2938T", "C3103T", "A3301C", "T3358C", "C3379T", "A3608T", + "A3877G", "C3919T", "T3956C", "T3982C", @@ -22512,7 +18748,6 @@ "G6538A", "T6625A", "T6946C", - "G7174A", "A7240G", "A7558G", "A7624G", @@ -22526,28 +18761,19 @@ "G9310A", "T9691C", "T9890C" - ], - "NS2A": [ - "M45L" - ], - "NS2B": [ - "E58K" ] - }, - "labels": { - "aa": "NS2A: M45L; NS2B: E58K" } }, "children": [ { "name": "OK469341.1|1992", "node_attrs": { - "div": 0.07020831, - "country": { - "value": "Singapore" - }, + "div": 0.0702, "clade_membership": { "value": "1IV_A" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -22556,7 +18782,6 @@ "C538T", "G1183A", "A1480G", - "C2068T", "A2209T", "A3295G", "C3673T", @@ -22571,24 +18796,14 @@ "G9202A", "G9233A", "C9394T" - ], - "NS2B": [ - "V109M" - ], - "NS5": [ - "I135M", - "D554N" ] - }, - "labels": { - "aa": "NS2B: V109M; NS5: I135M, D554N" } } }, { - "name": "NODE_0000151", + "name": "NODE_0000159", "node_attrs": { - "div": 0.08093195, + "div": 0.0809, "clade_membership": { "value": "1IV_A" } @@ -22625,6 +18840,7 @@ "C1793T", "A1825G", "T1906C", + "T2068C", "C2104T", "T2203C", "T2251C", @@ -22714,54 +18930,19 @@ "C10066T", "A10162G", "C10255T" - ], - "C": [ - "A112V" - ], - "E": [ - "S222T", - "I297M" - ], - "NS1": [ - "I224V" - ], - "NS2A": [ - "A38V", - "E121D", - "F159L" - ], - "NS2B": [ - "Y122H" - ], - "NS3": [ - "R15K" - ], - "NS4A": [ - "L55I", - "M89T" - ], - "NS4B": [ - "A18T" - ], - "NS5": [ - "Y127H", - "D544E" ] - }, - "labels": { - "aa": "C: A112V; E: S222T, I297M; NS1: I224V; NS2A: A38V, E121D, F159L; NS2B: Y122H; NS3: R15K; NS4A: L55I, M89T; NS4B: A18T; NS5: Y127H, D544E" } }, "children": [ { "name": "MW265693.1|2012-04-28", "node_attrs": { - "div": 0.08709518000000001, - "country": { - "value": "New Caledonia" - }, + "div": 0.0871, "clade_membership": { "value": "1IV_A" + }, + "country": { + "value": "New Caledonia" } }, "branch_attrs": { @@ -22829,48 +19010,19 @@ "G9537A", "T9778C", "A10093G" - ], - "E": [ - "V55I", - "K363R" - ], - "NS1": [ - "P138Q", - "A213T", - "I242V" - ], - "NS2A": [ - "T34I" - ], - "NS2B": [ - "I33V", - "A70T" - ], - "NS3": [ - "T91M", - "T115I", - "I520V", - "V551A" - ], - "NS5": [ - "E24Q", - "R655K" ] - }, - "labels": { - "aa": "E: V55I, K363R; NS1: P138Q, A213T, I242V; NS2A: T34I; NS2B: I33V, A70T; NS3: T91M, T115I, I520V, V551A; NS5: E24Q, R655K" } } }, { "name": "JQ915076.1|2009-06-09", "node_attrs": { - "div": 0.08507074, - "country": { - "value": "French Polynesia" - }, + "div": 0.0851, "clade_membership": { "value": "1IV_A" + }, + "country": { + "value": "French Polynesia" } }, "branch_attrs": { @@ -22916,20 +19068,7 @@ "A9847G", "C9907T", "T10012C" - ], - "NS1": [ - "N293H" - ], - "NS3": [ - "A170T", - "I474V" - ], - "NS5": [ - "T27I" ] - }, - "labels": { - "aa": "NS1: N293H; NS3: A170T, I474V; NS5: T27I" } } } @@ -22942,9 +19081,9 @@ ] }, { - "name": "NODE_0000152", + "name": "NODE_0000160", "node_attrs": { - "div": 0.04814628000000001, + "div": 0.0481, "clade_membership": { "value": "1IV" } @@ -22952,16 +19091,16 @@ "branch_attrs": { "mutations": { "nuc": [ - "C2947T", - "C5581T" + "T328C", + "C2947T" ] } }, "children": [ { - "name": "NODE_0000153", + "name": "NODE_0000161", "node_attrs": { - "div": 0.05585036000000001, + "div": 0.0522, "clade_membership": { "value": "1IV" } @@ -22969,125 +19108,57 @@ "branch_attrs": { "mutations": { "nuc": [ - "G334A", - "G388A", "C410T", "C538T", - "T643C", "G892A", "G1072A", - "T1123C", - "C1399T", "T1486C", - "C1687T", "A1711G", "A1823G", "G1825A", - "T1856C", "G1861A", "A1909G", + "T2068C", "C2341T", "C2437T", "T2698C", "A2704G", "G2855A", - "C2983T", - "T3156C", "C3287A", - "T3339C", - "A3565G", - "T3802C", "T3982C", "G3991A", - "A4015G", - "A4123G", "A4128G", - "T4138C", - "T4372C", "C4439T", "C4882T", - "T4909C", "A5080G", "G5113A", - "A5116G", "G5266A", - "C5296T", "T5347C", "T5353C", - "T5848C", - "T5878C", "A5916C", - "A5939G", - "T5941G", "T6034C", - "C6095T", - "C6265T", "G6435A", "C6454T", "T6499C", - "C6682T", - "A7207G", - "C7246T", "G7378A", "C7415T", - "T7504C", - "A7546G", "G7591A", - "A7597G", "G7639A", "C7653T", - "A7807T", "T7843C", - "C8650T", "C9058T", - "C9409T", - "C9490T", "C9694T", - "A9790C", "T9890C", "T9904C", - "T9928C", - "T10198C", - "C10216T" - ], - "C": [ - "L106F" - ], - "E": [ - "M297V" - ], - "NS1": [ - "D146N", - "I246T", - "H290N", - "I307T" - ], - "NS2A": [ - "K218R" - ], - "NS3": [ - "Q466P", - "I474V" - ], - "NS4A": [ - "R20K" - ], - "NS5": [ - "T27I" + "T10198C" ] - }, - "labels": { - "aa": "C: L106F; E: M297V; NS1: D146N, I246T, H290N, I307T; NS2A: K218R; NS3: Q466P, I474V; NS4A: R20K; NS5: T27I" } }, "children": [ { - "name": "OK605753.1|1983", + "name": "OQ061266.1|1983", "node_attrs": { - "div": 0.059814950000000006, - "country": { - "value": "Australia" - }, + "div": 0.0623, "clade_membership": { "value": "1IV" } @@ -23095,320 +19166,296 @@ "branch_attrs": { "mutations": { "nuc": [ - "G559A", - "C598T", - "C698A", - "G763C", - "C1024T", - "C1027T", - "A1451G", - "G1900A", - "G1987A", - "A2143G", - "A2242G", - "A2866G", - "G3060A", - "C3550T", - "T3703C", - "A4934G", - "T5017C", - "T5365C", - "A5402G", - "C5617T", - "T5833C", - "C6082T", - "G6511A", - "T6666C", - "C6850T", - "T6901A", - "C7138T", + "T375C", + "C403T", + "G421A", + "C431T", + "T511C", + "G565A", + "T667C", + 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"T8419C", + "T8464C", + "C8656T", + "A8665G", "C8704T", - "C9265T", - "A9316G", - "C9466T", - "C9586T" - ], - "E": [ - "I173V" - ], - "NS1": [ - "R214K" - ], - "NS3": [ - "I139V", - "I295V" - ], - "NS4A": [ - "M45I", - "M97T" - ], - "NS4B": [ - "H25Q" - ], - "NS5": [ - "I181V" + "T8815C", + "C8926T", + "T9157C", + "A9301G", + "C9406T", + "C9459T", + "C9502T", + "A9513G", + "C9526T", + "G9745A", + "T9898C", + "C9916T", + "C10153T" ] - }, - "labels": { - "aa": "E: I173V; NS1: R214K; NS3: I139V, I295V; NS4A: M45I, M97T; NS4B: H25Q; NS5: I181V" } } }, { - "name": "NODE_0000154", + "name": "NODE_0000162", "node_attrs": { - "div": 0.06108953000000001, + "div": 0.0558, "clade_membership": { - "value": "1IV_C" + "value": "1IV" } }, "branch_attrs": { "mutations": { "nuc": [ - "G370A", - "G610A", - "C664T", - "C847T", - "C1060T", - "T1093A", - "C1135T", - "C1336T", - "A1585G", - "A1795G", - "C1933T", - "G1948A", - "C1971T", - "C2176T", - "T2227C", - "C2485T", - "T2677C", - "A2785G", - "A3170G", 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+ "C4690T", + "C5083T", + "C5569A", + "C6379T", + "G6436A", + "C6439T", + "C6526T", + "A6661G", + "A6749C", + "T7033C", + "T7180C", + "A7660G", + "G7960A", + "G8056A", + "C8098T", + "A8167G", + "G8317A", + "A8683G", + "A8758G", + "C8767T", + "C8779T", + "C8863T", + "C9223A", + "C9463T", + "T9484C", + "C9500T", + "T9658C", + "T10048C", + "T10204C" ] - }, - "labels": { - "aa": "C: M104V; E: D37N, V55I; NS2A: V101I, S142P, F159L, F178L; NS2B: A105V; NS4A: Q19L" } }, "children": [ { - "name": "JN544410.2|2011-04", + "name": "KU509261.1|2010", "node_attrs": { - "div": 0.08061778, - "country": { - "value": "Singapore" - }, + "div": 0.089, "clade_membership": { "value": "1IV_C" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { "mutations": { "nuc": [ - "C328T", - "A363G", - "A473G", - "A479G", - "G553A", - "C595T", - "T667C", - "T742C", - "A871G", - "C1100T", - "C1109T", - "G1177A", - "A1327G", - "T1330C", - "T1441C", - "G1483A", - "C1574T", - "A1636G", - "T1654C", - "T1906C", - "T1933C", - "C1945T", + "C448T", + "C451A", + "A489G", + "A493G", + "A502C", + "G508T", + "T544C", + "C757A", + "G763A", + "A844G", + "A892G", + "C955T", + "T1285C", + "T1399C", + "C1643T", + "T1769A", + "G1909A", + "G2041A", + "G2044A", + "A2047G", + "G2055T", + "C2062T", + "G2072A", "T2092C", - "C2177T", - "T2203C", - "C2376T", - "G2560A", - "A2689G", - "T2708C", - "C2824T", - "T2947C", - "C3118T", - "C3339T", - "C3433T", - "T3519C", - "C3588T", - "G3706A", - "C3712T", - "C3742T", - "T3784C", - "A3823T", - "T3833C", + "G2131A", + "C2227T", + "C2458T", + "C2470T", + "C2473T", + "G2563A", + "C2686T", + "A2968G", + "T3053C", + "A3061G", + "C3088T", + "G3565A", + "T3584C", + "C3596T", + "C3606T", + "G3640A", + "C3641T", + "T3646C", + "T3664C", + "A3670C", + "T3675G", + "A3691G", + "T3704C", + "C3718T", + "G3720A", + "C3736T", + "A3739T", + "C3742A", + "T3754C", + "T3761C", + "T3769C", + "T3787A", + "G3791A", + "C3802T", + "G3805A", + "A3817G", + "A3820G", + "C3821T", + "A3835G", + 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"K72R", - "R325K", - "L503F", - "F643S" + "G3938A", + "A3946G", + "T3949G", + "C3982T", + "A3986G", + "A3991G", + "T4012C", + "T4030C", + "T4033C", + "C4061T", + "T4072C", + "A4103G", + "T4117C", + "G4123A", + "G4128A", + "T4153C", + "A4160G", + "T4192C", + "A4210G", + "C4219G", + "G4273A", + "G4288A", + "G4297A", + "G4303A", + "T4318A", + "G4337A", + "C4352T", + "C4372T", + "A4411G", + "C4414A", + "C4426T", + "T4439C", + "A4445G", + "C4447T", + "A4456G", + "A4463T", + "G4465A", + "G4474A", + "C4483T", + "T4495C", + "A4522T", + "C4543T", + "G4553A", + "C4570T", + "C4576T", + "T4585C", + "C4595A", + "C4597G", + "A4627G", + "A4630G", + "A4633G", + "T4639C", + "T4772C", + "T4813C", + "T4819A", + "G4825A", + "G4831A", + "A4897T", + "T4900C", + "G4981A", + "G5080A", + "A5122G", + "G5180A", + "C5182T", + "T5183C", + "C5188T", + "T5248C", + "G5278A", + "A5281G", + "T5299C", + "C5641T", + "G5659A", + "C5671T", + "G5707A", + "T5734C", + "G5890A", + "G5935A", + "C6302A", + "T6457C", + "A6535G", + "G6580A", + "C6670T", + "G6730A", + "C6757T", + "C6882T", + "A6967G", + "T6976C", + "C6991T", + "G7054A", + "G7147A", + "C7169T", + "G7174A", + "T7219C", + "C7273T", + "A7303G", + "C7408T", + "C7474T", + "G7663A", + "T7757C", + "G7759A", + "T7828C", + "C7882T", + "A7888G", + "T7975C", + "A8035G", + "T8137C", + "C8156A", + "T8293C", + "C8527T", + "C8596T", + "T8647C", + "T8719G", + "A8845T", + "C8926T", + "T9019C", + "C9064T", + "C9256T", + "C9499A", + "C9610T", + "T9691A", + "T9823C", + "T9854G", + "G9895A", + "T9901C", + "C9920T", + "C9928T", + "C9943A", + "G9958A", + "C9970T", + "T9973C", + "C9974A", + "T10207C" ] - }, - "labels": { - "aa": "C: N90S; E: A481V; M: I13V, S15G, M39I; NS1: T307I; NS2A: I15T, A38V; NS3: P466S; NS4B: A27T; NS5: K72R, R325K, L503F, F643S" } } }, { - "name": "NODE_0000158", + "name": "NODE_0000166", "node_attrs": { - "div": 0.07111411, + "div": 0.0709, "clade_membership": { "value": "1IV_C" } @@ -24124,85 +19969,174 @@ "branch_attrs": { "mutations": { "nuc": [ - "T1513C", - "A4960G" + "T335C", + "A388G", + "A404G", + "C880T", + "C1033A", + "G1043A", + "G1097A", + "C1138T", + "C1307T", + "A1390G", + "A2086G", + "T2809C", + "C3379T", + "G3745A", + "A3748C", + "G3776A", + "G3838A", + "T3899C", + "T3950C", + "A4000G", + "T4007C", + "T4030A", + "A4042G", + "T4171A", + "G4390A", + "C4443T", + "G4858A", + "C4894T", + "C5227T", + "C5353T", + "T5938C", + "A6432T", + "T6554C", + "T6584C", + "C7474A", + "G7873A", + "A8266G", + "C8521T", + "T8794C", + "A8824G", + "G8887A", + "C9127T", + "A9775G", + "A9976G", + "C10255T" ] } }, "children": [ { - "name": "KT827364.1|2002", + "name": "JN544410.2|2011-04", "node_attrs": { - "div": 0.07398025999999999, - "country": { - "value": "China" - }, + "div": 0.0806, "clade_membership": { "value": "1IV_C" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { "mutations": { "nuc": [ - "A1993G", - "C2321T", - "C2389T", - "C2407T", - "T2557A", - "A2943T", - "C3319T", - "C3469T", - "T3497C", - "T3952G", - "C4280T", - "A4432T", - "C4480T", - "A4912G", - "G5079A", - "G6127A", - "A6490T", - "C6654T", - "T6970C", - "G7445A", - "G7774A", - "C7957T", - "A8317G", - "C8404G", - "C8605T", - "T8815C", - "G9628A", - "A10051G", - "G10261A", - "A10272G" - ], - "NS1": [ - "Y175F" - ], - "NS2A": [ - "F8L" - ], - "NS3": [ - "R187K" - ], - "NS4A": [ - "A93V" - ], - "NS4B": [ - "E207K" + "C328T", + "A363G", + "A473G", + "A479G", + "G553A", + "C595T", + "T667C", + "T742C", + "A871G", + "C1100T", + "C1109T", + "G1177A", + "A1327G", + "T1330C", + "T1441C", + "G1483A", + "C1574T", + "A1636G", + "T1654C", + "T1906C", + "T1933C", + "C1945T", + "T2092C", + "C2177T", + "T2203C", + "C2376T", + "G2560A", + "A2689G", + "T2708C", + "C2824T", + "T2947C", + "C3118T", + "C3339T", + "C3433T", + "T3519C", + "C3588T", + "G3706A", + "C3712T", + "C3742T", + "T3784C", + "A3823T", + "T3833C", + "A3931G", + "T4003C", + "A4462T", + "T4607C", + "T4765C", + "C5140T", + "C5191A", + "T5338C", + "C5347T", + "C5398T", + "T5692C", + "T5719C", + "C5915T", + "T5920C", + "G6052A", + "A6148G", + "T6239C", + "A6280G", + "A6295G", + "T6398C", + "T6562C", + "T6685C", + "A6838T", + "T6877C", + "G6905A", + "A6937G", + "G7069A", + "A7285T", + "T7357C", + "C7408A", + "C7636T", + "G7708A", + "A7788G", + "A7945G", + "A8197G", + "G8314A", + "G8547A", + "T8569C", + "T8635C", + "A8770G", + "C8830T", + "T8911C", + "C9080T", + "C9235T", + "C9289T", + "C9346G", + "C9394T", + "T9445C", + "T9470C", + "T9501C", + "T9509C", + "T9706C", + "G9838A", + "C10075T", + "C10156T" ] - }, - "labels": { - "aa": "NS1: Y175F; NS2A: F8L; NS3: R187K; NS4A: A93V; NS4B: E207K" } } }, { - "name": "KC762630.1|2008-02-06", + "name": "NODE_0000167", "node_attrs": { - "div": 0.07784933999999999, - "country": { - "value": "Indonesia" - }, + "div": 0.0711, "clade_membership": { "value": "1IV_C" } @@ -24210,95 +20144,146 @@ "branch_attrs": { "mutations": { "nuc": [ - "A318G", - "C409G", - "G463A", - "T511C", - "T556C", - "T853C", - "G907A", - "G946A", - "C1024T", - "C1084T", - "T1204C", - "C1475T", - "T1654C", - "G1810A", - "T1831C", - "C2200T", - "T2464C", - "A2593G", - "G2926A", - "T2947C", - "G2953A", - "T3079C", - "G3130T", - "C3415T", - "T3496C", - "T3655C", - "C3884T", - "G4207A", - "A4469G", - "G4886A", - "A4897C", - "C5028T", - "C5168T", - "T5299C", - "T5305C", - "C5401T", - "T5443C", - "T5590A", - "A5683G", - "T5719C", - "G5815A", - "T6037C", - "G6109A", - "G6262A", - "A6484G", - "A6493G", - "A6823T", - "G7276T", - "G7304A", - "A7333G", - "C7471T", - "T7501C", - "A7522G", - "T8128C", - "T8149C", - "A8170G", - "C8390T", - "T8767C", - "T8920C", - "T9037A", - "A9052G", - "C9082T", - "C9321G", - "C9550T", - "G9814A", - "G10006A", - "C10033T" - ], - "C": [ - "N75S" - ], - "NS2B": [ - "I114V" - ], - "NS3": [ - "V123I", - "A170V" - ], - "NS4B": [ - "V160I" - ], - "NS5": [ - "A583G" + "T1513C", + "A4960G" ] + } + }, + "children": [ + { + "name": "KT827364.1|2002", + "node_attrs": { + "div": 0.074, + "clade_membership": { + "value": "1IV_C" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A1993G", + "C2321T", + "C2389T", + "C2407T", + "T2557A", + "A2943T", + "C3319T", + "C3469T", + "T3497C", + "T3952G", + "C4280T", + "A4432T", + "C4480T", + "A4912G", + "G5079A", + "G6127A", + "A6490T", + "C6654T", + "T6970C", + "G7445A", + "G7774A", + "C7957T", + "A8317G", + "C8404G", + "C8605T", + "T8815C", + "G9628A", + "A10051G", + "G10261A", + "A10272G" + ] + } + } }, - "labels": { - "aa": "C: N75S; NS2B: I114V; NS3: V123I, A170V; NS4B: V160I; NS5: A583G" + { + "name": "KC762630.1|2008-02-06", + "node_attrs": { + "div": 0.0778, + "clade_membership": { + "value": "1IV_C" + }, + "country": { + "value": "Indonesia" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A318G", + "C409G", + "G463A", + "T511C", + "T556C", + "T853C", + "G907A", + "G946A", + "C1024T", + "C1084T", + "T1204C", + "C1475T", + "T1654C", + "G1810A", + "T1831C", + "C2200T", + "T2464C", + "A2593G", + "G2926A", + "T2947C", + "G2953A", + "T3079C", + "G3130T", + "C3415T", + "T3496C", + "T3655C", + "C3884T", + "G4207A", + "A4469G", + "G4886A", + "A4897C", + "C5028T", + "C5168T", + "T5299C", + "T5305C", + "C5401T", + "T5443C", + "T5590A", + "A5683G", + "T5719C", + "G5815A", + "T6037C", + "G6109A", + "G6262A", + "A6484G", + "A6493G", + "A6823T", + "G7276T", + "G7304A", + "A7333G", + "C7471T", + "T7501C", + "A7522G", + "T8128C", + "T8149C", + "A8170G", + "C8390T", + "T8767C", + "T8920C", + "T9037A", + "A9052G", + "C9082T", + "C9321G", + "C9550T", + "G9814A", + "G10006A", + "C10033T" + ] + } + } } - } + ] } ] } @@ -24311,9 +20296,9 @@ ] }, { - "name": "NODE_0000159", + "name": "NODE_0000168", "node_attrs": { - "div": 0.053356110000000005, + "div": 0.0534, "clade_membership": { "value": "1IV_B" } @@ -24330,7 +20315,6 @@ "G1672A", "C1846G", "G2038A", - "C2068T", "A2215G", "G2240A", "A2257G", @@ -24342,13 +20326,14 @@ "A3271T", "T3749C", "A3751G", + "G4015A", "C4058T", "T4132C", "A4180T", "C4264T", - "C4861T", "C5359T", "C5419T", + "C5581T", "T5833C", "T5881C", "T6448C", @@ -24371,21 +20356,17 @@ "C8150T", "G8371A", "T10048C" - ], - "E": [ - "V436I" ] }, "labels": { - "aa": "E: V436I", "lineage": "1IV_B" } }, "children": [ { - "name": "NODE_0000160", + "name": "NODE_0000169", "node_attrs": { - "div": 0.055287960000000004, + "div": 0.0553, "clade_membership": { "value": "1IV_B" } @@ -24416,37 +20397,19 @@ "T9525C", "A10051G", "A10215T" - ], - "NS1": [ - "D146N", - "I307T" - ], - "NS3": [ - "T91A" - ], - "NS4A": [ - "M89I" - ], - "NS5": [ - "E647K", - "I651T", - "Y881F" ] - }, - "labels": { - "aa": "NS1: D146N, I307T; NS3: T91A; NS4A: M89I; NS5: E647K, I651T, Y881F" } }, "children": [ { "name": "MW945952.1|1974", "node_attrs": { - "div": 0.05617391000000001, - "country": { - "value": "Nauru" - }, + "div": 0.0562, "clade_membership": { "value": "1IV_B" + }, + "country": { + "value": "Nauru" } }, "branch_attrs": { @@ -24461,35 +20424,19 @@ "T6445C", "T7173C", "C9946T" - ], - "E": [ - "K202E", - "E203K" - ], - "M": [ - "A127V" - ], - "NS3": [ - "N481K" - ], - "NS4B": [ - "V116A" ] - }, - "labels": { - "aa": "E: K202E, E203K; M: A127V; NS3: N481K; NS4B: V116A" } } }, { "name": "OK469344.1|1975", "node_attrs": { - "div": 0.05607509, - "country": { - "value": "Fiji" - }, + "div": 0.0561, "clade_membership": { "value": "1IV_B" + }, + "country": { + "value": "Fiji" } }, "branch_attrs": { @@ -24503,25 +20450,16 @@ "C6352T", "T7531C", "C8148A" - ], - "NS3": [ - "I520V" - ], - "NS5": [ - "T192N" ] - }, - "labels": { - "aa": "NS3: I520V; NS5: T192N" } } } ] }, { - "name": "NODE_0000161", + "name": "NODE_0000170", "node_attrs": { - "div": 0.06332222000000001, + "div": 0.0633, "clade_membership": { "value": "1IV_B" } @@ -24630,47 +20568,19 @@ "A9775G", "T9812C", "T9973C" - ], - "C": [ - "G70S" - ], - "E": [ - "M297V", - "I378L" - ], - "M": [ - "K118R" - ], - "NS1": [ - "S94N", - "I123V" - ], - "NS2A": [ - "T148A" - ], - "NS3": [ - "R33K", - "V323M", - "V332A" - ], - "NS5": [ - "I181V" ] - }, - "labels": { - "aa": "C: G70S; E: M297V, I378L; M: K118R; NS1: S94N, I123V; NS2A: T148A; NS3: R33K, V323M, V332A; NS5: I181V" } }, "children": [ { "name": "MF033231.1|2015-03", "node_attrs": { - "div": 0.08398972000000002, - "country": { - "value": "Singapore" - }, + "div": 0.084, "clade_membership": { "value": "1IV_B" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -24873,47 +20783,14 @@ "C10150T", "C10153T", "C10213T" - ], - "C": [ - "N21S", - "T103N" - ], - "M": [ - "S28F" - ], - "NS1": [ - "D92E", - "D278E" - ], - "NS2A": [ - "M133T", - "F159L" - ], - "NS3": [ - "R15K", - "V384I" - ], - "NS5": [ - "I34M", - "Y127H", - "T135I", - "K166R", - "V190I", - "D274N", - "R378K", - "S629T", - "I651T" ] - }, - "labels": { - "aa": "C: N21S, T103N; M: S28F; NS1: D92E, D278E; NS2A: M133T, F159L; NS3: R15K, V384I; NS5: I34M, Y127H, T135I, K166R, V190I, D274N, R378K, S629T, I651T" } } }, { - "name": "NODE_0000162", + "name": "NODE_0000171", "node_attrs": { - "div": 0.06897450000000001, + "div": 0.069, "clade_membership": { "value": "1IV_B" } @@ -24971,34 +20848,14 @@ "C9490T", "G9646A", "A9922G" - ], - "NS1": [ - "A213T", - "D278G" - ], - "NS2A": [ - "T44I" - ], - "NS4B": [ - "A18V", - "N22S" - ], - "NS5": [ - "S629L" ] - }, - "labels": { - "aa": "NS1: A213T, D278G; NS2A: T44I; NS4B: A18V, N22S; NS5: S629L" } }, "children": [ { "name": "GQ868602.1|2004", "node_attrs": { - "div": 0.07615014, - "country": { - "value": "Philippines" - }, + "div": 0.0761, "clade_membership": { "value": "1IV_B" } @@ -25081,39 +20938,14 @@ "T10018C", "G10248A", "C10255T" - ], - "C": [ - "I94X", - "M95X", - "N96S" - ], - "NS1": [ - "I96V", - "T131I" - ], - "NS2A": [ - "A148T" - ], - "NS3": [ - "T91M", - "E575L", - "E576K" - ], - "NS5": [ - "H263N", - "V413I", - "S892N" ] - }, - "labels": { - "aa": "C: I94X, M95X, N96S; NS1: I96V, T131I; NS2A: A148T; NS3: T91M, E575L, E576K; NS5: H263N, V413I, S892N" } } }, { - "name": "NODE_0000163", + "name": "NODE_0000172", "node_attrs": { - "div": 0.06940549000000001, + "div": 0.0694, "clade_membership": { "value": "1IV_B" } @@ -25127,795 +20959,14 @@ "A5683G", "T7513C", "C9518T" - ], - "NS5": [ - "H649Y" ] - }, - "labels": { - "aa": "NS5: H649Y" } }, "children": [ { - "name": "NODE_0000164", - "node_attrs": { - "div": 0.07269792000000001, - "clade_membership": { - "value": "1IV_B.1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C451T", - "C781T", - "G1003A", - "C1135T", - "A1534G", - "A1777G", - "G1903A", - "T2155C", - "A3089G", - "T3236C", - "A3616G", - "G3640A", - "A3643G", - "A3691G", - "T3781C", - "C4195A", - "C4582T", - "G4870A", - "G5224A", - "C5536T", - "T5590A", - "T6070C", - "C6256T", - "T7501C", - "A7624G", - "C7636T", - "C8089T", - "C8251T", - "A8671G", - "C9058T", - "A9100G", - "T9658C", - "C9784T", - "T9919C", - "A10272G" - ], - "NS1": [ - "I224V" - ] - }, - "labels": { - "aa": "NS1: I224V", - "lineage": "1IV_B.1" - } - }, - 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"T9525C", "A9625G" - ], - "NS1": [ - "I246T" - ], - "NS5": [ - "I34M", - "I651T" ] }, "labels": { - "aa": "NS1: I246T; NS5: I34M, I651T", "lineage": "1IV_B.2" } }, @@ -25994,12 +21037,12 @@ { "name": "MT832037.1|2012", "node_attrs": { - "div": 0.08043460000000001, - "country": { - "value": "Philippines" - }, + "div": 0.0804, "clade_membership": { "value": "1IV_B.2" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -26066,29 +21109,14 @@ "A9301G", "T9778C", "C10263T" - ], - "NS1": [ - "K112R", - "A265V", - "K341R" - ], - "NS5": [ - "A245T", - "K248R", - "K366R", - "D432E", - "A897V" ] - }, - "labels": { - "aa": "NS1: K112R, A265V, K341R; NS5: A245T, K248R, K366R, D432E, A897V" } } }, { - "name": "NODE_0000169", + "name": "NODE_0000174", "node_attrs": { - "div": 0.07601478000000002, + "div": 0.076, "clade_membership": { "value": "1IV_B.2" } @@ -26109,21 +21137,14 @@ "T6898C", "T8104C", "A8851G" - ], - "NS2A": [ - "V175I", - "L182M" ] - }, - "labels": { - "aa": "NS2A: 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"C2200T", + "G2224A", + "G2230T", + "G2239A", + "T2290C", + "A2315G", + "C2374T", + "A2384C", "C2389A", "C2422T", "C2437T", @@ -26845,52 +22512,17 @@ "C10085T", "C10189A", "A10272G" - ], - "E": [ - "T155S", - "I461V", - "M484L" - ], - "M": [ - "K122R" - ], - "NS1": [ - "I224V" - ], - "NS2A": [ - "M133I", - "T210A" - ], - "NS2B": [ - "M112L" - ], - "NS3": [ - "L26M", - "G44N", - "F85L", - "A293S" - ], - "NS4A": [ - "K39R" - ], - "NS4B": [ - "A20V" - ], - "NS5": [ - "N285H", - "H649Y" ] }, "labels": { - "aa": "E: T155S, I461V, M484L; M: K122R; NS1: I224V; NS2A: M133I, T210A; NS2B: M112L; NS3: L26M, G44N, F85L, A293S; NS4A: K39R; NS4B: A20V; NS5: N285H, H649Y", "lineage": "1I" } }, "children": [ { - "name": "NODE_0000173", + "name": "NODE_0000183", "node_attrs": { - "div": 0.05582542, + "div": 0.0558, "clade_membership": { "value": "1I_B" } @@ -26898,7 +22530,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "C328T", "A391G", "C439T", "C469T", @@ -26965,26 +22596,9 @@ "A10090G", "C10153T", "T10249C" - ], - "E": [ - "L351V" - ], - "M": [ - "S15T" - ], - "NS1": [ - "T131S" - ], - "NS2A": [ - "T148A" - ], - "NS5": [ - "P108A", - "R367Q" ] }, "labels": { - "aa": "E: L351V; M: S15T; NS1: T131S; NS2A: T148A; NS5: P108A, R367Q", "lineage": "1I_B" } }, @@ -26992,12 +22606,12 @@ { "name": "AY732483.1|1981", "node_attrs": { - "div": 0.05937958, - "country": { - "value": "Thailand" - }, + "div": 0.0594, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -27039,41 +22653,14 @@ "A9913C", "T9925C", "G9992A" - ], - "E": [ - "T145S" - ], - "M": [ - "A29T" - ], - "NS1": [ - "V286I" - ], - "NS2A": [ - "H143Y", - "F159Y" - ], - "NS3": [ - "E536D", - "M538L" - ], - "NS4B": [ - "L113S" - ], - "NS5": [ - "R378K", - "D807N" ] - }, - "labels": { - "aa": "E: T145S; M: A29T; NS1: V286I; NS2A: H143Y, F159Y; NS3: E536D, M538L; NS4B: L113S; NS5: R378K, D807N" } } }, { - "name": "NODE_0000174", + "name": "NODE_0000184", "node_attrs": { - "div": 0.05947401, + "div": 0.0595, "clade_membership": { "value": "1I_B" } @@ -27081,7 +22668,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "T478C", "C724T", "T1607A", "T1654C", @@ -27116,30 +22702,19 @@ "T9676C", "A9790G", "A10114T" - ], - "E": [ - "S225T", - "S397T" - ], - "NS5": [ - "M34I", - "K513R" ] - }, - "labels": { - "aa": "E: S225T, S397T; NS5: M34I, K513R" } }, "children": [ { "name": "MW945829.1|1995", "node_attrs": { - "div": 0.06988661, - "country": { - "value": "Thailand" - }, + "div": 0.0699, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -27147,6 +22722,7 @@ "nuc": [ "G109A", "G428A", + "T478C", "G550A", "G565A", "C595T", @@ -27252,38 +22828,14 @@ "C10150T", "T10153C", "A10242C" - ], - "C": [ - "A112T" - ], - "NS1": [ - "H111Y", - "V224A" - ], - "NS3": [ - "N482S" - ], - "NS4B": [ - "V20A", - "V152I" - ], - "NS5": [ - "A245V", - "R253K", - "Q621L", - "D807N", - "N890T" ] - }, - "labels": { - "aa": "C: A112T; NS1: H111Y, V224A; NS3: N482S; NS4B: V20A, V152I; NS5: A245V, R253K, Q621L, D807N, N890T" } } }, { - "name": "NODE_0000175", + "name": "NODE_0000185", "node_attrs": { - "div": 0.06243925, + "div": 0.0624, "clade_membership": { "value": "1I_B" } @@ -27315,32 +22867,19 @@ "A10060G", "C10216T", "G10246T" - ], - "C": [ - "A112V" - ], - "NS2A": [ - "L182M" - ], - "NS5": [ - "I372V", - "E891D" ] - }, - "labels": { - "aa": "C: A112V; NS2A: L182M; NS5: I372V, E891D" } }, "children": [ { "name": "MW946065.1|1996", "node_attrs": { - "div": 0.07272735, - "country": { - "value": "Thailand" - }, + "div": 0.0727, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -27348,7 +22887,6 @@ "nuc": [ "A337G", "T375C", - "C478T", "C538T", "A982G", "T1204C", @@ -27447,31 +22985,14 @@ "C9523T", "C9934T", "C10249T" - ], - "C": [ - "I94T" - ], - "NS3": [ - "Y405F", - "N467S" - ], - "NS5": [ - "A245V", - "A370V", - "E374G", - "D432E", - "R436K" ] - }, - "labels": { - "aa": "C: I94T; NS3: Y405F, N467S; NS5: A245V, A370V, E374G, D432E, R436K" } } }, { - "name": "NODE_0000176", + "name": "NODE_0000186", "node_attrs": { - "div": 0.06658346, + "div": 0.0666, "clade_membership": { "value": "1I_B" } @@ -27480,6 +23001,7 @@ "mutations": { "nuc": [ "T382C", + "T478C", "G521A", "C595T", "T843C", @@ -27516,29 +23038,19 @@ "G9568T", "A9631G", "A9634G" - ], - "M": [ - "A29T", - "I136T" - ], - "NS2A": [ - "F159C" ] - }, - "labels": { - "aa": "M: A29T, I136T; NS2A: F159C" } }, "children": [ { "name": "KJ649286.1|2011-12-31", "node_attrs": { - "div": 0.07733326, - "country": { - "value": "Saudi Arabia" - }, + "div": 0.0773, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Saudi Arabia" } }, "branch_attrs": { @@ -27652,50 +23164,14 @@ "C10168T", "G10185A", "T10207C" - ], - "E": [ - "A313V", - "S338L" - ], - "M": [ - "V64I" - ], - "NS2B": [ - "I33V" - ], - "NS3": [ - "Q61K", - "S68T" - ], - "NS4A": [ - "N23S", - "R76K", - "V93M" - ], - "NS4B": [ - "L106M", - "A120T" - ], - "NS5": [ - "Y127H", - "T135I", - "Q367R", - "I627L", - "D644N", - "E647G", - "D807N", - "R871K" ] - }, - "labels": { - "aa": "E: A313V, S338L; M: V64I; NS2B: I33V; NS3: Q61K, S68T; NS4A: N23S, R76K, V93M; NS4B: L106M, A120T; NS5: Y127H, T135I, Q367R, I627L, D644N, E647G, D807N, R871K" } } }, { - "name": "NODE_0000177", + "name": "NODE_0000187", "node_attrs": { - "div": 0.07364408, + "div": 0.0736, "clade_membership": { "value": "1I_B" } @@ -27752,32 +23228,19 @@ "C9811T", "T10084C", "C10237T" - ], - "E": [ - "T81A" - ], - "NS2A": [ - "S2L", - "F40L" - ], - "NS5": [ - "A108P" ] - }, - "labels": { - "aa": "E: T81A; NS2A: S2L, F40L; NS5: A108P" } }, "children": [ { "name": "OK040060.1|2011", "node_attrs": { - "div": 0.08378128, - "country": { - "value": "Somalia" - }, + "div": 0.0838, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Somalia" } }, "branch_attrs": { @@ -27872,58 +23335,19 @@ "T10153C", "C10221T", "C10255A" - ], - "C": [ - "T8A", - "G42V", - "I65V" - ], - "E": [ - "W212C", - "P219T" - ], - "M": [ - "P54S", - "G132R" - ], - "NS1": [ - "G47W", - "S174P" - ], - "NS3": [ - "T398P" - ], - "NS4A": [ - "A40X", - "Y41X" - ], - "NS4B": [ - "N59Y", - "A96S", - "S239-" - ], - "NS5": [ - "S39F", - "A245V", - "A377V", - "E458K", - "T883I" ] - }, - "labels": { - "aa": "C: T8A, G42V, I65V; E: W212C, P219T; M: P54S, G132R; NS1: G47W, S174P; NS3: T398P; NS4A: A40X, Y41X; NS4B: N59Y, A96S, S239-; NS5: S39F, A245V, A377V, E458K, T883I" } } }, { "name": "KU509258.1|2010", "node_attrs": { - "div": 0.08562318, - "country": { - "value": "Eritrea" - }, + "div": 0.0856, "clade_membership": { "value": "1I_B" + }, + "country": { + "value": "Eritrea" } }, "branch_attrs": { @@ -28072,52 +23496,7 @@ "T9895A", "T9901C", "A9985G" - ], - "E": [ - "I140V", - "L237M", - "S452T", - "I459K" - ], - "M": [ - "V64I" - ], - "NS1": [ - "W168R", - "I251T" - ], - "NS2A": [ - "G35R", - "I54V" - ], - "NS2B": [ - "I74M", - "D80E", - "D88K" - ], - "NS3": [ - "R185K", - "N401S", - "W403G" - ], - "NS4B": [ - "M88K", - "I90V" - ], - "NS5": [ - "K14R", - "I34M", - "I114V", - "Y127H", - "W381S", - "T399I", - "E500D", - "S629L", - "I669V" ] - }, - "labels": { - "aa": "E: I140V, L237M, S452T, I459K; M: V64I; NS1: W168R, I251T; NS2A: G35R, I54V; NS2B: I74M, D80E, D88K; NS3: R185K, N401S, W403G; NS4B: M88K, I90V; NS5: K14R, I34M, I114V, Y127H, W381S, T399I, E500D, S629L, I669V" } } } @@ -28132,9 +23511,9 @@ ] }, { - "name": "NODE_0000178", + "name": "NODE_0000188", "node_attrs": { - "div": 0.05742453, + "div": 0.0574, "clade_membership": { "value": "1I" } @@ -28143,6 +23522,7 @@ "mutations": { "nuc": [ "G120C", + "T328C", "T335C", "C397T", "C448T", @@ -28235,35 +23615,14 @@ "C9640T", "C9802T", "G10186A" - ], - "C": [ - "G9A" - ], - "E": [ - "N8S", - "V324I", - "V380I" - ], - "NS1": [ - "S94V" - ], - "NS3": [ - "D350E", - "Q466H" - ], - "NS5": [ - "R325K" ] - }, - "labels": { - "aa": "C: G9A; E: N8S, V324I, V380I; NS1: S94V; NS3: D350E, Q466H; NS5: R325K" } }, "children": [ { - "name": "NODE_0000179", + "name": "NODE_0000189", "node_attrs": { - "div": 0.061086310000000005, + "div": 0.0611, "clade_membership": { "value": "1I_A" } @@ -28309,16 +23668,9 @@ "C7066T", "T7216G", "T8725C" - ], - "E": [ - "K343R" - ], - "NS4A": [ - "R76K" ] }, "labels": { - "aa": "E: K343R; NS4A: R76K", "lineage": "1I_A" } }, @@ -28326,12 +23678,12 @@ { "name": "FJ196847.1|1997", "node_attrs": { - "div": 0.08929571, - "country": { - "value": "China" - }, + "div": 0.0893, "clade_membership": { "value": "1I_A" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -28614,54 +23966,14 @@ "T10213C", "G10240A", "G10272A" - ], - "E": [ - "D37N", - "V55I", - "A88T", - "S155T", - "T163I", - "G408A", - "D417G" - ], - "M": [ - "A29T" - ], - "NS1": [ - "I308V" - ], - "NS2A": [ - "N63S", - "H143Y" - ], - "NS3": [ - "L435P", - "H466P", - "I474V" - ], - "NS4B": [ - "T61S" - ], - "NS5": [ - "M34I", - "Y127H", - "T135I", - "H285N", - "L608V", - "L643F", - "Y649H", - "V651I" ] - }, - "labels": { - "aa": "E: D37N, V55I, A88T, S155T, T163I, G408A, D417G; M: A29T; NS1: I308V; NS2A: N63S, H143Y; NS3: L435P, H466P, I474V; NS4B: T61S; NS5: M34I, Y127H, T135I, H285N, L608V, L643F, Y649H, V651I" } } }, { - "name": "NODE_0000180", + "name": "NODE_0000190", "node_attrs": { - "div": 0.06283097, + "div": 0.0628, "clade_membership": { "value": "1I_A" } @@ -28691,12 +24003,12 @@ { "name": "MW946016.1|1995", "node_attrs": { - "div": 0.06828597, - "country": { - "value": "Thailand" - }, + "div": 0.0683, "clade_membership": { "value": "1I_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -28762,38 +24074,14 @@ "G9442A", "A9519G", "T9919C" - ], - "C": [ - "V102M" - ], - "E": [ - "T51S" - ], - "NS2A": [ - "S7N", - "V39A", - "F159L" - ], - "NS2B": [ - "T102S" - ], - "NS4A": [ - "T81S" - ], - "NS5": [ - "R378K", - "Y649C" ] - }, - "labels": { - "aa": "C: V102M; E: T51S; NS2A: S7N, V39A, F159L; NS2B: T102S; NS4A: T81S; NS5: R378K, Y649C" } } }, { - "name": "NODE_0000181", + "name": "NODE_0000191", "node_attrs": { - "div": 0.06340099, + "div": 0.0634, "clade_membership": { "value": "1I_A" } @@ -28812,12 +24100,12 @@ { "name": "MW946160.1|1998", "node_attrs": { - "div": 0.07099275000000001, - "country": { - "value": "Thailand" - }, + "div": 0.071, "clade_membership": { "value": "1I_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -28897,32 +24185,14 @@ "C9526T", "A9790G", "C10237T" - ], - "E": [ - "T145N", - "K361R", - "L447M" - ], - "NS2A": [ - "I155V", - "F159L" - ], - "NS2B": [ - "D88E" - ], - "NS4A": [ - "V93A" ] - }, - "labels": { - "aa": "E: T145N, K361R, L447M; NS2A: I155V, F159L; NS2B: D88E; NS4A: V93A" } } }, { - "name": "NODE_0000182", + "name": "NODE_0000192", "node_attrs": { - "div": 0.06743447000000001, + "div": 0.0674, "clade_membership": { "value": "1I_A" } @@ -28966,34 +24236,19 @@ "G9814A", "C9868T", "G10231A" - ], - "C": [ - "I65V" - ], - "NS2A": [ - "N63S" - ], - "NS4B": [ - "T61S" - ], - "NS5": [ - "E634D" ] - }, - "labels": { - "aa": "C: I65V; NS2A: N63S; NS4B: T61S; NS5: E634D" } }, "children": [ { "name": "KY586545.1|2004", "node_attrs": { - "div": 0.07777377, - "country": { - "value": "Thailand" - }, + "div": 0.0778, "clade_membership": { "value": "1I_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -29082,39 +24337,19 @@ "C10144T", "C10192T", "T10204C" - ], - "NS1": [ - "K9R", - "V224I", - "K324R" - ], - "NS2B": [ - "L75S" - ], - "NS3": [ - "P119L" - ], - "NS5": [ - "Y127H", - "K284R", - "H285Y", - "K288R" ] - }, - "labels": { - "aa": "NS1: K9R, V224I, K324R; NS2B: L75S; NS3: P119L; NS5: Y127H, K284R, H285Y, K288R" } } }, { "name": "MW945835.1|1997", "node_attrs": { - "div": 0.07227528000000001, - "country": { - "value": "Thailand" - }, + "div": 0.0723, "clade_membership": { "value": "1I_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -29173,33 +24408,7 @@ "C10126T", "A10189G", "G10248C" - ], - "E": [ - "T33I", - "N52D", - "I114M" - ], - "M": [ - "S15N", - "A29T" - ], - "NS1": [ - "A121V" - ], - "NS2A": [ - "H143Y" - ], - "NS3": [ - "S293C" - ], - "NS5": [ - "H285Q", - "Y649H", - "S892T" ] - }, - "labels": { - "aa": "E: T33I, N52D, I114M; M: S15N, A29T; NS1: A121V; NS2A: H143Y; NS3: S293C; NS5: H285Q, Y649H, S892T" } } } @@ -29212,9 +24421,9 @@ ] }, { - "name": "NODE_0000183", + "name": "NODE_0000193", "node_attrs": { - "div": 0.06034446, + "div": 0.0603, "clade_membership": { "value": "1I" } @@ -29256,27 +24465,14 @@ "T9706C", "T9895C", "A10071G" - ], - "C": [ - "L109M" - ], - "NS1": [ - "V224I" - ], - "NS5": [ - "Y127H", - "E833G" ] - }, - "labels": { - "aa": "C: L109M; NS1: V224I; NS5: Y127H, E833G" } }, "children": [ { - "name": "NODE_0000184", + "name": "NODE_0000194", "node_attrs": { - "div": 0.061130130000000005, + "div": 0.0611, "clade_membership": { "value": "1I" } @@ -29292,23 +24488,14 @@ "C7129A", "G7948A", "T9121C" - ], - "M": [ - "S15T" ] - }, - "labels": { - "aa": "M: S15T" } }, "children": [ { "name": "AB608789.1|1994", "node_attrs": { - "div": 0.06803113000000001, - "country": { - "value": "Taiwan" - }, + "div": 0.068, "clade_membership": { "value": "1I" } @@ -29385,41 +24572,14 @@ "A9620G", "A10060G", "C10255T" - ], - "E": [ - "K394R" - ], - "M": [ - "V64I" - ], - "NS1": [ - "H111Y" - ], - "NS2A": [ - "I15M", - "F159V" - ], - "NS3": [ - "D20E" - ], - "NS5": [ - "L45V", - "K468P", - "G469E", - "P630S", - "E647G", - "M683V" ] - }, - "labels": { - "aa": "E: K394R; M: V64I; NS1: H111Y; NS2A: I15M, F159V; NS3: D20E; NS5: L45V, K468P, G469E, P630S, E647G, M683V" } } }, { - "name": "NODE_0000185", + "name": "NODE_0000195", "node_attrs": { - "div": 0.07163923, + "div": 0.0716, "clade_membership": { "value": "1I_C" } @@ -29453,6 +24613,7 @@ "G2362A", "A2455G", "T2698A", + "G2719A", "C2917T", "T3088C", "C3091T", @@ -29535,36 +24696,17 @@ "A10090G", "A10151T", "A10247G" - ], - "E": [ - "V83M" - ], - "NS2A": [ - "F159L" - ], - "NS2B": [ - "I13V" - ], - "NS5": [ - "T27I", - "K52R", - "H435Q", - "R436K", - "S629L", - "T860S", - "S892G" ] }, "labels": { - "aa": "E: V83M; NS2A: F159L; NS2B: I13V; NS5: T27I, K52R, H435Q, R436K, S629L, T860S, S892G", "lineage": "1I_C" } }, "children": [ { - "name": "NODE_0000186", + "name": "NODE_0000196", "node_attrs": { - "div": 0.07173714, + "div": 0.0722, "clade_membership": { "value": "1I_C" } @@ -29572,214 +24714,106 @@ "branch_attrs": { "mutations": { "nuc": [ - "T3121C", - "T4699C" + "T511C", + "A2667G", + "A4828G", + "T7555C", + "A8158G", + "G9493A", + "C9860T" ] } }, "children": [ { - "name": "EU677173.1|2007", + "name": "GQ199837.1|2005", "node_attrs": { - "div": 0.0768678, - "country": { - "value": "Vietnam" - }, + "div": 0.0747, "clade_membership": { "value": "1I_C" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { "mutations": { "nuc": [ - "G320A", - "T373C", - "T505C", - "C781T", - "C854T", - "T991C", - "C1246T", - "T1408C", - "G1456A", - "T1561C", - "C1597T", - 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} }, { - "name": "GQ199805.1|2007", + "name": "GQ199833.1|2004", "node_attrs": { - "div": 0.07666271000000001, - "country": { - "value": "Vietnam" - }, + "div": 0.0734, "clade_membership": { "value": "1I_C" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { "mutations": { "nuc": [ - "T290C", - "C403T", - "C864T", - "G916A", - "C1099T", - "A1303T", - "T1432C", - "C1457T", - "T1477C", - "T1639C", - "T2251C", - "T2260C", - "A2309T", - "A2491G", - "C2677T", - "T2731C", - "T2942C", - "C3184T", - "A3463G", - "T3636C", - "A4088G", - "C4153T", - "T4348C", - "C4693T", - "G4714A", - "C4783T", - "G4858A", - "C5461T", - "A5485G", - "G5683A", - "T5842C", - "G5875A", - "T6034C", - "A6148G", - "C6379T", - "T6566C", - "A7330G", - "C7816T", - "C8125T", - "T8200C", - "G8287A", - "G8542A", - "T9055C", - "C9133T", - "A9225G", - "C9277T", - "G9448A", - "C9480A", - "C10150T" - ], - "E": [ - "I459L" - ], - "M": [ - "A143V" - ], - "NS1": [ - "Y175H" - ], - "NS2A": [ - "I54T", - "T205A" - ], - 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+ "children": [ + { + "name": "GQ199805.1|2007", + "node_attrs": { + "div": 0.0767, + "clade_membership": { + "value": "1I_C" + }, + "country": { + "value": "Viet Nam" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T290C", + "C403T", + "C864T", + "G916A", + "C1099T", + "A1303T", + "T1432C", + "C1457T", + "T1477C", + "T1639C", + "T2251C", + "T2260C", + "A2309T", + "A2491G", + "C2677T", + "A2719G", + "T2731C", + "T2942C", + "C3184T", + "A3463G", + "T3636C", + "A4088G", + "C4153T", + "T4348C", + "C4693T", + "T4699C", + "G4714A", + "C4783T", + "G4858A", + "C5461T", + "A5485G", + "G5683A", + "T5842C", + "G5875A", + "T6034C", + "A6148G", + "C6379T", + "T6566C", + "A7330G", + "C7816T", + "C8125T", + "T8200C", + "G8287A", + "G8542A", + "T9055C", + "C9133T", + "A9225G", + "C9277T", + "G9448A", + "C9480A", + "C10150T" + ] + } + } }, - "labels": { - "aa": "E: L125M; NS4B: G246R; NS5: N585S" + { + "name": "NODE_0000199", + "node_attrs": { + "div": 0.0717, + "clade_membership": { + "value": "1I_C" + } + }, + "branch_attrs": { + "mutations": {} + }, + "children": [ + { + "name": "FJ898412.1|2006", + "node_attrs": { + "div": 0.0743, + "clade_membership": { + "value": "1I_C" + }, + "country": { + "value": "Viet Nam" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A112G", + "T628C", + "T1180C", + "A1351G", + "C1366T", + "C1441T", + "T1481C", + "C1933T", + "T3289C", + "T3778C", + "C4936T", + "A5593G", + "T5629C", + "C5782T", + "T6772C", + "C6903T", + "A7162G", + "T7216C", + "C7517T", + "T7666C", + "T8362C", + "G9535A", + "C9754T", + "T9904C", + "G10090A" + ] + } + } + }, + { + "name": "EU677173.1|2007", + "node_attrs": { + "div": 0.0769, + "clade_membership": { + "value": "1I_C" + }, + "country": { + "value": "Viet Nam" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G320A", + "T373C", + "T505C", + "C781T", + "C854T", + "T991C", + "C1246T", + "T1408C", + "G1456A", + "T1561C", + "C1597T", + "T1607A", + "G1834A", + "T1985C", + "G2047A", + 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Nam" } }, "branch_attrs": { "mutations": { "nuc": [ - "T230A", - "T409G", - "T412C", - "T628A", - "C640T", - "T1477A", - "T1720C", - "C1971T", - "T1996A", - "C2079T", - "A2242G", - "C2598T", - "T2654C", - "C2812A", - "C2947T", - "T2952C", - "C2966T", - "A3133G", - "A3143G", - "G3154A", - "C3358T", - "C3584T", - "C3649T", - "A3721G", - "T3821A", - "G3838A", - "T4201C", - "C4276T", - "C4423T", - "C4459T", - "G4681A", - "A4798G", - "G5041T", - "C5428T", - "T6010C", - "C6154T", - "C6448T", - "A6841G", - "C6916T", - "A7213G", - "G7432A", - "C7504T", - "T7897C", - "C7999A", - "T8293C", - "C8390T", - "A8737G", - "T8752C", - "A8773G", - "T9232C", - "T9518C", - "A9556G", - "A10060G", - "C10243T" - ], - "C": [ - "L46M" - ], - "E": [ - "T346I", - "A382V" - ], - "NS1": [ - "A60V", - "V178A", - "I242V" - ], - "NS2A": [ - "L116I" - ], - "NS5": [ - "Y649H" + "C826T", + "C1307A", + "C1846T", + "T2273C", + "A2719G", + "C5941T", + "A6616G", + "G7562A", + "T9040C", + "A9327G" ] - }, - "labels": { - "aa": 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+ "mutations": { + "nuc": [ + "A99C", + "A809C", + "T895C", + "A963C", + "G1003A", + "A1200C", + "T1210C", + "A1213C", + "A1460C", + "A1507G", + "C1553T", + "C1722G", + "T1978C", + "A2161C", + "A2207G", + "T2422C", + "T2449A", + "T2476C", + "T2481G", + "G2564C", + "T2605G", + "A2689G", + "C2809T", + "T2942C", + "T2972G", + "C2992G", + "A3044C", + "T3067C", + "G3211A", + "C3379T", + "T3415C", + "T3499C", + "G4103A", + "C4306T", + "T4352C", + "G4614C", + "C4894T", + "C5476T", + "C5536T", + "C5740T", + "C6346T", + "A6412G", + "G6520A", + "C6656T", + "A6751G", + "A6781G", + "C6850T", + "T7270A", + "C7355T", + "T7387C", + "A7459G", + "T7544C", + "C7753T", + "C7831T", + "C7999T", + "G8140A", + "T8212C", + "G8887A", + "G8953A", + "C9133T", + "T9910C" + ] + } + } }, - "labels": { - "aa": "E: V358I, V432I; M: I136T; NS1: L171M; NS2A: F178I; NS3: I213M; NS4A: M89T; NS5: R52K, R253K, A370V, Q435K, L643F" + { + "name": "GU131753.1|2008", + "node_attrs": { + "div": 0.0787, + "clade_membership": { + "value": "1I_C" + }, + "country": { + "value": "Viet Nam" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C310T", + "G550A", + "T843C", + "C1462T", + "T1561C", + "T1873C", + "G2006A", + "G2228A", + "A2338G", + "A2452G", + "T2713C", + "C2743T", + "A2803G", + "T2930A", + "C3019T", + "A3562G", + "G3838A", + "T4007A", + "C4153T", + "C4192T", + "C4195A", + "G4390A", + "T4543C", + "C4594A", + "G4858A", + "T5008C", + "A5158G", + "G5332C", + "A5548G", + "T5695C", + "C5845T", + "C6019T", + "A6277G", + "A6403G", + "T6562C", + "T6642C", + "G6679A", + "G6844A", + "T6863C", + "T7048C", + "T7180C", + "T7192C", + "C7202T", + "C7411T", + "G7728A", + "T8011C", + "C8089T", + "G8331A", + "G8380A", + "A8431G", + "T8617C", + "C8682T", + "A8683G", + "C8876A", + "A8942C", + "T9157C", + "C9334T", + "A9397G", + "C9500T", + "T9925C" + ] + } + } } - } + ] } ] } @@ -30173,9 +25349,9 @@ ] }, { - "name": "NODE_0000190", + "name": "NODE_0000203", "node_attrs": { - "div": 0.06257069, + "div": 0.0626, "clade_membership": { "value": "1I" } @@ -30205,24 +25381,14 @@ "T9067C", "C9592T", "G10058A" - ], - "NS2A": [ - "L41F" - ], - "NS5": [ - "T135I", - "V829I" ] - }, - "labels": { - "aa": "NS2A: L41F; NS5: T135I, V829I" } }, "children": [ { - "name": "NODE_0000191", + "name": "NODE_0000204", "node_attrs": { - "div": 0.06505285, + "div": 0.0651, "clade_membership": { "value": "1I_D" } @@ -30255,20 +25421,9 @@ "A8392G", "A9148T", "G9859A" - ], - "M": [ - "A59V", - "T107A" - ], - "NS2A": [ - "F178L" - ], - "NS4A": [ - "V93A" ] }, "labels": { - "aa": "M: A59V, T107A; NS2A: F178L; NS4A: V93A", "lineage": "1I_D" } }, @@ -30276,12 +25431,12 @@ { "name": "FJ639678.1|2003", "node_attrs": { - "div": 0.07619524999999999, - "country": { - "value": "Cambodia" - }, + "div": 0.0762, "clade_membership": { "value": "1I_D" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -30400,47 +25555,14 @@ "T10012C", "G10071A", "T10084C" - ], - "C": [ - "I94T" - ], - "E": [ - "S8N" - ], - "M": [ - "S22A", - "S81P", - "K90R" - ], - "NS1": [ - "H111Y", - "V128I" - ], - "NS2B": [ - "V120L" - ], - "NS3": [ - "P439Q" - ], - "NS4A": [ - "R20K" - ], - "NS5": [ - "K52R", - "R367Q", - "Q547R", - "G833E" ] - }, - "labels": { - "aa": "C: I94T; E: S8N; M: S22A, S81P, K90R; NS1: H111Y, V128I; NS2B: V120L; NS3: P439Q; NS4A: R20K; NS5: K52R, R367Q, Q547R, G833E" } } }, { - "name": "NODE_0000192", + "name": "NODE_0000205", "node_attrs": { - "div": 0.069433, + "div": 0.0694, "clade_membership": { "value": "1I_D" } @@ -30489,32 +25611,14 @@ "T9121C", "A9469G", "C10208T" - ], - "M": [ - "A70T" - ], - "NS1": [ - "K69R" - ], - "NS2A": [ - "H143Y" - ], - "NS3": [ - "K255R" - ], - "NS5": [ - "K46R" ] - }, - "labels": { - "aa": "M: A70T; NS1: K69R; NS2A: H143Y; NS3: K255R; NS5: K46R" } }, "children": [ { - "name": "NODE_0000193", + "name": "NODE_0000206", "node_attrs": { - "div": 0.07436126, + "div": 0.0744, "clade_membership": { "value": "1I_D" } @@ -30573,28 +25677,19 @@ "G9733A", "C9946T", "T10066C" - ], - "M": [ - "R122K" - ], - "NS2A": [ - "L56S" ] - }, - "labels": { - "aa": "M: R122K; NS2A: L56S" } }, "children": [ { "name": "FJ882549.1|2007", "node_attrs": { - "div": 0.07868732, - "country": { - "value": "Vietnam" - }, + "div": 0.0787, "clade_membership": { "value": "1I_D" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -30641,35 +25736,19 @@ "C9601T", "A9605T", "C10255T" - ], - "C": [ - "M44I" - ], - "NS4A": [ - "R76K" - ], - "NS5": [ - "F354L", - "R378K", - "K584R", - "Y649H", - "T678S" ] - }, - "labels": { - "aa": "C: M44I; NS4A: R76K; NS5: F354L, R378K, K584R, Y649H, T678S" } } }, { "name": "GQ199775.1|2007", "node_attrs": { - "div": 0.07889594, - "country": { - "value": "Vietnam" - }, + "div": 0.0789, "clade_membership": { "value": "1I_D" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -30720,39 +25799,16 @@ "C8844G", "C9509T", "C9716T" - ], - "E": [ - "T161I", - "S273T", - "V485I" - ], - "NS1": [ - "I104V", - "K339R" - ], - "NS5": [ - "Q195H", - "C393W", - "F398V", - "A407G", - "V411G", - "F412V", - "V413G", - "E423K", - "A424G" ] - }, - "labels": { - "aa": "E: T161I, S273T, V485I; NS1: I104V, K339R; NS5: Q195H, C393W, F398V, A407G, V411G, F412V, V413G, E423K, A424G" } } } ] }, { - "name": "NODE_0000194", + "name": "NODE_0000207", "node_attrs": { - "div": 0.07162748999999999, + "div": 0.0716, "clade_membership": { "value": "1I_D" } @@ -30781,36 +25837,19 @@ "A9595G", "G10071A", "C10253A" - ], - "M": [ - "A143V" - ], - "NS2A": [ - "L208F" - ], - "NS4A": [ - "V2I" - ], - "NS5": [ - "M34L", - "G833E", - "P894T" ] - }, - "labels": { - "aa": "M: A143V; NS2A: L208F; NS4A: V2I; NS5: M34L, G833E, P894T" } }, "children": [ { "name": "JQ287664.1|2004", "node_attrs": { - "div": 0.07539258999999998, - "country": { - "value": "Cambodia" - }, + "div": 0.0754, "clade_membership": { "value": "1I_D" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -30853,28 +25892,19 @@ "C10117T", "C10187T", "C10237T" - ], - "NS3": [ - "R203K" - ], - "NS5": [ - "V784F" ] - }, - "labels": { - "aa": "NS3: R203K; NS5: V784F" } } }, { "name": "FJ850069.1|2003", "node_attrs": { - "div": 0.07476333999999998, - "country": { - "value": "Cambodia" - }, + "div": 0.0748, "clade_membership": { "value": "1I_D" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -30913,19 +25943,7 @@ "A8705G", "C9043T", "T9640C" - ], - "M": [ - "S15G" - ], - "NS2A": [ - "A147V" - ], - "NS5": [ - "R378G" ] - }, - "labels": { - "aa": "M: S15G; NS2A: A147V; NS5: R378G" } } } @@ -30936,9 +25954,9 @@ ] }, { - "name": "NODE_0000195", + "name": "NODE_0000208", "node_attrs": { - "div": 0.06679652, + "div": 0.0668, "clade_membership": { "value": "1I" } @@ -30993,31 +26011,14 @@ "C9586T", "T9998C", "G10105A" - ], - "E": [ - "S171T" - ], - "NS1": [ - "V94A", - "H111Y", - "K324R" - ], - "NS4B": [ - "T27A" - ], - "NS5": [ - "T565K" ] - }, - "labels": { - "aa": "E: S171T; NS1: V94A, H111Y, K324R; NS4B: T27A; NS5: T565K" } }, "children": [ { - "name": "NODE_0000196", + "name": "NODE_0000209", "node_attrs": { - "div": 0.07115989, + "div": 0.0712, "clade_membership": { "value": "1I_E" } @@ -31070,29 +26071,17 @@ "C8878T", "A9225G", "G9932A" - ], - "C": [ - "N75S" - ], - "NS2A": [ - "K218R" - ], - "NS5": [ - "R378K", - "K551R", - "V787I" ] }, "labels": { - "aa": "C: N75S; NS2A: K218R; NS5: R378K, K551R, V787I", "lineage": "1I_E" } }, "children": [ { - "name": "NODE_0000197", + "name": "NODE_0000210", "node_attrs": { - "div": 0.07165513, + "div": 0.0717, "clade_membership": { "value": "1I_E" } @@ -31114,12 +26103,12 @@ { "name": "KY586530.1|2002", "node_attrs": { - "div": 0.07367272999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0737, "clade_membership": { "value": "1I_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -31146,30 +26135,14 @@ "C9884T", "G10000A", "G10046A" - ], - "M": [ - "S81P", - "I144V" - ], - "NS1": [ - "H290R" - ], - "NS3": [ - "T115I" - ], - "NS5": [ - "D825N" ] - }, - "labels": { - "aa": "M: S81P, I144V; NS1: H290R; NS3: T115I; NS5: D825N" } } }, { - "name": "NODE_0000198", + "name": "NODE_0000211", "node_attrs": { - "div": 0.0750145, + "div": 0.075, "clade_membership": { "value": "1I_E" } @@ -31212,31 +26185,19 @@ "A9850G", "A10090G", "T10207C" - ], - "E": [ - "V55I" - ], - "NS2A": [ - "F41L" - ], - "NS4B": [ - "E21G" ] - }, - "labels": { - "aa": "E: V55I; NS2A: F41L; NS4B: E21G" } }, "children": [ { "name": "MW265667.1|2016-02-09", "node_attrs": { - "div": 0.08303386, - "country": { - "value": "Cambodia" - }, + "div": 0.083, "clade_membership": { "value": "1I_E" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -31323,52 +26284,19 @@ "T10057C", "G10070A", "C10141T" - ], - "2K": [ - "T20A" - ], - "C": [ - "M104I" - ], - "E": [ - "A386V", - "V432A" - ], - "NS1": [ - "I6V", - "A98G" - ], - "NS2B": [ - "E62A" - ], - "NS3": [ - "V452A" - ], - "NS4B": [ - "I151V" - ], - "NS5": [ - "R436K", - "N528I", - "K569R", - "V784A", - "G833R" ] - }, - "labels": { - "aa": "2K: T20A; C: M104I; E: A386V, V432A; NS1: I6V, A98G; NS2B: E62A; NS3: V452A; NS4B: I151V; NS5: R436K, N528I, K569R, V784A, G833R" } } }, { "name": "KC759167.1|2012-01-09", "node_attrs": { - "div": 0.08273131, - "country": { - "value": "China" - }, + "div": 0.0827, "clade_membership": { "value": "1I_E" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -31452,47 +26380,7 @@ "A9637G", "T9692C", "G10006A" - ], - "C": [ - "A77T" - ], - "E": [ - "T81P", - "L82E", - "E370K", - "Y377C" - ], - "M": [ - "I148V" - ], - "NS1": [ - "L318P" - ], - "NS2A": [ - "T36A", - "R95K" - ], - "NS2B": [ - "Q125R" - ], - "NS3": [ - "E94G", - "H252Y", - "F534Y", - "C564Y" - ], - "NS5": [ - "S23L", - "T27S", - "A316S", - "G626E", - "V651I", - "D671N", - "F707L" ] - }, - "labels": { - "aa": "C: A77T; E: T81P, L82E, E370K, Y377C; M: I148V; NS1: L318P; NS2A: T36A, R95K; NS2B: Q125R; NS3: E94G, H252Y, F534Y, C564Y; NS5: S23L, T27S, A316S, G626E, V651I, D671N, F707L" } } } @@ -31501,9 +26389,9 @@ ] }, { - "name": "NODE_0000199", + "name": "NODE_0000212", "node_attrs": { - "div": 0.07646284, + "div": 0.0765, "clade_membership": { "value": "1I_E" } @@ -31564,23 +26452,14 @@ "C9946T", "T10057C", "T10102C" - ], - "E": [ - "V312L" - ], - "M": [ - "A59T" ] - }, - "labels": { - "aa": "E: V312L; M: A59T" } }, "children": [ { - "name": "NODE_0000200", + "name": "NODE_0000213", "node_attrs": { - "div": 0.07739865, + "div": 0.0766, "clade_membership": { "value": "1I_E" } @@ -31588,25 +26467,15 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1234T", - "T1441C", - "A1969G", - "T2935C", - "T3833C", - "T6797C", - "T7513C", - "T9484C" + "A3580T" ] } }, "children": [ { - "name": "GU131824.1|2008", + "name": "NODE_0000214", "node_attrs": { - "div": 0.07779621, - "country": { - "value": "Vietnam" - }, + "div": 0.0771, "clade_membership": { "value": "1I_E" } @@ -31614,1235 +26483,665 @@ "branch_attrs": { "mutations": { "nuc": [ - "A8560G", - "A8644G", - "T8749A" - ] - } - } - }, - { - "name": "NODE_0000201", - "node_attrs": { - "div": 0.08001196, - "clade_membership": { - "value": "1I_E.1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T368C", - "C409T", - "T571C", - "A1088G", - "C1580T", - "A1699G", - "G2563A", - "C2770T", - "T3001C", - "C3053T", - "C3184T", - "T3956C", - "T4072A", - "C4141T", - "T4447C", - "A4531G", - "T4969C", - "A5281G", - "T5617C", - "G6603A", - "A6631T", - "A6931C", - "C7939T", - "C7940T", - "A8590G", - "C9406T", - "A9436G", - "T9784C" - ], - "E": [ - "N52D" - ], - "NS4A": [ - "R76K" + "G733A", + "T1513C", + "T2750C", + "A2845G", + "G6644T", + "C8461T" ] - }, - "labels": { - "aa": "E: N52D; NS4A: R76K", - "lineage": "1I_E.1" } }, "children": [ { - "name": "NODE_0000202", + "name": "FJ410230.1|2008", "node_attrs": { - "div": 0.08330752999999999, + "div": 0.0777, "clade_membership": { - "value": "1I_E.1" + "value": "1I_E" } }, "branch_attrs": { "mutations": { "nuc": [ - "G418T", - "T424C", - "G484A", 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{ + "value": "1I_E" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T5656C", + "C7129T", + "T7300C" + ] + } + } + }, + { + "name": "NODE_0000227", "node_attrs": { - "div": 0.08230760999999999, + "div": 0.0823, "clade_membership": { "value": "1I_E.3" } @@ -33776,101 +27317,96 @@ "branch_attrs": { "mutations": { "nuc": [ - "G313A", - "C625T", - "T1942C", - "C2485T", - "G2911A", - "T3199C", - "T3451C", - "G3538A", - "T4393C", "T4420C", - "A4627G", - "C5005T", "A5257G", - "T5974C", "T6010C", - "A6148G", - "C6478T", - "C9067T", - "C9406T", - "T9498C", - "A9513G", - "A9649G" - ], - "NS5": [ - "V642A", - "E647G" + "C9406T" ] }, "labels": { - "aa": "NS5: V642A, E647G", "lineage": "1I_E.3" } }, "children": [ { - "name": "OQ426707.1|2017-07-06", + "name": "NODE_0000228", "node_attrs": { - "div": 0.08457790999999999, - "country": { - "value": "Vietnam" - }, + "div": 0.0823, "clade_membership": { "value": "1I_E.3" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "A1843G", - 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"name": "MW315188.1|2017-03-17", + "name": "MN912190.1|2017-07-31", "node_attrs": { - "div": 0.08444771, - "country": { - "value": "New Caledonia" - }, + "div": 0.0866, "clade_membership": { - "value": "1I_E.2" + "value": "1I_E.1.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { "mutations": { "nuc": [ - "T448C", - "T811C", - "T2938C", - "G3442A", - "T3950A", - "C7853T", - "C8954T" - ], - "NS2A": [ - "F159I" + "G1541A" ] - }, - "labels": { - "aa": "NS2A: F159I" } } } @@ -34518,9 +28890,9 @@ ] }, { - "name": "NODE_0000236", + "name": "NODE_0000254", "node_attrs": { - "div": 0.06698239, + "div": 0.067, "clade_membership": { "value": "1I" } @@ -34534,9 +28906,9 @@ }, "children": [ { - "name": "NODE_0000237", + "name": "NODE_0000255", "node_attrs": { - "div": 0.06716938, + "div": 0.0672, "clade_membership": { "value": "1I" } @@ -34551,9 +28923,9 @@ }, "children": [ { - "name": "NODE_0000238", + "name": "NODE_0000256", "node_attrs": { - "div": 0.06717183, + "div": 0.0672, "clade_membership": { "value": "1I" } @@ -34563,9 +28935,9 @@ }, "children": [ { - "name": "NODE_0000239", + "name": "NODE_0000257", "node_attrs": { - "div": 0.06835363, + "div": 0.0684, "clade_membership": { "value": "1I_G" } @@ -34586,17 +28958,9 @@ "T9518C", "A9631T", "C10255T" - ], - "E": [ - "T170S" - ], - "NS5": [ - "R378K", - "Y649H" ] }, "labels": { - "aa": "E: T170S; NS5: R378K, Y649H", "lineage": "1I_G" } }, @@ -34604,12 +28968,12 @@ { "name": "MW946158.1|1999", "node_attrs": { - "div": 0.07091677, - "country": { - "value": "Thailand" - }, + "div": 0.0709, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -34640,34 +29004,14 @@ "A9097G", "A9190G", "T9499C" - ], - "C": [ - "A112T" - ], - "E": [ - "S305P", - "A386T" - ], - "NS1": [ - "K101R", - "D278N" - ], - "NS2A": [ - "K213R" - ], - "NS4B": [ - "A27T" ] - }, - "labels": { - "aa": "C: A112T; E: S305P, A386T; NS1: K101R, D278N; NS2A: K213R; NS4B: A27T" } } }, { - "name": "NODE_0000240", + "name": "NODE_0000258", "node_attrs": { - "div": 0.06904165, + "div": 0.069, "clade_membership": { "value": "1I_G" } @@ -34686,12 +29030,12 @@ { "name": "KY586528.1|2002", "node_attrs": { - "div": 0.07426769, - "country": { - "value": "Thailand" - }, + "div": 0.0743, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -34749,38 +29093,14 @@ "T9583C", "G9781A", "T10085C" - ], - "E": [ - "S338L", - "S390N" - ], - "NS1": [ - "I167V", - "M349I" - ], - "NS2A": [ - "S142T", - "K213R" - ], - "NS3": [ - "M26V" - ], - "NS4B": [ - "M28L" - ], - "NS5": [ - "E40G" ] - }, - "labels": { - "aa": "E: S338L, S390N; NS1: I167V, M349I; NS2A: S142T, K213R; NS3: M26V; NS4B: M28L; NS5: E40G" } } }, { - "name": "NODE_0000241", + "name": "NODE_0000259", "node_attrs": { - "div": 0.07278989999999999, + "div": 0.0728, "clade_membership": { "value": "1I_G" } @@ -34826,31 +29146,19 @@ "T9217C", "C9286A", "A9436G" - ], - "M": [ - "L44F" - ], - "NS1": [ - "R324K" - ], - "NS3": [ - "P119S" ] - }, - "labels": { - "aa": "M: L44F; NS1: R324K; NS3: P119S" } }, "children": [ { "name": "HQ624983.1|2007", "node_attrs": { - "div": 0.07978405, - "country": { - "value": "Cambodia" - }, + "div": 0.0798, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -34921,35 +29229,14 @@ "G10071A", "C10153T", "A10186G" - ], - "C": [ - "M109V" - ], - "M": [ - "T57S" - ], - "NS2A": [ - "T72M" - ], - "NS5": [ - "Q19H", - "I135V", - "P525S", - "K565N", - "H649Y", - "T805A", - "G833E" ] - }, - "labels": { - "aa": "C: M109V; M: T57S; NS2A: T72M; NS5: Q19H, I135V, P525S, K565N, H649Y, T805A, G833E" } } }, { - "name": "NODE_0000242", + "name": "NODE_0000260", "node_attrs": { - "div": 0.07397079, + "div": 0.074, "clade_membership": { "value": "1I_G" } @@ -34968,25 +29255,19 @@ "T8635C", "T9005C", "A9492G" - ], - "NS5": [ - "E640G" ] - }, - "labels": { - "aa": "NS5: E640G" } }, "children": [ { "name": "GU131811.1|2008", "node_attrs": { - "div": 0.08074324999999999, - "country": { - "value": "Vietnam" - }, + "div": 0.0807, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -35061,41 +29342,14 @@ "T9640C", "A10190C", "C10243T" - ], - "E": [ - "A382V", - "A404T" - ], - "M": [ - "T83I" - ], - "NS1": [ - "F86L" - ], - "NS2A": [ - "L152M", - "K156R" - ], - "NS2B": [ - "E58V" - ], - "NS3": [ - "I146V" - ], - "NS5": [ - "V642A", - "I873L" ] - }, - "labels": { - "aa": "E: A382V, A404T; M: T83I; NS1: F86L; NS2A: L152M, K156R; NS2B: E58V; NS3: I146V; NS5: V642A, I873L" } } }, { - "name": "NODE_0000243", + "name": "NODE_0000261", "node_attrs": { - "div": 0.07529877, + "div": 0.0753, "clade_membership": { "value": "1I_G" } @@ -35123,12 +29377,12 @@ { "name": "GU131805.1|2008", "node_attrs": { - "div": 0.08174442, - "country": { - "value": "Vietnam" - }, + "div": 0.0817, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -35200,63 +29454,19 @@ "C9829T", "T10057C", "T10204C" - ], - "C": [ - "N2S" - ], - "E": [ - "N52D", - "I114M", - "T171P", - "T176P", - "T189P", - "T200P", - "Q234K", - "V238G", - "K247E", - "P372A", - "F392V" - ], - "NS1": [ - "V21G", - "D83A", - "F86L", - "T209P", - "T304P", - "R336S" - ], - "NS2A": [ - "T36P", - "A38P", - "T49P", - "T73P", - "V101G", - "S151A", - "H162D" - ], - "NS2B": [ - "S20A", - "A70G", - "D93A" - ], - "NS5": [ - "T675A" ] - }, - "labels": { - "aa": "C: N2S; E: N52D, I114M, T171P, T176P, T189P, T200P, Q234K, V238G, K247E, P372A, F392V; NS1: V21G, D83A, F86L, T209P, T304P, R336S; NS2A: T36P, A38P, T49P, T73P, V101G, S151A, H162D; NS2B: S20A, A70G, D93A; NS5: T675A" } } }, { "name": "KT827369.1|2011", "node_attrs": { - "div": 0.08193595000000001, - "country": { - "value": "China" - }, + "div": 0.0819, "clade_membership": { "value": "1I_G" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -35323,24 +29533,7 @@ "T9898C", "G10071A", "T10084C" - ], - "2K": [ - "M17I" - ], - "E": [ - "D37G", - "V55I", - "A386T" - ], - "NS2A": [ - "R26K" - ], - "NS5": [ - "G833E" ] - }, - "labels": { - "aa": "2K: M17I; E: D37G, V55I, A386T; NS2A: R26K; NS5: G833E" } } } @@ -35355,9 +29548,9 @@ ] }, { - "name": "NODE_0000244", + "name": "NODE_0000262", "node_attrs": { - "div": 0.06805682, + "div": 0.0681, "clade_membership": { "value": "1I" } @@ -35381,10 +29574,7 @@ { "name": "KY586516.1|1998", "node_attrs": { - "div": 0.07121087000000001, - "country": { - "value": "Thailand" - }, + "div": 0.0712, "clade_membership": { "value": "1I" } @@ -35424,30 +29614,14 @@ "A9154G", "T9265C", "T10057C" - ], - "E": [ - "T81I" - ], - "NS2B": [ - "R91K" - ], - "NS3": [ - "D354N", - "I474V" - ], - "NS5": [ - "R30K" ] - }, - "labels": { - "aa": "E: T81I; NS2B: R91K; NS3: D354N, I474V; NS5: R30K" } } }, { - "name": "NODE_0000245", + "name": "NODE_0000263", "node_attrs": { - "div": 0.06904262, + "div": 0.069, "clade_membership": { "value": "1I_F" } @@ -35465,21 +29639,17 @@ "C8098T", "C9260T", "T10084C" - ], - "NS3": [ - "I462V" ] }, "labels": { - "aa": "NS3: I462V", "lineage": "1I_F" } }, "children": [ { - "name": "NODE_0000246", + "name": "NODE_0000264", "node_attrs": { - "div": 0.06923958, + "div": 0.0692, "clade_membership": { "value": "1I_F" } @@ -35496,12 +29666,12 @@ { "name": "MW946055.1|2003", "node_attrs": { - "div": 0.07594237999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0759, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -35575,41 +29745,19 @@ "T10057C", "G10065C", "C10126T" - ], - "C": [ - "T103I" - ], - "E": [ - "N52D", - "S227P", - "V432F" - ], - "NS1": [ - "N7S", - "A213V" - ], - "NS2A": [ - "I174M" - ], - "NS5": [ - "K551R", - "S831T" ] - }, - "labels": { - "aa": "C: T103I; E: N52D, S227P, V432F; NS1: N7S, A213V; NS2A: I174M; NS5: K551R, S831T" } } }, { "name": "MW946093.1|1996", "node_attrs": { - "div": 0.06953453999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0695, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -35618,22 +29766,16 @@ "C403T", "A1455G", "T4909C" - ], - "E": [ - "Q174R" ] - }, - "labels": { - "aa": "E: Q174R" } } } ] }, { - "name": "NODE_0000247", + "name": "NODE_0000265", "node_attrs": { - "div": 0.06963712, + "div": 0.0696, "clade_membership": { "value": "1I_F" } @@ -35656,12 +29798,12 @@ { "name": "FJ196848.1|1999", "node_attrs": { - "div": 0.09084522, - "country": { - "value": "China" - }, + "div": 0.0908, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -35875,60 +30017,14 @@ "T9610C", "C9611T", "G10272A" - ], - "2K": [ - "T20A" - ], - "C": [ - "I59L", - "A77Q", - "A112D" - ], - "E": [ - "W20C", - "D22Y", - "V23M", - "D37N", - "V55I", - "A88T", - "S155T", - "T163I", - "T171S", - "A386V", - "G490A" - ], - "NS2A": [ - "M168I" - ], - "NS3": [ - "I221V", - "V462I", - "H466P", - "I474V" - ], - "NS4A": [ - "Q19L", - "R20K", - "R39K" - ], - "NS4B": [ - "T196P" - ], - "NS5": [ - "I135T", - "H285N", - "K648R" ] - }, - "labels": { - "aa": "2K: T20A; C: I59L, A77Q, A112D; E: W20C, D22Y, V23M, D37N, V55I, A88T, S155T, T163I, T171S, A386V, G490A; NS2A: M168I; NS3: I221V, V462I, H466P, I474V; NS4A: Q19L, R20K, R39K; NS4B: T196P; NS5: I135T, H285N, K648R" } } }, { - "name": "NODE_0000248", + "name": "NODE_0000266", "node_attrs": { - "div": 0.07486453, + "div": 0.0749, "clade_membership": { "value": "1I_F" } @@ -35982,34 +30078,19 @@ "G9613A", "G9958A", "G10071A" - ], - "E": [ - "F96L" - ], - "NS3": [ - "E12K", - "V123I", - "S368A", - "N401S" - ], - "NS5": [ - "G833E" ] - }, - "labels": { - "aa": "E: F96L; NS3: E12K, V123I, S368A, N401S; NS5: G833E" } }, "children": [ { "name": "ON038484.1|2009-12-14", "node_attrs": { - "div": 0.0798975, - "country": { - "value": "Thailand" - }, + "div": 0.0799, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -36061,34 +30142,14 @@ "G9532A", "C9757T", "C9812T" - ], - "C": [ - "K7R" - ], - "E": [ - "A88T", - "S222T" - ], - "NS3": [ - "G438A" - ], - "NS4B": [ - "V20A", - "A117T" - ], - "NS5": [ - "I541V" ] - }, - "labels": { - "aa": "C: K7R; E: A88T, S222T; NS3: G438A; NS4B: V20A, A117T; NS5: I541V" } } }, { - "name": "NODE_0000249", + "name": "NODE_0000267", "node_attrs": { - "div": 0.07614778999999999, + "div": 0.0761, "clade_membership": { "value": "1I_F" } @@ -36113,25 +30174,19 @@ "T9037C", "G9475A", "C10187T" - ], - "NS5": [ - "G174K" ] - }, - "labels": { - "aa": "NS5: G174K" } }, "children": [ { "name": "MW946075.1|2010", "node_attrs": { - "div": 0.08077580999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0808, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -36183,43 +30238,19 @@ "A8035G", "G9307A", "C9606T" - ], - "E": [ - "L96F", - "E384G", - "V446I" - ], - "M": [ - "R55Q" - ], - "NS2B": [ - "K126R" - ], - "NS3": [ - "L480I" - ], - "NS4A": [ - "Q15H", - "T18A" - ], - "NS5": [ - "T678I" ] - }, - "labels": { - "aa": "E: L96F, E384G, V446I; M: R55Q; NS2B: K126R; NS3: L480I; NS4A: Q15H, T18A; NS5: T678I" } } }, { "name": "KU509260.1|2008", "node_attrs": { - "div": 0.08049269999999999, - "country": { - "value": "Cambodia" - }, + "div": 0.0805, "clade_membership": { "value": "1I_F" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -36270,42 +30301,7 @@ "C9709T", "C9967A", "T10249C" - ], - "C": [ - "G42V", - "M48V", - "G76R", - "I78V", - "G83V" - ], - "E": [ - "L237M", - "K343T", - "F440L" - ], - "M": [ - "M33T" - ], - "NS2A": [ - "G1E", - "L102H", - "G126A", - "L195P", - "K213N" - ], - "NS2B": [ - "M37I", - "A56P" - ], - "NS3": [ - "P356Q" - ], - "NS5": [ - "K389R" ] - }, - "labels": { - "aa": "C: G42V, M48V, G76R, I78V, G83V; E: L237M, K343T, F440L; M: M33T; NS2A: G1E, L102H, G126A, L195P, K213N; NS2B: M37I, A56P; NS3: P356Q; NS5: K389R" } } } @@ -36322,9 +30318,9 @@ ] }, { - "name": "NODE_0000250", + "name": "NODE_0000268", "node_attrs": { - "div": 0.06823794, + "div": 0.0682, "clade_membership": { "value": "1I" } @@ -36343,29 +30339,14 @@ "C7996T", "A10056G", "C10117T" - ], - "NS3": [ - "S368A" - ], - "NS4A": [ - "R76K" - ], - "NS5": [ - "H828R" ] - }, - "labels": { - "aa": "NS3: S368A; NS4A: R76K; NS5: H828R" } }, "children": [ { "name": "MW946134.1|1996", "node_attrs": { - "div": 0.06892663, - "country": { - "value": "Thailand" - }, + "div": 0.0689, "clade_membership": { "value": "1I" } @@ -36380,20 +30361,14 @@ "T7783C", "A8245G", "C9454T" - ], - "NS2A": [ - "H143Y" ] - }, - "labels": { - "aa": "NS2A: H143Y" } } }, { - "name": "NODE_0000251", + "name": "NODE_0000269", "node_attrs": { - "div": 0.06921133, + "div": 0.0692, "clade_membership": { "value": "1I_H" } @@ -36411,13 +30386,9 @@ "C8065T", "T9592C", "T10085C" - ], - "NS1": [ - "T131S" ] }, "labels": { - "aa": "NS1: T131S", "lineage": "1I_H" } }, @@ -36425,12 +30396,12 @@ { "name": "MW946178.1|1997", "node_attrs": { - "div": 0.06960481, - "country": { - "value": "Thailand" - }, + "div": 0.0696, "clade_membership": { "value": "1I_H" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -36445,9 +30416,9 @@ } }, { - "name": "NODE_0000252", + "name": "NODE_0000270", "node_attrs": { - "div": 0.07186984, + "div": 0.0719, "clade_membership": { "value": "1I_H" } @@ -36480,30 +30451,14 @@ "C10208T", "T10209C", "T10252A" - ], - "E": [ - "I114L" - ], - "NS4B": [ - "V148I" - ], - "NS5": [ - "E428D", - "S631N", - "G833E", - "L879S", - "D893E" ] - }, - "labels": { - "aa": "E: I114L; NS4B: V148I; NS5: E428D, S631N, G833E, L879S, D893E" } }, "children": [ { - "name": "NODE_0000253", + "name": "NODE_0000271", "node_attrs": { - "div": 0.07216102, + "div": 0.0722, "clade_membership": { "value": "1I_H" } @@ -36514,25 +30469,19 @@ "T2750C", "C6265T", "G10006A" - ], - "NS1": [ - "Y111H" ] - }, - "labels": { - "aa": "NS1: Y111H" } }, "children": [ { "name": "MW945936.1|2011", "node_attrs": { - "div": 0.08220132000000001, - "country": { - "value": "Thailand" - }, + "div": 0.0822, "clade_membership": { "value": "1I_H" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -36635,44 +30584,14 @@ "C10002T", "T10018G", "C10216T" - ], - "E": [ - "F96L", - "F392Y" - ], - "M": [ - "S28P", - "A29V" - ], - "NS1": [ - "A94V", - "V178A", - "V338I" - ], - "NS2A": [ - "F41L", - "M68V", - "H143Y" - ], - "NS3": [ - "T115I", - "E173D" - ], - "NS5": [ - "N631S", - "L643F", - "S810L" ] - }, - "labels": { - "aa": "E: F96L, F392Y; M: S28P, A29V; NS1: A94V, V178A, V338I; NS2A: F41L, M68V, H143Y; NS3: T115I, E173D; NS5: N631S, L643F, S810L" } } }, { - "name": "NODE_0000254", + "name": "NODE_0000272", "node_attrs": { - "div": 0.07400938, + "div": 0.074, "clade_membership": { "value": "1I_H" } @@ -36697,32 +30616,14 @@ "G8717A", "C9934T", "A10210G" - ], - "C": [ - "K99R" - ], - "NS2A": [ - "L152M" - ], - "NS3": [ - "L217M" - ], - "NS5": [ - "G382S" ] - }, - "labels": { - "aa": "C: K99R; NS2A: L152M; NS3: L217M; NS5: G382S" } }, "children": [ { "name": "MW945932.1|2003", "node_attrs": { - "div": 0.0749932, - "country": { - "value": "Thailand" - }, + "div": 0.075, "clade_membership": { "value": "1I_H" } @@ -36739,20 +30640,14 @@ "T4258C", "G5923A", "G9298A" - ], - "M": [ - "I156V" ] - }, - "labels": { - "aa": "M: I156V" } } }, { - "name": "NODE_0000255", + "name": "NODE_0000273", "node_attrs": { - "div": 0.07722531, + "div": 0.0772, "clade_membership": { "value": "1I_H.1" } @@ -36789,20 +30684,9 @@ "C9952T", "T10084C", "A10090G" - ], - "C": [ - "R100K" - ], - "NS1": [ - "S117N", - "P144S" - ], - "NS3": [ - "E12K" ] }, "labels": { - "aa": "C: R100K; NS1: S117N, P144S; NS3: E12K", "lineage": "1I_H.1" } }, @@ -36810,12 +30694,12 @@ { "name": "MW386867.1|2019-10", "node_attrs": { - "div": 0.08721754000000001, - "country": { - "value": "China" - }, + "div": 0.0872, "clade_membership": { "value": "1I_H.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -36912,36 +30796,14 @@ "T10057C", "T10066C", "C10126T" - ], - "E": [ - "A382V", - "L463A", - "T464S", - "W465R" - ], - "NS1": [ - "D278N" - ], - "NS2A": [ - "V114M" - ], - "NS3": [ - "I77V" - ], - "NS5": [ - "S629L", - "S746G" ] - }, - "labels": { - "aa": "E: A382V, L463A, T464S, W465R; NS1: D278N; NS2A: V114M; NS3: I77V; NS5: S629L, S746G" } } }, { - "name": "NODE_0000256", + "name": "NODE_0000274", "node_attrs": { - "div": 0.07863308000000001, + "div": 0.0786, "clade_membership": { "value": "1I_H.1" } @@ -36965,25 +30827,19 @@ "C6217T", "T6654C", "G7759A" - ], - "NS4A": [ - "V93A" ] - }, - "labels": { - "aa": "NS4A: V93A" } }, "children": [ { "name": "MN960676.1|2019-11-16", "node_attrs": { - "div": 0.09139438000000001, - "country": { - "value": "China" - }, + "div": 0.0914, "clade_membership": { "value": "1I_H.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -37118,33 +30974,14 @@ "G10165A", "C10168T", "A10225T" - ], - "NS1": [ - "A98T" - ], - "NS2B": [ - "V109M" - ], - "NS3": [ - "G159V", - "T160S", - "Y161D", - "V162F", - "S163W", - "Q167L", - "R203K", - "D437E" ] - }, - "labels": { - "aa": "NS1: A98T; NS2B: V109M; NS3: G159V, T160S, Y161D, V162F, S163W, Q167L, R203K, D437E" } } }, { - "name": "NODE_0000257", + "name": "NODE_0000275", "node_attrs": { - "div": 0.07962074000000001, + "div": 0.0796, "clade_membership": { "value": "1I_H.1" } @@ -37159,26 +30996,19 @@ "C8584T", "G9450A", "A10058G" - ], - "NS5": [ - "G626E", - "I829V" ] - }, - "labels": { - "aa": "NS5: G626E, I829V" } }, "children": [ { "name": "OQ080034.1|2020-08-17", "node_attrs": { - "div": 0.08901804, - "country": { - "value": "Sri Lanka" - }, + "div": 0.089, "clade_membership": { "value": "1I_H.1" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -37275,45 +31105,14 @@ "C9994T", "T10061A", "A10123T" - ], - "E": [ - "N52D", - "V139I", - "N194T" - ], - "NS1": [ - "I123F", - "K347R" - ], - "NS3": [ - "N90S", - "N401S" - ], - "NS4A": [ - "S99N" - ], - "NS4B": [ - "M53V", - "G247S" - ], - "NS5": [ - "M244I", - "Q278K", - "R378G", - "K551R", - "V784A", - "S830T" ] - }, - "labels": { - "aa": "E: N52D, V139I, N194T; NS1: I123F, K347R; NS3: N90S, N401S; NS4A: S99N; NS4B: M53V, G247S; NS5: M244I, Q278K, R378G, K551R, V784A, S830T" } } }, { - "name": "NODE_0000258", + "name": "NODE_0000276", "node_attrs": { - "div": 0.08207747000000001, + "div": 0.0821, "clade_membership": { "value": "1I_H.1" } @@ -37343,29 +31142,19 @@ "T9229C", "T9904C", "T9970C" - ], - "M": [ - "T107A" - ], - "NS4B": [ - "V18A", - "V31I" ] - }, - "labels": { - "aa": "M: T107A; NS4B: V18A, V31I" } }, "children": [ { "name": "KJ755855.1|2013-07", "node_attrs": { - "div": 0.09539017000000001, - "country": { - "value": "India" - }, + "div": 0.0954, "clade_membership": { "value": "1I_H.1" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -37504,104 +31293,19 @@ "C10063T", "G10090A", "A10189G" - ], - "2K": [ - "G13R" - ], - "E": [ - "V24E", - "G106E", - "T145I", - "G146A", - "D147A", - "T163I", - "Q234L", - "D235F", - "E269A", - "I270L", - "S273F", - "C285X", - "V320I" - ], - "NS1": [ - "M84L", - "I224T", - "R257S" - ], - "NS2A": [ - "D6V", - "F8L", - "L42R", - "L43K", - "M45R", - "M70T", - "G71R", - "A88S", - "D125V", - "G126L", - "K135T", - "A164T" - ], - "NS3": [ - "R15K", - "A70G", - "S71R", - "R84G", - "Q86K", - "Q167H", - "I179T", - "D181V", - "V183A", - "I295L", - "R419P", - "K431N", - "A456N", - "F611K" - ], - "NS4A": [ - "T81A", - "S82G", - "I83N", - "S99N" - ], - "NS4B": [ - "C99F", - "Y100L", - "T203S", - "T204P", - "F213S" - ], - "NS5": [ - "S23T", - "T98S", - "K101R", - "N122D", - "V124L", - "L126R", - "H127C", - "D131E", - "V132F", - "T142S", - "L143F", - "C145G", - "L162V", - "I716V" ] - }, - "labels": { - "aa": "2K: G13R; E: V24E, G106E, T145I, G146A, D147A, T163I, Q234L, D235F, E269A, I270L, S273F, C285X, V320I; NS1: M84L, I224T, R257S; NS2A: D6V, F8L, L42R, L43K, M45R, M70T, G71R, A88S, D125V, G126L, K135T, A164T; NS3: R15K, A70G, S71R, R84G, Q86K, Q167H, I179T, D181V, V183A, I295L, R419P, K431N, A456N, F611K; NS4A: T81A, S82G, I83N, S99N; NS4B: C99F, Y100L, T203S, T204P, F213S; NS5: S23T, T98S, K101R, N122D, V124L, L126R, H127C, D131E, V132F, T142S, L143F, C145G, L162V, I716V" } } }, { "name": "ON123666.1|2018", "node_attrs": { - "div": 0.10106447000000002, - "country": { - "value": "India" - }, + "div": 0.101, "clade_membership": { "value": "1I_H.1" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -37789,39 +31493,7 @@ "A10252T", "G10261A", "G10272A" - ], - "E": [ - "T272M" - ], - "NS1": [ - "N117S" - ], - "NS2A": [ - "I19V", - "L208F" - ], - "NS3": [ - "R15I", - "L85F", - "T91A", - "H466Q" - ], - "NS4A": [ - "R39K", - "K76R", - "M89I" - ], - "NS5": [ - "D428E", - "K466T", - "R828H", - "I873V", - "S879L", - "E893D" ] - }, - "labels": { - "aa": "E: T272M; NS1: N117S; NS2A: I19V, L208F; NS3: R15I, L85F, T91A, H466Q; NS4A: R39K, K76R, M89I; NS5: D428E, K466T, R828H, I873V, S879L, E893D" } } } @@ -37838,9 +31510,9 @@ ] }, { - "name": "NODE_0000259", + "name": "NODE_0000277", "node_attrs": { - "div": 0.07226907, + "div": 0.0723, "clade_membership": { "value": "1I_H" } @@ -37853,20 +31525,14 @@ "G5486A", "T9388C", "T9640C" - ], - "NS3": [ - "V323M" ] - }, - "labels": { - "aa": "NS3: V323M" } }, "children": [ { - "name": "NODE_0000260", + "name": "NODE_0000278", "node_attrs": { - "div": 0.07483216000000001, + "div": 0.0748, "clade_membership": { "value": "1I_H" } @@ -37898,26 +31564,14 @@ "T7048C", "T7397C", "T9928C" - ], - "NS1": [ - "A98V" - ], - "NS2A": [ - "H143Y" ] - }, - "labels": { - "aa": "NS1: A98V; NS2A: H143Y" } }, "children": [ { "name": "MW946067.1|2003", "node_attrs": { - "div": 0.07552016, - "country": { - "value": "Thailand" - }, + "div": 0.0755, "clade_membership": { "value": "1I_H" } @@ -37937,9 +31591,9 @@ } }, { - "name": "NODE_0000261", + "name": "NODE_0000279", "node_attrs": { - "div": 0.07740284000000001, + "div": 0.0774, "clade_membership": { "value": "1I_H.2" } @@ -37973,22 +31627,9 @@ "G8953A", "C9028T", "C9459T" - ], - "M": [ - "D89E" - ], - "NS1": [ - "Y247H" - ], - "NS2B": [ - "Y122H" - ], - "NS5": [ - "S629L" ] }, "labels": { - "aa": "M: D89E; NS1: Y247H; NS2B: Y122H; NS5: S629L", "lineage": "1I_H.2" } }, @@ -37996,12 +31637,12 @@ { "name": "HM181952.1|2007", "node_attrs": { - "div": 0.07917897000000002, - "country": { - "value": "Cambodia" - }, + "div": 0.0792, "clade_membership": { "value": "1I_H.2" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -38025,23 +31666,14 @@ "C7804T", "G8287A", "C9907T" - ], - "NS1": [ - "R214K" - ], - "NS4B": [ - "I122V" ] - }, - "labels": { - "aa": "NS1: R214K; NS4B: I122V" } } }, { - "name": "NODE_0000262", + "name": "NODE_0000280", "node_attrs": { - "div": 0.07789147000000002, + "div": 0.0779, "clade_membership": { "value": "1I_H.2" } @@ -38054,25 +31686,19 @@ "A8113G", "A9097G", "A9492G" - ], - "NS5": [ - "E640G" ] - }, - "labels": { - "aa": "NS5: E640G" } }, "children": [ { "name": "EU482811.1|2006", "node_attrs": { - "div": 0.07848187000000002, - "country": { - "value": "Vietnam" - }, + "div": 0.0785, "clade_membership": { "value": "1I_H.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -38089,9 +31715,9 @@ } }, { - "name": "NODE_0000263", + "name": "NODE_0000281", "node_attrs": { - "div": 0.07946978000000002, + "div": 0.0795, "clade_membership": { "value": "1I_H.2" } @@ -38115,25 +31741,19 @@ "C7532T", "T7975C", "C8128T" - ], - "NS3": [ - "L85F" ] - }, - "labels": { - "aa": "NS3: L85F" } }, "children": [ { "name": "GU131749.1|2008", "node_attrs": { - "div": 0.08133798000000002, - "country": { - "value": "Vietnam" - }, + "div": 0.0813, "clade_membership": { "value": "1I_H.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -38158,26 +31778,14 @@ "T9485C", "C9907T", "T10057C" - ], - "C": [ - "R97T" - ], - "E": [ - "G445R" - ], - "NS5": [ - "V231I" ] - }, - "labels": { - "aa": "C: R97T; E: G445R; NS5: V231I" } } }, { - "name": "NODE_0000264", + "name": "NODE_0000282", "node_attrs": { - "div": 0.07966578000000002, + "div": 0.0797, "clade_membership": { "value": "1I_H.2" } @@ -38194,12 +31802,12 @@ { "name": "GU131801.1|2008", "node_attrs": { - "div": 0.08084791000000002, - "country": { - "value": "Vietnam" - }, + "div": 0.0808, "clade_membership": { "value": "1I_H.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -38217,33 +31825,19 @@ "T2500C", "A5971G", "T7882C" - ], - "C": [ - "T8P", - "A9G", - "R10D", - "A30G" - ], - "E": [ - "V379G", - "F392V", - "F402V" ] - }, - "labels": { - "aa": "C: T8P, A9G, R10D, A30G; E: V379G, F392V, F402V" } } }, { "name": "GU131678.1|2008", "node_attrs": { - "div": 0.08262600000000002, - "country": { - "value": "Vietnam" - }, + "div": 0.0826, "clade_membership": { "value": "1I_H.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -38279,47 +31873,7 @@ "A9882C", "G10133C", "G10148C" - ], - "E": [ - "V122M", - "E403K" - ], - "NS2A": [ - "S9L" - ], - "NS3": [ - "H466P", - "D566A", - "R593L" - ], - "NS4A": [ - "A98G" - ], - "NS4B": [ - "D80A" - ], - "NS5": [ - "T59P", - "N69T", - "K72N", - "D79A", - "G86A", - "V97G", - "N122D", - "E267D", - "A447P", - "A472P", - "G510A", - "A550G", - "S746T", - "H767P", - "D770A", - "A854P", - "A859P" ] - }, - "labels": { - "aa": "E: V122M, E403K; NS2A: S9L; NS3: H466P, D566A, R593L; NS4A: A98G; NS4B: D80A; NS5: T59P, N69T, K72N, D79A, G86A, V97G, N122D, E267D, A447P, A472P, G510A, A550G, S746T, H767P, D770A, A854P, A859P" } } } @@ -38334,9 +31888,9 @@ ] }, { - "name": "NODE_0000265", + "name": "NODE_0000283", "node_attrs": { - "div": 0.07344929, + "div": 0.0734, "clade_membership": { "value": "1I_H" } @@ -38356,27 +31910,14 @@ "T8725C", "A9809G", "T10078C" - ], - "NS3": [ - "S347L" - ], - "NS5": [ - "I135V", - "S746G" ] - }, - "labels": { - "aa": "NS3: S347L; NS5: I135V, S746G" } }, "children": [ { "name": "MW945886.1|2004", "node_attrs": { - "div": 0.0758175, - "country": { - "value": "Thailand" - }, + "div": 0.0758, "clade_membership": { "value": "1I_H" } @@ -38408,24 +31949,14 @@ "C6256T", "C9835G", "C9940T" - ], - "NS1": [ - "V5A", - "T301K" - ], - "NS2A": [ - "K135R" ] - }, - "labels": { - "aa": "NS1: V5A, T301K; NS2A: K135R" } } }, { - "name": "NODE_0000266", + "name": "NODE_0000284", "node_attrs": { - "div": 0.07542422, + "div": 0.0754, "clade_membership": { "value": "1I_H.3" } @@ -38463,12 +31994,12 @@ { "name": "KY586396.1|2004", "node_attrs": { - "div": 0.076013, - "country": { - "value": "Thailand" - }, + "div": 0.076, "clade_membership": { "value": "1I_H.3" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -38480,23 +32011,14 @@ "C4006T", "A5212G", "G6905A" - ], - "E": [ - "S338L" - ], - "NS4B": [ - "A27T" ] - }, - "labels": { - "aa": "E: S338L; NS4B: A27T" } } }, { - "name": "NODE_0000267", + "name": "NODE_0000285", "node_attrs": { - "div": 0.07735393, + "div": 0.0774, "clade_membership": { "value": "1I_H.3" } @@ -38530,12 +32052,12 @@ { "name": "MW946105.1|2006", "node_attrs": { - "div": 0.07897124, - "country": { - "value": "Thailand" - }, + "div": 0.079, "clade_membership": { "value": "1I_H.3" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -38558,24 +32080,14 @@ "T8428C", "A9278G", "C9757T" - ], - "NS3": [ - "E12K", - "V274L" - ], - "NS5": [ - "K569E" ] - }, - "labels": { - "aa": "NS3: E12K, V274L; NS5: K569E" } } }, { - "name": "NODE_0000268", + "name": "NODE_0000286", "node_attrs": { - "div": 0.0775095, + "div": 0.0775, "clade_membership": { "value": "1I_H.3" } @@ -38591,12 +32103,12 @@ { "name": "MW946070.1|2006", "node_attrs": { - "div": 0.07868995, - "country": { - "value": "Thailand" - }, + "div": 0.0787, "clade_membership": { "value": "1I_H.3" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -38614,20 +32126,14 @@ "C8769T", "A8773G", "T10057C" - ], - "NS5": [ - "T399I" ] - }, - "labels": { - "aa": "NS5: T399I" } } }, { - "name": "NODE_0000269", + "name": "NODE_0000287", "node_attrs": { - "div": 0.08055831, + "div": 0.0806, "clade_membership": { "value": "1I_H.3" } @@ -38666,32 +32172,19 @@ "T8038C", "T9583C", "G10120A" - ], - "M": [ - "T83A" - ], - "NS3": [ - "L85F", - "Y349H" - ], - "NS4A": [ - "M30I" ] - }, - "labels": { - "aa": "M: T83A; NS3: L85F, Y349H; NS4A: M30I" } }, "children": [ { "name": "KY849741.1|2008-10-06", "node_attrs": { - "div": 0.08055931, - "country": { - "value": "Laos" - }, + "div": 0.0806, "clade_membership": { "value": "1I_H.3" + }, + "country": { + "value": "Laos" } }, "branch_attrs": { @@ -38701,12 +32194,12 @@ { "name": "KC172834.1|2008-10-06", "node_attrs": { - "div": 0.08055931, - "country": { - "value": "Laos" - }, + "div": 0.0806, "clade_membership": { "value": "1I_H.3" + }, + "country": { + "value": "Laos" } }, "branch_attrs": { @@ -38734,9 +32227,9 @@ ] }, { - "name": "NODE_0000270", + "name": "NODE_0000288", "node_attrs": { - "div": 0.06782108, + "div": 0.0678, "clade_membership": { "value": "1I" } @@ -38758,9 +32251,9 @@ }, "children": [ { - "name": "NODE_0000271", + "name": "NODE_0000289", "node_attrs": { - "div": 0.06925053, + "div": 0.0693, "clade_membership": { "value": "1I" } @@ -38782,29 +32275,14 @@ "T6733C", "G6905T", "C7420T" - ], - "M": [ - "R122K" - ], - "NS1": [ - "T131A" - ], - "NS4B": [ - "A27S" ] - }, - "labels": { - "aa": "M: R122K; NS1: T131A; NS4B: A27S" } }, "children": [ { "name": "MW945806.1|1998", "node_attrs": { - "div": 0.07089773, - "country": { - "value": "Thailand" - }, + "div": 0.0709, "clade_membership": { "value": "1I" } @@ -38829,26 +32307,14 @@ "G7144A", "T7387A", "A7963G" - ], - "E": [ - "G274V" - ], - "NS2A": [ - "V60I" - ], - "NS3": [ - "L85F" ] - }, - "labels": { - "aa": "E: G274V; NS2A: V60I; NS3: L85F" } } }, { - "name": "NODE_0000272", + "name": "NODE_0000290", "node_attrs": { - "div": 0.07026287, + "div": 0.0703, "clade_membership": { "value": "1I_J" } @@ -38863,24 +32329,17 @@ "C8288T", "G8953A", "G10071A" - ], - "NS4A": [ - "M45L" - ], - "NS5": [ - "G833E" ] }, "labels": { - "aa": "NS4A: M45L; NS5: G833E", "lineage": "1I_J" } }, "children": [ { - "name": "NODE_0000273", + "name": "NODE_0000291", "node_attrs": { - "div": 0.07307956, + "div": 0.0731, "clade_membership": { "value": "1I_J" } @@ -38919,25 +32378,19 @@ "C8896T", "C9257T", "C9425T" - ], - "M": [ - "A29T" ] - }, - "labels": { - "aa": "M: A29T" } }, "children": [ { "name": "MW945782.1|2000", "node_attrs": { - "div": 0.07327858, - "country": { - "value": "Thailand" - }, + "div": 0.0733, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -38950,9 +32403,9 @@ } }, { - "name": "NODE_0000274", + "name": "NODE_0000292", "node_attrs": { - "div": 0.07357203, + "div": 0.0736, "clade_membership": { "value": "1I_J" } @@ -38976,12 +32429,12 @@ { "name": "MG840548.1|2015", "node_attrs": { - "div": 0.08736772999999999, - "country": { - "value": "China" - }, + "div": 0.0874, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -39102,56 +32555,19 @@ "C9907A", "T10057C", "T10204C" - ], - "C": [ - "N2I", - "G70S" - ], - "E": [ - "V55I" - ], - "NS1": [ - "I246T", - "F323Y" - ], - "NS2A": [ - "M31T", - "I174L", - "W215R", - "K218R" - ], - "NS2B": [ - "V78I" - ], - "NS3": [ - "A170T", - "S387G" - ], - "NS4B": [ - "H23Q", - "K81R", - "V148I" - ], - "NS5": [ - "I78V", - "K422R", - "V666A" ] - }, - "labels": { - "aa": "C: N2I, G70S; E: V55I; NS1: I246T, F323Y; NS2A: M31T, I174L, W215R, K218R; NS2B: V78I; NS3: A170T, S387G; NS4B: H23Q, K81R, V148I; NS5: I78V, K422R, V666A" } } }, { "name": "MW793709.1|2018-07", "node_attrs": { - "div": 0.08607772999999999, - "country": { - "value": "Myanmar" - }, + "div": 0.0861, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "Myanmar" } }, "branch_attrs": { @@ -39277,31 +32693,7 @@ "C10055T", "C10150T", "C10168T" - ], - "C": [ - "T103A" - ], - "E": [ - "V320I", - "T339A" - ], - "NS1": [ - "Y111H", - "I251T" - ], - "NS3": [ - "I443V" - ], - "NS4B": [ - "H24R" - ], - "NS5": [ - "I340T", - "H828Y" ] - }, - "labels": { - "aa": "C: T103A; E: V320I, T339A; NS1: Y111H, I251T; NS3: I443V; NS4B: H24R; NS5: I340T, H828Y" } } } @@ -39310,9 +32702,9 @@ ] }, { - "name": "NODE_0000275", + "name": "NODE_0000293", "node_attrs": { - "div": 0.07517744000000001, + "div": 0.0752, "clade_membership": { "value": "1I_J" } @@ -39350,28 +32742,19 @@ "T8821C", "C9884T", "T9970C" - ], - "NS1": [ - "I224V" - ], - "NS4A": [ - "V93A" ] - }, - "labels": { - "aa": "NS1: I224V; NS4A: V93A" } }, "children": [ { "name": "MN933656.1|2014-09-23", "node_attrs": { - "div": 0.08720294, - "country": { - "value": "China" - }, + "div": 0.0872, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -39505,65 +32888,14 @@ "A10189C", "G10240A", "T10252C" - ], - "2K": [ - "Q3H" - ], - "E": [ - "E203G" - ], - "M": [ - "T73S" - ], - "NS1": [ - "D37H", - "S117N", - "R324K" - ], - "NS2A": [ - "T34A" - ], - "NS2B": [ - "K85R" - ], - "NS3": [ - "G2E", - "V3E", - "A112V" - ], - "NS4A": [ - "L55S", - "M56L", - "F72L", - "G75R" - ], - "NS4B": [ - "E2D", - "K10R", - "N22T", - "H24P", - "S27T" - ], - "NS5": [ - "E24D", - "T59A", - "R253K", - "V324E", - "P330S", - "V642A", - "D785N", - "V787I" ] - }, - "labels": { - "aa": "2K: Q3H; E: E203G; M: T73S; NS1: D37H, S117N, R324K; NS2A: T34A; NS2B: K85R; NS3: G2E, V3E, A112V; NS4A: L55S, M56L, F72L, G75R; NS4B: E2D, K10R, N22T, H24P, S27T; NS5: E24D, T59A, R253K, V324E, P330S, V642A, D785N, V787I" } } }, { - "name": "NODE_0000276", + "name": "NODE_0000294", "node_attrs": { - "div": 0.08225917, + "div": 0.0823, "clade_membership": { "value": "1I_J" } @@ -39637,33 +32969,19 @@ "C2290T", "T6928C", "G8005A" - ], - "E": [ - "S8N", - "A88T", - "S155T", - "T171S", - "T339S" - ], - "M": [ - "A59T", - "D72E" ] - }, - "labels": { - "aa": "E: S8N, A88T, S155T, T171S, T339S; M: A59T, D72E" } }, "children": [ { "name": "MT397276.1|2015-11", "node_attrs": { - "div": 0.09606637000000001, - "country": { - "value": "Thailand" - }, + "div": 0.0961, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -39822,84 +33140,19 @@ "C9703T", "T9823C", "C10055T" - ], - "C": [ - "T62S", - "L81T", - "K85N", - "E87Q", - "I88T", - "P110T" - ], - "E": [ - "E203K", - "E249G", - "L253V", - "E257D", - "G258L", - "L264I", - "G266R", - "A267E", - "L283P", - "T293S", - "S339C", - "V436I" - ], - "M": [ - "K21T", - "P54T", - "W74F", - "V75L", - "C80S", - "Q82E", - "G84V", - "E85D", - "H86K", - "D89V", - "K90E" - ], - "NS1": [ - "S117N", - "R324K" - ], - "NS2A": [ - "L120V" - ], - "NS3": [ - "V13M", - "V72I", - "K104R", - "D285V", - "A296P" - ], - "NS4A": [ - "V2I" - ], - "NS4B": [ - "R227K" - ], - "NS5": [ - "M34I", - "R253K", - "F412Y", - "V642A", - "H828Y" ] - }, - "labels": { - "aa": "C: T62S, L81T, K85N, E87Q, I88T, P110T; E: E203K, E249G, L253V, E257D, G258L, L264I, G266R, A267E, L283P, T293S, S339C, V436I; M: K21T, P54T, W74F, V75L, C80S, Q82E, G84V, E85D, H86K, D89V, K90E; NS1: S117N, R324K; NS2A: L120V; NS3: V13M, V72I, K104R, D285V, A296P; NS4A: V2I; NS4B: R227K; NS5: M34I, R253K, F412Y, V642A, H828Y" } } }, { "name": "JF459993.1|2002", "node_attrs": { - "div": 0.09861477, - "country": { - "value": "Myanmar" - }, + "div": 0.0986, "clade_membership": { "value": "1I_J" + }, + "country": { + "value": "Myanmar" } }, "branch_attrs": { @@ -40050,37 +33303,7 @@ "A9976G", "A10058G", "G10240A" - ], - "C": [ - "A9G", - "E87G", - "L106F", - "M109L", - "A112S" - ], - "E": [ - "V55I", - "M297V", - "I324V", - "T346I", - "I380V", - "V461I", - "L484M" - ], - "M": [ - "R129G" - ], - "NS1": [ - "Y256H" - ], - "NS5": [ - "G626E", - "I723V", - "I829V" ] - }, - "labels": { - "aa": "C: A9G, E87G, L106F, M109L, A112S; E: V55I, M297V, I324V, T346I, I380V, V461I, L484M; M: R129G; NS1: Y256H; NS5: G626E, I723V, I829V" } } } @@ -40093,9 +33316,9 @@ ] }, { - "name": "NODE_0000277", + "name": "NODE_0000295", "node_attrs": { - "div": 0.06840087, + "div": 0.0684, "clade_membership": { "value": "1I" } @@ -40116,10 +33339,7 @@ { "name": "MW946069.1|1999", "node_attrs": { - "div": 0.0712583, - "country": { - "value": "Thailand" - }, + "div": 0.0713, "clade_membership": { "value": "1I" } @@ -40156,20 +33376,14 @@ "A9631G", "G9736A", "G10231A" - ], - "C": [ - "A112V" ] - }, - "labels": { - "aa": "C: A112V" } } }, { - "name": "NODE_0000278", + "name": "NODE_0000296", "node_attrs": { - "div": 0.06956935, + "div": 0.0696, "clade_membership": { "value": "1I_K" } @@ -40199,12 +33413,12 @@ { "name": "MW945798.1|1999", "node_attrs": { - "div": 0.07202284, - "country": { - "value": "Thailand" - }, + "div": 0.072, "clade_membership": { "value": "1I_K" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -40235,34 +33449,14 @@ "C9500T", "T10018C", "T10084C" - ], - "C": [ - "A112T" - ], - "E": [ - "E362D" - ], - "NS1": [ - "F86L", - "V350A" - ], - "NS2A": [ - "F159L" - ], - "NS5": [ - "K445R", - "L643F" ] - }, - "labels": { - "aa": "C: A112T; E: E362D; NS1: F86L, V350A; NS2A: F159L; NS5: K445R, L643F" } } }, { - "name": "NODE_0000279", + "name": "NODE_0000297", "node_attrs": { - "div": 0.07063318, + "div": 0.0706, "clade_membership": { "value": "1I_K" } @@ -40281,21 +33475,14 @@ "T9269G", "C9553T", "G10071A" - ], - "NS5": [ - "S566A", - "G833E" ] - }, - "labels": { - "aa": "NS5: S566A, G833E" } }, "children": [ { - "name": "NODE_0000280", + "name": "NODE_0000298", "node_attrs": { - "div": 0.07280449, + "div": 0.0728, "clade_membership": { "value": "1I_K.7" } @@ -40325,17 +33512,9 @@ "T9498C", "C9940T", "C10168T" - ], - "NS1": [ - "F86L" - ], - "NS5": [ - "A259T", - "V642A" ] }, "labels": { - "aa": "NS1: F86L; NS5: A259T, V642A", "lineage": "1I_K.7" } }, @@ -40343,12 +33522,12 @@ { "name": "KY586366.1|2001", "node_attrs": { - "div": 0.07447739, - "country": { - "value": "Thailand" - }, + "div": 0.0745, "clade_membership": { "value": "1I_K.7" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -40372,23 +33551,14 @@ "C8125G", "T8449C", "C8677T" - ], - "C": [ - "L106F" - ], - "NS2A": [ - "T34I" ] - }, - "labels": { - "aa": "C: L106F; NS2A: T34I" } } }, { - "name": "NODE_0000281", + "name": "NODE_0000299", "node_attrs": { - "div": 0.07280893, + "div": 0.0728, "clade_membership": { "value": "1I_K.7" } @@ -40400,12 +33570,12 @@ { "name": "MW946221.1|2006", "node_attrs": { - "div": 0.07645589, - "country": { - "value": "Thailand" - }, + "div": 0.0765, "clade_membership": { "value": "1I_K.7" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -40449,30 +33619,14 @@ "T9592C", "C9874T", "T10057C" - ], - "C": [ - "S27P" - ], - "E": [ - "V485I" - ], - "NS2A": [ - "M45V" - ], - "NS5": [ - "I627V", - "P636L" ] - }, - "labels": { - "aa": "C: S27P; E: V485I; NS2A: M45V; NS5: I627V, P636L" } } }, { - "name": "NODE_0000282", + "name": "NODE_0000300", "node_attrs": { - "div": 0.0729031, + "div": 0.0729, "clade_membership": { "value": "1I_K.7" } @@ -40482,25 +33636,19 @@ "nuc": [ "T2802C", "G8953A" - ], - "NS1": [ - "V128A" ] - }, - "labels": { - "aa": "NS1: V128A" } }, "children": [ { "name": "GQ868619.1|2003", "node_attrs": { - "div": 0.075266, - "country": { - "value": "Cambodia" - }, + "div": 0.0753, "clade_membership": { "value": "1I_K.7" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -40528,31 +33676,14 @@ "T8227C", "T9016G", "C10150T" - ], - "2K": [ - "I12M" - ], - "NS2A": [ - "A38V" - ], - "NS3": [ - "V323M", - "V433I" - ], - "NS4A": [ - "T69M", - "V93G" ] - }, - "labels": { - "aa": "2K: I12M; NS2A: A38V; NS3: V323M, V433I; NS4A: T69M, V93G" } } }, { - "name": "NODE_0000283", + "name": "NODE_0000301", "node_attrs": { - "div": 0.07727898, + "div": 0.0773, "clade_membership": { "value": "1I_K.7" } @@ -40604,29 +33735,19 @@ "C9562T", "G9886A", "T10066C" - ], - "NS1": [ - "A98G" - ], - "NS3": [ - "Q86R", - "I520V" ] - }, - "labels": { - "aa": "NS1: A98G; NS3: Q86R, I520V" } }, "children": [ { "name": "FJ410257.1|2008", "node_attrs": { - "div": 0.07993749, - "country": { - "value": "Vietnam" - }, + "div": 0.0799, "clade_membership": { "value": "1I_K.7" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -40656,29 +33777,14 @@ "G7606A", "T10102C", "C10255T" - ], - "C": [ - "L46F" - ], - "E": [ - "S338T" - ], - "NS3": [ - "P356S", - "H466Y", - "E588D", - "F611L" ] - }, - "labels": { - "aa": "C: L46F; E: S338T; NS3: P356S, H466Y, E588D, F611L" } } }, { - "name": "NODE_0000284", + "name": "NODE_0000302", "node_attrs": { - "div": 0.07786706, + "div": 0.0779, "clade_membership": { "value": "1I_K.7" } @@ -40699,12 +33805,12 @@ { "name": "HM181970.1|2008", "node_attrs": { - "div": 0.0808213, - "country": { - "value": "Vietnam" - }, + "div": 0.0808, "clade_membership": { "value": "1I_K.7" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -40741,760 +33847,122 @@ "T9253C", "A9682G", "G9877A" - ], - "E": [ - "V436I" - ], - "NS2A": [ - "S65F" - ], - "NS3": [ - "N44D", - "Y349H" - ] - }, - "labels": { - "aa": "E: V436I; NS2A: S65F; NS3: N44D, Y349H" - } - } - }, - { - "name": "GU131752.1|2008", - "node_attrs": { - "div": 0.08111098, - "country": { - "value": "Vietnam" - }, - "clade_membership": { - "value": "1I_K.7" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A109G", - "T556C", - "C816T", - "T1210C", - "C1360T", - "C1856T", - "C1879A", - "C1951A", - "T2336C", - "G2419A", - "C2431T", - "C2608T", - "A2722G", - "C2836T", - "C3128T", - "T3415C", - "T3697C", - "A4960G", - "A5086G", - "A5449G", - "C5737T", - "G6556A", - "C7598T", - "G8080A", - "C8278T", - "A8818G", - "G8971A", - "T9016G", - "C9067T", - "G10248C" - ], - "M": [ - "A127V" - ], - "NS5": [ - "S892T" - ] - }, - "labels": { - "aa": "M: A127V; NS5: S892T" - } - } - } - ] - } - ] - } - ] - } - ] - } - ] - }, - { - "name": 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+ "T4594C", + "A4951G", + "C5410T", + "C5632T", + "C6199T", + "G6676A", + "C7186T", + "A7315G", + "T7441C", + "A8740G", + "T8815C", + "T9658C", + "T9823C" + ] + } + }, + "children": [ + { + "name": "NODE_0000304", + "node_attrs": { + "div": 0.0727, + "clade_membership": { + "value": "1I_K" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T850C", + "A2866G", + "G7084A" + ] + } + }, + "children": [ { - "name": "NODE_0000292", + "name": "NODE_0000305", "node_attrs": { - "div": 0.07706347, + "div": 0.0771, "clade_membership": { "value": "1I_K" } @@ -41547,31 +34015,14 @@ "A9513G", "T9904C", "G10065A" - ], - "M": [ - "I13M" - ], - "NS2B": [ - "Y110F" - ], - "NS5": [ - "Q16R", - "E647G", - "S831N" ] - }, - "labels": { - "aa": "M: I13M; NS2B: Y110F; NS5: Q16R, E647G, S831N" } }, "children": [ { "name": "MW946128.1|2006", "node_attrs": { - "div": 0.07745708, - "country": { - "value": "Thailand" - }, + "div": 0.0775, "clade_membership": { "value": "1I_K" } @@ -41588,9 +34039,9 @@ } }, { - "name": "NODE_0000293", + "name": "NODE_0000306", "node_attrs": { - "div": 0.0797273, + "div": 0.0797, "clade_membership": { "value": "1I_K.6" } @@ -41625,13 +34076,9 @@ "T9040A", "T9121C", "T9721C" - ], - "NS2A": [ - "V114A" ] }, "labels": { - "aa": "NS2A: V114A", "lineage": "1I_K.6" } }, @@ -41639,12 +34086,12 @@ { "name": "ON038487.1|2011-06-09", "node_attrs": { - "div": 0.08051303, - "country": { - "value": "Thailand" - }, + "div": 0.0805, "clade_membership": { "value": "1I_K.6" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -41658,23 +34105,14 @@ "G9584A", "G9613A", "C9895T" - ], - "NS3": [ - "I443V" - ], - "NS5": [ - "D671N" ] - }, - "labels": { - "aa": "NS3: I443V; NS5: D671N" } } }, { - "name": "NODE_0000294", + "name": "NODE_0000307", "node_attrs": { - "div": 0.08110728, + "div": 0.0811, "clade_membership": { "value": "1I_K.6" } @@ -41696,23 +34134,14 @@ "C9425T", "C9502A", "A9805G" - ], - "NS2A": [ - "T34I" - ], - "NS5": [ - "V413I" ] - }, - "labels": { - "aa": "NS2A: T34I; NS5: V413I" } }, "children": [ { - "name": "NODE_0000295", + "name": "NODE_0000308", "node_attrs": { - "div": 0.08347489000000001, + "div": 0.0835, "clade_membership": { "value": "1I_K.6" } @@ -41741,39 +34170,19 @@ "G6905A", "G7621A", "A9304G" - ], - "E": [ - "N89I", - "L113F", - "T346F", - "Q347E" - ], - "NS3": [ - "V3E" - ], - "NS4A": [ - "L55S" - ], - "NS4B": [ - "G14R", - "H24P", - "A27T" ] - }, - "labels": { - "aa": "E: N89I, L113F, T346F, Q347E; NS3: V3E; NS4A: L55S; NS4B: G14R, H24P, A27T" } }, "children": [ { "name": "MN933654.1|2014-07-24", "node_attrs": { - "div": 0.08427741000000001, - "country": { - "value": "China" - }, + "div": 0.0843, "clade_membership": { "value": "1I_K.6" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -41788,32 +34197,19 @@ "A8731G", "C9238T", "C9801T" - ], - "E": [ - "V345E", - "H437L" - ], - "NS4B": [ - "L33I" - ], - "NS5": [ - "A743V" ] - }, - "labels": { - "aa": "E: V345E, H437L; NS4B: L33I; NS5: A743V" } } }, { "name": "MN933659.1|2015-04-21", "node_attrs": { - "div": 0.08879887000000002, - "country": { - "value": "China" - }, + "div": 0.0888, "clade_membership": { "value": "1I_K.6" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -41872,45 +34268,16 @@ "C9146T", "G9512A", "A10210G" - ], - "2K": [ - "Q3H" - ], - "E": [ - "E84G", - "E85R", - "A117D", - "T268I", - "L294I", - "L308V", - "F337L", - "F346L" - ], - "NS4A": [ - "E101K" - ], - "NS4B": [ - "H23P" - ], - "NS5": [ - "V231I", - "H285C", - "I413V", - "P525S", - "G647R" ] - }, - "labels": { - "aa": "2K: Q3H; E: E84G, E85R, A117D, T268I, L294I, L308V, F337L, F346L; NS4A: E101K; NS4B: H23P; NS5: V231I, H285C, I413V, P525S, G647R" } } } ] }, { - "name": "NODE_0000296", + "name": "NODE_0000309", "node_attrs": { - "div": 0.08110928, + "div": 0.0811, "clade_membership": { "value": "1I_K.6" } @@ -41922,12 +34289,12 @@ { "name": "KF971870.1|2013-08-23", "node_attrs": { - "div": 0.08258505000000001, - "country": { - "value": "China" - }, + "div": 0.0826, "clade_membership": { "value": "1I_K.6" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -41948,35 +34315,19 @@ "G6442A", "G6479C", "G6501C" - ], - "NS1": [ - "A186S", - "E208D" - ], - "NS3": [ - "K590E", - "D598G", - "E610D" - ], - "NS4A": [ - "E35Q", - "R42T" ] - }, - "labels": { - "aa": "NS1: A186S, E208D; NS3: K590E, D598G, E610D; NS4A: E35Q, R42T" } } }, { "name": "MW945860.1|2013", "node_attrs": { - "div": 0.08297975, - "country": { - "value": "Thailand" - }, + "div": 0.083, "clade_membership": { "value": "1I_K.6" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -42001,24 +34352,542 @@ "C8482T", "T9232C", "T9518A" - ], - "E": [ - "S227P" - ], - "NS1": [ - "D278N" - ], - "NS3": [ - "A112V" - ], - "NS5": [ - "Y649N" ] + } + } + } + ] + } + ] + } + ] + } + ] + }, + { + "name": "NODE_0000310", + "node_attrs": { + "div": 0.0728, + "clade_membership": { + "value": "1I_K" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T3655C" + ] + } + }, + "children": [ + { + "name": "FJ469907.1|2003", + "node_attrs": { + "div": 0.0752, + "clade_membership": { + "value": "1I_K" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G349A", + "A844G", + "A2719G", + "T2800C", + "C3493T", + "A4105G", + "A4243G", + "A4831G", + "A5035G", + "T5365C", + "G5569C", + "G5659A", + "C5822T", + "T6034C", + "C6308T", + "T6352C", + "G6667A", + "T7048G", + "G7483A", + "A7507G", + "T8488C", + "C8878T", + "T9295C", + "A9991G", + "G10015A" + ] + } + } + }, + { + "name": "NODE_0000311", + "node_attrs": { + "div": 0.0751, + "clade_membership": { + "value": "1I_K.5" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T2399C", + "T2731C", + "G2866T", + "C3469T", + "C3712T", + "C3955T", + "T3956C", + "A4825G", + "A5919G", + "A6106G", + "T6121C", + "T6463C", + "G6694A", + "A7201T", + "A7756G", + "T7882C", + "G8020A", + "A8083G", + "C8869T", + "C9064T", + "C9235T", + "T9586C", + "G10006A" + ] + }, + "labels": { + "lineage": "1I_K.5" + } + }, + "children": [ + { + "name": "KY586336.1|2006", + "node_attrs": { + "div": 0.0768, + "clade_membership": { + "value": "1I_K.5" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T448C", + "A1765G", + "A2719G", + "C2872T", + "T3367C", + "C3379T", + "C4915T", + "G4984A", + "T5293C", + "T5599C", + "C5977T", + "T6383G", + "A6532G", + "C9058T", + "G10165T" + ] + } + } + }, + { + "name": "NODE_0000312", + "node_attrs": { + "div": 0.0752, + "clade_membership": { + "value": "1I_K.5" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C3053T" + ] + } + }, + "children": [ + { + "name": "KY586334.1|2008", + "node_attrs": { + "div": 0.0794, + "clade_membership": { + "value": "1I_K.5" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T397C", + "T643C", + "C678T", + "G1036A", + "A1315G", + "T1441C", + "T1942A", + "A1962G", + "G2103A", + "T3415C", + "G3442A", + "T3472C", + "T3628A", + "G3694A", + "T3712C", + "C3915T", + "A4243G", + "C4480A", + "C4693T", + "T5365C", + "G6118A", + "C6187T", + "C6472T", + "A6610G", + "C6850T", + "T7216C", + "G7237A", + "G7447A", + "T7516C", + "C7966T", + "T7977C", + "T8038C", + "T8200A", + "G8416A", + "T8831A", + "C9085T", + "A9370T", + "A9596G", + "C9754T", + "C9871T", + "C9939T" + ] + } + } + }, + { + "name": "NODE_0000313", + "node_attrs": { + "div": 0.0757, + "clade_membership": { + "value": "1I_K.5" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C679T", + "G1975A", + "T3148C", + "T4463C", + "C6895T" + ] + } + }, + "children": [ + { + "name": "MN448635.1|2010-08-03", + "node_attrs": { + "div": 0.0801, + "clade_membership": { + "value": "1I_K.5" }, - "labels": { - "aa": "E: S227P; NS1: D278N; NS3: A112V; NS5: Y649N" + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A217T", + "T448A", + "A673G", + "C1793T", + "C1840T", + "C2002T", + "A2003G", + "A2119G", + "C2188T", + "A2332G", + "G2368A", + "G2575A", + "A2719G", + "C2830T", + "T2866C", + "A3089G", + "T3364G", + "C3532T", + "C3813T", + "A4509G", + "G4516A", + "G4654A", + "C5168T", + "C5173T", + "C5191T", + "C5518T", + "A5530G", + "T5770C", + "C5794T", + "T6398C", + "G6586A", + "C6628T", + "T6654C", + "C6916T", + "T7376C", + "C8125T", + "G8331A", + "C8335T", + "T8395G", + "A9230G", + "T9518C", + "G9532A", + "A9538G", + "G9688A", + "C10216T" + ] } } + }, + { + "name": "NODE_0000314", + "node_attrs": { + "div": 0.0758, + "clade_membership": { + "value": "1I_K.5" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G2779A", + "T5514C" + ] + } + }, + "children": [ + { + "name": "KY849723.1|2010-07-06", + "node_attrs": { + "div": 0.0814, + "clade_membership": { + "value": "1I_K.5" + }, + "country": { + "value": "Laos" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G436A", + "C901T", + "A1150T", + "A1213G", + "C1462T", + "T1495C", + "G1600A", + "C1630T", + "A1748G", + "G1898T", + "T2273C", + "A2803G", + "A2928G", + "C2992T", + "G3052A", + "T3067C", + "A3565G", + "T3667C", + "T3916C", + "T4099C", + "A4105G", + "C4417T", + "C4675T", + "C4783A", + "T4906C", + "A5122G", + "T5452C", + "A5626G", + "T5830C", + "G6435A", + "T6566C", + "C6697T", + "T7052C", + "T7173G", + "G7243A", + "A7795G", + "C7846T", + "C7927T", + "T7975C", + "T8116C", + "T8137C", + "G8152A", + "C8527T", + "T8752C", + "G8782A", + "A8950G", + "G9151A", + "A9154T", + "G9233A", + "G9262A", + "G9781A", + "C9934T", + "G10027A" + ] + } + } + }, + { + "name": "NODE_0000315", + "node_attrs": { + "div": 0.0813, + "clade_membership": { + "value": "1I_K.5" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T373C", + "A520G", + "G574T", + "T598C", + "T742C", + "T895C", + "T1441C", + "T1613C", + "T1789C", + "A2146G", + "A2242G", + "C2321T", + "C2707T", + "A2722G", + "C2809T", + "T3559C", + "C4117T", + "A4165G", + "C4181T", + "G4609A", + "T4819C", + "C4837A", + "C5011T", + "C5099T", + "T5617C", + "C5704T", + "C5887T", + "T6172C", + "A6523G", + "C6776T", + "C6973T", + "C6991T", + "T7216C", + "G7315A", + "C7598T", + "G7876A", + "C7996T", + "T8209C", + "T8293C", + "C8307T", + "C8350T", + "C8482T", + "G8707A", + "C8863T", + "C8878T", + "C9028T", + "T9232C", + "C9409T", + "A9513G", + "C9757T", + "C10117T", + "C10150T", + "A10189G", + "C10253T" + ] + } + }, + "children": [ + { + "name": "MN448692.1|2012-10-01", + "node_attrs": { + "div": 0.0834, + "clade_membership": { + "value": "1I_K.5" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T1489C", + "A1504G", + "C1926T", + "C1971T", + "C2125T", + "C2960T", + "A3643G", + "T4255C", + "T5200C", + "C5317T", + "C5470T", + "C5586G", + "A5800G", + "T6070C", + "A6820G", + "T7465C", + "A7528T", + "G8410A", + "G8718T", + "T8854C", + "C9238T" + ] + } + } + }, + { + "name": "ON038490.1|2012-11-26", + "node_attrs": { + "div": 0.0832, + "clade_membership": { + "value": "1I_K.5" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G466A", + "G1855A", + "A1921G", + "T1945C", + "T2698A", + "A2755G", + "C2788T", + "G3652A", + "G3835A", + "C4024T", + "T4099C", + "C5177T", + "G6880A", + "A7060G", + "C7297A", + "C8521T", + "C8830T", + "C8929T", + "A9641G" + ] + } + } + } + ] + } + ] } ] } @@ -42031,9 +34900,9 @@ ] }, { - "name": "NODE_0000297", + "name": "NODE_0000316", "node_attrs": { - "div": 0.07323904, + "div": 0.0732, "clade_membership": { "value": "1I_K" } @@ -42051,20 +34920,14 @@ "C6608T", "C8539T", "G8962A" - ], - "NS1": [ - "Y111H" ] - }, - "labels": { - "aa": "NS1: Y111H" } }, "children": [ { - "name": "NODE_0000298", + "name": "NODE_0000317", "node_attrs": { - "div": 0.0737304, + "div": 0.0737, "clade_membership": { "value": "1I_K" } @@ -42084,10 +34947,7 @@ { "name": "FJ469909.1|2003", "node_attrs": { - "div": 0.07540571, - "country": { - "value": "Singapore" - }, + "div": 0.0754, "clade_membership": { "value": "1I_K" } @@ -42113,27 +34973,14 @@ "T8720C", "C9421T", "T9518C" - ], - "NS1": [ - "N139D" - ], - "NS2A": [ - "V89I" - ], - "NS5": [ - "F383L", - "Y649H" ] - }, - "labels": { - "aa": "NS1: N139D; NS2A: V89I; NS5: F383L, Y649H" } } }, { - "name": "NODE_0000299", + "name": "NODE_0000318", "node_attrs": { - "div": 0.07659392, + "div": 0.0766, "clade_membership": { "value": "1I_K.4" } @@ -42170,19 +35017,9 @@ "G8681A", "C8914T", "G9781A" - ], - "M": [ - "M49L" - ], - "NS3": [ - "I462V" - ], - "NS5": [ - "A370T" ] }, "labels": { - "aa": "M: M49L; NS3: I462V; NS5: A370T", "lineage": "1I_K.4" } }, @@ -42190,12 +35027,12 @@ { "name": "KC762631.1|2008-02-15", "node_attrs": { - "div": 0.07955361, - "country": { - "value": "Indonesia" - }, + "div": 0.0796, "clade_membership": { "value": "1I_K.4" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -42230,30 +35067,14 @@ "T9232C", "C9883T", "A10081T" - ], - "M": [ - "I13T" - ], - "NS3": [ - "V45L", - "S347L" - ], - "NS4A": [ - "D50E" - ], - "NS5": [ - "D432E" ] - }, - "labels": { - "aa": "M: I13T; NS3: V45L, S347L; NS4A: D50E; NS5: D432E" } } }, { - "name": "NODE_0000300", + "name": "NODE_0000319", "node_attrs": { - "div": 0.07668973999999999, + "div": 0.0767, "clade_membership": { "value": "1I_K.4" } @@ -42267,9 +35088,9 @@ }, "children": [ { - "name": "NODE_0000301", + "name": "NODE_0000320", "node_attrs": { - "div": 0.07708411, + "div": 0.0771, "clade_membership": { "value": "1I_K.4" } @@ -42286,12 +35107,12 @@ { "name": "KC762621.1|2008-02-15", "node_attrs": { - "div": 0.08033406, - "country": { - "value": "Indonesia" - }, + "div": 0.0803, "clade_membership": { "value": "1I_K.4" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -42329,31 +35150,19 @@ "A7945G", "C8503T", "A10058G" - ], - "NS1": [ - "I251T" - ], - "NS4B": [ - "H17Y" - ], - "NS5": [ - "I829V" ] - }, - "labels": { - "aa": "NS1: I251T; NS4B: H17Y; NS5: I829V" } } }, { "name": "KC762647.1|2010-03-03", "node_attrs": { - "div": 0.08033055, - "country": { - "value": "Indonesia" - }, + "div": 0.0803, "clade_membership": { "value": "1I_K.4" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -42391,33 +35200,16 @@ "A9742T", "A9821C", "T9970C" - ], - "C": [ - "M109T" - ], - "NS1": [ - "K192R", - "I224V" - ], - "NS4A": [ - "R20K" - ], - "NS5": [ - "I181V", - "T750P" ] - }, - "labels": { - "aa": "C: M109T; NS1: K192R, I224V; NS4A: R20K; NS5: I181V, T750P" } } } ] }, { - "name": "NODE_0000302", + "name": "NODE_0000321", "node_attrs": { - "div": 0.07727854999999999, + "div": 0.0773, "clade_membership": { "value": "1I_K.4" } @@ -42439,12 +35231,12 @@ { "name": "KC762629.1|2008-03-15", "node_attrs": { - "div": 0.0803308, - "country": { - "value": "Indonesia" - }, + "div": 0.0803, "clade_membership": { "value": "1I_K.4" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -42481,35 +35273,19 @@ "G8056A", "T8401C", "A9072G" - ], - "E": [ - "A386T" - ], - "M": [ - "I13V", - "K118R" - ], - "NS1": [ - "D278N" - ], - "NS5": [ - "E500G" ] - }, - "labels": { - "aa": "E: A386T; M: I13V, K118R; NS1: D278N; NS5: E500G" } } }, { "name": "KC762627.1|2008-04-17", "node_attrs": { - "div": 0.07974312999999998, - "country": { - "value": "Indonesia" - }, + "div": 0.0797, "clade_membership": { "value": "1I_K.4" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -42540,20 +35316,7 @@ "T9466C", "C9479T", "T9484C" - ], - "E": [ - "V436I" - ], - "NS2A": [ - "I17M" - ], - "NS5": [ - "G382S", - "P636S" ] - }, - "labels": { - "aa": "E: V436I; NS2A: I17M; NS5: G382S, P636S" } } } @@ -42566,9 +35329,9 @@ ] }, { - "name": "NODE_0000303", + "name": "NODE_0000322", "node_attrs": { - "div": 0.07378575000000001, + "div": 0.0738, "clade_membership": { "value": "1I_K" } @@ -42586,9 +35349,9 @@ }, "children": [ { - "name": "NODE_0000304", + "name": "NODE_0000323", "node_attrs": { - "div": 0.07550205000000001, + "div": 0.0755, "clade_membership": { "value": "1I_K" } @@ -42615,23 +35378,14 @@ "G9025A", "C9127T", "T9799G" - ], - "NS4A": [ - "R76K" ] - }, - "labels": { - "aa": "NS4A: R76K" } }, "children": [ { "name": "KY057369.1|2012", "node_attrs": { - "div": 0.08275833000000002, - "country": { - "value": "Indonesia" - }, + "div": 0.0828, "clade_membership": { "value": "1I_K" } @@ -42711,48 +35465,14 @@ "C10055T", "G10090A", "C10237T" - ], - "E": [ - "S338L", - "A481V" - ], - "M": [ - "A29V", - "Q119H", - "V123M" - ], - "NS1": [ - "D127N" - ], - "NS2A": [ - "E4K", - "K82E", - "F159L", - "A210V" - ], - "NS2B": [ - "Y122H" - ], - "NS3": [ - "S559F" - ], - "NS4B": [ - "H17Y", - "V20A" - ], - "NS5": [ - "H828Y" ] - }, - "labels": { - "aa": "E: S338L, A481V; M: A29V, Q119H, V123M; NS1: D127N; NS2A: E4K, K82E, F159L, A210V; NS2B: Y122H; NS3: S559F; NS4B: H17Y, V20A; NS5: H828Y" } } }, { - "name": "NODE_0000305", + "name": "NODE_0000324", "node_attrs": { - "div": 0.07971987000000001, + "div": 0.0797, "clade_membership": { "value": "1I_K.3" } @@ -42801,21 +35521,9 @@ "T9602C", "A9790G", "G10043A" - ], - "NS1": [ - "F323Y" - ], - "NS5": [ - "V231I", - "H285C", - "P525S", - "D554E", - "L562Q", - "E824K" ] }, "labels": { - "aa": "NS1: F323Y; NS5: V231I, H285C, P525S, D554E, L562Q, E824K", "lineage": "1I_K.3" } }, @@ -42823,12 +35531,12 @@ { "name": "MN933660.1|2016-04-28", "node_attrs": { - "div": 0.08475461000000001, - "country": { - "value": "China" - }, + "div": 0.0848, "clade_membership": { "value": "1I_K.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -42884,39 +35592,14 @@ "A10186G", "A10189C", "T10192C" - ], - "E": [ - "N89I", - "L113F", - "T346A", - "Q347P" - ], - "NS2B": [ - "V106L" - ], - "NS3": [ - "G2E", - "N346S" - ], - "NS5": [ - "S21I", - "N26D", - "T27P", - "D37N", - "A60D", - "L182M", - "D671N" ] - }, - "labels": { - "aa": "E: N89I, L113F, T346A, Q347P; NS2B: V106L; NS3: G2E, N346S; NS5: S21I, N26D, T27P, D37N, A60D, L182M, D671N" } } }, { - "name": "NODE_0000306", + "name": "NODE_0000325", "node_attrs": { - "div": 0.07999569000000001, + "div": 0.08, "clade_membership": { "value": "1I_K.3" } @@ -42935,12 +35618,12 @@ { "name": "MF033230.1|2015-02", "node_attrs": { - "div": 0.08443744, - "country": { - "value": "Singapore" - }, + "div": 0.0844, "clade_membership": { "value": "1I_K.3" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -42993,36 +35676,14 @@ "A10043G", "C10187T", "C10267T" - ], - "E": [ - "T95V", - "I129T" - ], - "NS1": [ - "G95R" - ], - "NS3": [ - "N401S" - ], - "NS4A": [ - "A40V", - "I61M" - ], - "NS5": [ - "K95R", - "E647K", - "K824E" ] - }, - "labels": { - "aa": "E: T95V, I129T; NS1: G95R; NS3: N401S; NS4A: A40V, I61M; NS5: K95R, E647K, K824E" } } }, { - "name": "NODE_0000307", + "name": "NODE_0000326", "node_attrs": { - "div": 0.08255811, + "div": 0.0826, "clade_membership": { "value": "1I_K.3" } @@ -43052,25 +35713,19 @@ "T9121C", "A9607T", "T9964C" - ], - "NS5": [ - "I114V" ] - }, - "labels": { - "aa": "NS5: I114V" } }, "children": [ { "name": "MN556094.1|2019-09-01", "node_attrs": { - "div": 0.08817982, - "country": { - "value": "China" - }, + "div": 0.0882, "clade_membership": { "value": "1I_K.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -43135,47 +35790,14 @@ "C9940T", "A10177G", "A10251C" - ], - "E": [ - "S305T", - "V320I" - ], - "NS1": [ - "S17N" - ], - "NS2A": [ - "S2L", - "F40L", - "M168I", - "F178L" - ], - "NS2B": [ - "V120L" - ], - "NS3": [ - "G81E", - "G567V" - ], - "NS4B": [ - "V20A" - ], - "NS5": [ - "I135T", - "I181V", - "F497L", - "A616V", - "D893A" ] - }, - "labels": { - "aa": "E: S305T, V320I; NS1: S17N; NS2A: S2L, F40L, M168I, F178L; NS2B: V120L; NS3: G81E, G567V; NS4B: V20A; NS5: I135T, I181V, F497L, A616V, D893A" } } }, { - "name": "NODE_0000308", + "name": "NODE_0000327", "node_attrs": { - "div": 0.08345097, + "div": 0.0835, "clade_membership": { "value": "1I_K.3" } @@ -43190,25 +35812,19 @@ "C8869T", "C9883T", "C9890T" - ], - "NS2A": [ - "Y163C" ] - }, - "labels": { - "aa": "NS2A: Y163C" } }, "children": [ { "name": "OM281571.1|2018-12", "node_attrs": { - "div": 0.08682406, - "country": { - "value": "China" - }, + "div": 0.0868, "clade_membership": { "value": "1I_K.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -43250,34 +35866,19 @@ "A8773G", "A9088G", "T9211C" - ], - "E": [ - "S338L", - "V436I" - ], - "NS2A": [ - "S109C", - "M168I", - "M170T" - ], - "NS2B": [ - "K126R" ] - }, - "labels": { - "aa": "E: S338L, V436I; NS2A: S109C, M168I, M170T; NS2B: K126R" } } }, { "name": "MN933665.1|2017-07-31", "node_attrs": { - "div": 0.08838016, - "country": { - "value": "China" - }, + "div": 0.0884, "clade_membership": { "value": "1I_K.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -43331,40 +35932,7 @@ "C10187T", "A10189C", "T10192C" - ], - "E": [ - "P75L", - "T76A", - "V432T", - "G433R", - "K434M" - ], - "NS1": [ - "K9E" - ], - "NS2A": [ - "K166T", - "T167R", - "A169T", - "L172I", - "V175L", - "C181R", - "S198C", - "L199F", - "L208F" - ], - "NS3": [ - "Q110E", - "P113S", - "L495P" - ], - "NS5": [ - "V869L", - "L872F" ] - }, - "labels": { - "aa": "E: P75L, T76A, V432T, G433R, K434M; NS1: K9E; NS2A: K166T, T167R, A169T, L172I, V175L, C181R, S198C, L199F, L208F; NS3: Q110E, P113S, L495P; NS5: V869L, L872F" } } } @@ -43379,9 +35947,9 @@ ] }, { - "name": "NODE_0000309", + "name": "NODE_0000328", "node_attrs": { - "div": 0.07689533000000001, + "div": 0.0769, "clade_membership": { "value": "1I_K" } @@ -43419,27 +35987,14 @@ "A9166T", "C9895T", "C9940T" - ], - "C": [ - "N90S" - ], - "NS4B": [ - "A27T" - ], - "NS5": [ - "H127Y", - "V413I" ] - }, - "labels": { - "aa": "C: N90S; NS4B: A27T; NS5: H127Y, V413I" } }, "children": [ { - "name": "NODE_0000310", + "name": "NODE_0000329", "node_attrs": { - "div": 0.07876617000000001, + "div": 0.0788, "clade_membership": { "value": "1I_K.2" } @@ -43475,9 +36030,9 @@ }, "children": [ { - "name": "NODE_0000311", + "name": "NODE_0000330", "node_attrs": { - "div": 0.08354672, + "div": 0.0835, "clade_membership": { "value": "1I_K.2" } @@ -43533,25 +36088,19 @@ "C8596T", "T8821C", "T9163C" - ], - "NS2B": [ - "V106I" ] - }, - "labels": { - "aa": "NS2B: V106I" } }, "children": [ { "name": "ON631278.1|2021", "node_attrs": { - "div": 0.08884941, - "country": { - "value": "Reunion" - }, + "div": 0.0888, "clade_membership": { "value": "1I_K.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -43601,41 +36150,19 @@ "T9721C", "G9745A", "A10058G" - ], - "NS1": [ - "R214K", - "N293S", - "K341R" - ], - "NS2B": [ - "I44M" - ], - "NS3": [ - "E12K" - ], - "NS5": [ - "K388R", - "K551R", - "E559D", - "Y649C", - "V686I", - "I829V" ] - }, - "labels": { - "aa": "NS1: R214K, N293S, K341R; NS2B: I44M; NS3: E12K; NS5: K388R, K551R, E559D, Y649C, V686I, I829V" } } }, { "name": "MZ291446.1|2020-08", "node_attrs": { - "div": 0.08907988, - "country": { - "value": "Italy" - }, + "div": 0.0891, "clade_membership": { "value": "1I_K.2" + }, + "country": { + "value": "Italy" } }, "branch_attrs": { @@ -43695,33 +36222,16 @@ "T9904C", "A10177G", "C10187T" - ], - "E": [ - "S227L", - "T329A" - ], - "NS2A": [ - "T36I", - "Y163C" - ], - "NS2B": [ - "E63K" - ], - "NS3": [ - "E43G" ] - }, - "labels": { - "aa": "E: S227L, T329A; NS2A: T36I, Y163C; NS2B: E63K; NS3: E43G" } } } ] }, { - "name": "NODE_0000312", + "name": "NODE_0000331", "node_attrs": { - "div": 0.07888971000000002, + "div": 0.0789, "clade_membership": { "value": "1I_K.2" } @@ -43739,12 +36249,12 @@ { "name": "MF033220.1|2014-06", "node_attrs": { - "div": 0.08433232000000002, - "country": { - "value": "Singapore" - }, + "div": 0.0843, "clade_membership": { "value": "1I_K.2" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -43804,34 +36314,14 @@ "C9830T", "T9925C", "C9943T" - ], - "E": [ - "V485A" - ], - "NS1": [ - "T131A", - "I202L" - ], - "NS2A": [ - "R24K", - "S113F" - ], - "NS4A": [ - "S99N" - ], - "NS5": [ - "E647G" ] - }, - "labels": { - "aa": "E: V485A; NS1: T131A, I202L; NS2A: R24K, S113F; NS4A: S99N; NS5: E647G" } } }, { - "name": "NODE_0000313", + "name": "NODE_0000332", "node_attrs": { - "div": 0.08084687000000002, + "div": 0.0808, "clade_membership": { "value": "1I_K.2" } @@ -43857,32 +36347,19 @@ "C8575T", "A9719G", "G9736A" - ], - "NS1": [ - "D278N" - ], - "NS3": [ - "V147L", - "N482S" - ], - "NS5": [ - "I716V" ] - }, - "labels": { - "aa": "NS1: D278N; NS3: V147L, N482S; NS5: I716V" } }, "children": [ { "name": "MN018323.1|2016-05-24", "node_attrs": { - "div": 0.08806611000000002, - "country": { - "value": "China" - }, + "div": 0.0881, "clade_membership": { "value": "1I_K.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -43963,54 +36440,19 @@ "C9874T", "T10057C", "T10066C" - ], - "C": [ - "A9V", - "A77T" - ], - "E": [ - "E154K", - "A180G", - "L181V", - "P187H", - "L214V", - "C479S" - ], - "M": [ - "L138F" - ], - "NS1": [ - "G47A" - ], - "NS3": [ - "M59R", - "A616L" - ], - "NS4A": [ - "S1K", - "V2S", - "S3P", - "G4S" - ], - "NS5": [ - "E647G", - "V651A" ] - }, - "labels": { - "aa": "C: A9V, A77T; E: E154K, A180G, L181V, P187H, L214V, C479S; M: L138F; NS1: G47A; NS3: M59R, A616L; NS4A: S1K, V2S, S3P, G4S; NS5: E647G, V651A" } } }, { "name": "OM281590.1|2019-12", "node_attrs": { - "div": 0.08928479000000002, - "country": { - "value": "Cambodia" - }, + "div": 0.0893, "clade_membership": { "value": "1I_K.2" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -44095,24 +36537,7 @@ "T9778C", "T9928C", "G10090A" - ], - "NS1": [ - "M349T" - ], - "NS2A": [ - "A38T", - "F41L", - "L127F" - ], - "NS4A": [ - "I61M" - ], - "NS5": [ - "I135V" ] - }, - "labels": { - "aa": "NS1: M349T; NS2A: A38T, F41L, L127F; NS4A: I61M; NS5: I135V" } } } @@ -44123,9 +36548,9 @@ ] }, { - "name": "NODE_0000314", + "name": "NODE_0000333", "node_attrs": { - "div": 0.07698244000000001, + "div": 0.077, "clade_membership": { "value": "1I_K" } @@ -44141,10 +36566,7 @@ { "name": "MH048670.1|2014-12", "node_attrs": { - "div": 0.08103076000000001, - "country": { - "value": "Malaysia" - }, + "div": 0.081, "clade_membership": { "value": "1I_K" } @@ -44194,32 +36616,14 @@ "G8917A", "C9523A", "T9772C" - ], - "NS1": [ - "V5A" - ], - "NS2A": [ - "V114A" - ], - "NS3": [ - "R338K" - ], - "NS4B": [ - "A117G" - ], - "NS5": [ - "K166R" ] - }, - "labels": { - "aa": "NS1: V5A; NS2A: V114A; NS3: R338K; NS4B: A117G; NS5: K166R" } } }, { - "name": "NODE_0000315", + "name": "NODE_0000334", "node_attrs": { - "div": 0.07848243000000002, + "div": 0.0785, "clade_membership": { "value": "1I_K" } @@ -44242,23 +36646,14 @@ "C9334T", "A9349T", "A9487G" - ], - "NS5": [ - "I135M" ] - }, - "labels": { - "aa": "NS5: I135M" } }, "children": [ { "name": "JQ048541.1|2011-09", "node_attrs": { - "div": 0.08074545000000002, - "country": { - "value": "China" - }, + "div": 0.0807, "clade_membership": { "value": "1I_K" } @@ -44289,31 +36684,14 @@ "G9262A", "T9457C", "A9809G" - ], - "E": [ - "S338L" - ], - "NS1": [ - "N255K", - "Y256L" - ], - "NS2A": [ - "L56S" - ], - "NS5": [ - "I181V", - "S746G" ] - }, - "labels": { - "aa": "E: S338L; NS1: N255K, Y256L; NS2A: L56S; NS5: I181V, S746G" } } }, { - "name": "NODE_0000316", + "name": "NODE_0000335", "node_attrs": { - "div": 0.08109988000000001, + "div": 0.0811, "clade_membership": { "value": "1I_K.1" } @@ -44348,21 +36726,17 @@ "A9595T", "A9655G", "G10261A" - ], - "NS5": [ - "E640K" ] }, "labels": { - "aa": "NS5: E640K", "lineage": "1I_K.1" } }, "children": [ { - "name": "NODE_0000317", + "name": "NODE_0000336", "node_attrs": { - "div": 0.08339007000000001, + "div": 0.0834, "clade_membership": { "value": "1I_K.1.1" } @@ -44394,25 +36768,9 @@ "T9940C", "C9961A", "C10141T" - ], - "C": [ - "T103A" - ], - "E": [ - "N52D" - ], - "NS1": [ - "D278G" - ], - "NS2B": [ - "K127R" - ], - "NS5": [ - "G626R" ] }, "labels": { - "aa": "C: T103A; E: N52D; NS1: D278G; NS2B: K127R; NS5: G626R", "lineage": "1I_K.1.1" } }, @@ -44420,12 +36778,12 @@ { "name": "OQ678061.1|2019-12-17", "node_attrs": { - "div": 0.08887543, - "country": { - "value": "Cambodia" - }, + "div": 0.0889, "clade_membership": { "value": "1I_K.1.1" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -44487,40 +36845,14 @@ "C9754T", "T9898A", "A9905G" - ], - "E": [ - "T170M" - ], - "NS2A": [ - "M31T" - ], - "NS2B": [ - "V11I" - ], - "NS3": [ - "L85F" - ], - "NS4A": [ - "V2I" - ], - "NS4B": [ - "S180A" - ], - "NS5": [ - "R436K", - "S629L", - "I778V" ] - }, - "labels": { - "aa": "E: T170M; NS2A: M31T; NS2B: V11I; NS3: L85F; NS4A: V2I; NS4B: S180A; NS5: R436K, S629L, I778V" } } }, { - "name": "NODE_0000318", + "name": "NODE_0000337", "node_attrs": { - "div": 0.08386821000000001, + "div": 0.0839, "clade_membership": { "value": "1I_K.1.1" } @@ -44540,12 +36872,12 @@ { "name": "MN923088.1|2019-10-25", "node_attrs": { - "div": 0.08912592000000001, - "country": { - "value": "China" - }, + "div": 0.0891, "clade_membership": { "value": "1I_K.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -44602,30 +36934,14 @@ "C9509T", "A9790G", "C9871T" - ], - "E": [ - "S338L" - ], - "M": [ - "G7R", - "S28L" - ], - "NS3": [ - "L480I" - ], - "NS5": [ - "H435R" ] - }, - "labels": { - "aa": "E: S338L; M: G7R, S28L; NS3: L480I; NS5: H435R" } } }, { - "name": "NODE_0000319", + "name": "NODE_0000338", "node_attrs": { - "div": 0.08410445000000001, + "div": 0.0841, "clade_membership": { "value": "1I_K.1.1" } @@ -44642,12 +36958,12 @@ { "name": "OP984871.1|2022-08-12", "node_attrs": { - "div": 0.08894840000000001, - "country": { - "value": "Myanmar" - }, + "div": 0.0889, "clade_membership": { "value": "1I_K.1.1" + }, + "country": { + "value": "Myanmar" } }, "branch_attrs": { @@ -44699,39 +37015,14 @@ "A9417G", "T10057C", "G10120A" - ], - "C": [ - "S71T" - ], - "E": [ - "L283V", - "H317R" - ], - "NS1": [ - "M333T" - ], - "NS2A": [ - "R29K", - "M129T", - "G130D", - "F178L" - ], - "NS5": [ - "V264A", - "R361P", - "T362A", - "E615G" ] - }, - "labels": { - "aa": "C: S71T; E: L283V, H317R; NS1: M333T; NS2A: R29K, M129T, G130D, F178L; NS5: V264A, R361P, T362A, E615G" } } }, { - "name": "NODE_0000320", + "name": "NODE_0000339", "node_attrs": { - "div": 0.08410726000000002, + "div": 0.0841, "clade_membership": { "value": "1I_K.1.1" } @@ -44743,12 +37034,12 @@ { "name": "OM281593.1|2019-12", "node_attrs": { - "div": 0.08942454000000001, - "country": { - "value": "Thailand" - }, + "div": 0.0894, "clade_membership": { "value": "1I_K.1.1" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -44807,38 +37098,19 @@ "G9932A", "C10117T", "T10141C" - ], - "E": [ - "T346S" - ], - "NS2A": [ - "L161V" - ], - "NS2B": [ - "L118F" - ], - "NS3": [ - "Q172K" - ], - "NS5": [ - "K640E", - "V787I" ] - }, - "labels": { - "aa": "E: T346S; NS2A: L161V; NS2B: L118F; NS3: Q172K; NS5: K640E, V787I" } } }, { "name": "OL411495.1|2020-07", "node_attrs": { - "div": 0.08923471000000002, - "country": { - "value": "Cambodia" - }, + "div": 0.0892, "clade_membership": { "value": "1I_K.1.1" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -44899,26 +37171,7 @@ "G9613A", "C9860T", "A10056C" - ], - "C": [ - "L37M" - ], - "NS2A": [ - "A38V", - "M168V" - ], - "NS4A": [ - "E101Q", - "L115M" - ], - "NS5": [ - "L209F", - "K551R", - "H828P" ] - }, - "labels": { - "aa": "C: L37M; NS2A: A38V, M168V; NS4A: E101Q, L115M; NS5: L209F, K551R, H828P" } } } @@ -44931,9 +37184,9 @@ ] }, { - "name": "NODE_0000321", + "name": "NODE_0000340", "node_attrs": { - "div": 0.08309815000000001, + "div": 0.0831, "clade_membership": { "value": "1I_K.1.2" } @@ -44948,13 +37201,12 @@ "C938A", "C1135T", "A1261G", - "C2824T", + "A2719G", "G3592A", "T3895C", "T3956C", "T4279C", "A4846G", - "T6499C", "A6820G", "T7501C", "A8320T", @@ -44963,24 +37215,17 @@ "T9619C", "C9709T", "A10203G" - ], - "M": [ - "A29V" - ], - "NS5": [ - "N877S" ] }, "labels": { - "aa": "M: A29V; NS5: N877S", "lineage": "1I_K.1.2" } }, "children": [ { - "name": "NODE_0000322", + "name": "NODE_0000341", "node_attrs": { - "div": 0.08481389, + "div": 0.0848, "clade_membership": { "value": "1I_K.1.2" } @@ -44991,6 +37236,7 @@ "T319C", "G320A", "G436A", + "C2824T", "C2941T", "T3636C", "C3908T", @@ -45000,35 +37246,24 @@ "C5227T", "T5539C", "A5593G", + "T6499C", "C8150T", "G8706A", "C8788T", "T9895C" - ], - "C": [ - "G76R" - ], - "NS2A": [ - "I54T" - ], - "NS5": [ - "R378K" ] - }, - "labels": { - "aa": "C: G76R; NS2A: I54T; NS5: R378K" } }, "children": [ { "name": "MN018298.1|2017-08-21", "node_attrs": { - "div": 0.08649090000000001, - "country": { - "value": "China" - }, + "div": 0.0865, "clade_membership": { "value": "1I_K.1.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -45038,7 +37273,6 @@ "C914T", "T1123C", "A2588T", - "A2719G", "T3355C", "T3589C", "A4042G", @@ -45052,36 +37286,19 @@ "A7837G", "T7838C", "C9127T" - ], - "M": [ - "A127G" - ], - "NS1": [ - "I57F" - ], - "NS3": [ - "D566F", - "G567E", - "E568G" - ], - "NS5": [ - "Y89H" ] - }, - "labels": { - "aa": "M: A127G; NS1: I57F; NS3: D566F, G567E, E568G; NS5: Y89H" } } }, { "name": "MN933667.1|2018-08-09", "node_attrs": { - "div": 0.08905804, - "country": { - "value": "China" - }, + "div": 0.0891, "clade_membership": { "value": "1I_K.1.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -45112,6 +37329,7 @@ "A1970G", "A1974G", "T1978G", + "G2719A", "C2980T", "A3640G", "T3884C", @@ -45129,50 +37347,16 @@ "G8953A", "A9156C", "G9608A" - ], - "E": [ - "E84R", - "E85G", - "N89I", - "G104V", - "L113F", - "T115M", - "A117D", - "P169H", - "A180S", - "L294I", - "F337C", - "T346A", - "Q347R", - "N348K" - ], - "NS2A": [ - "S160L" - ], - "NS3": [ - "E12K" - ], - "NS4A": [ - "L55S", - "M56L" - ], - "NS5": [ - "I392T", - "N528T", - "A679T" ] - }, - "labels": { - "aa": "E: E84R, E85G, N89I, G104V, L113F, T115M, A117D, P169H, A180S, L294I, F337C, T346A, Q347R, N348K; NS2A: S160L; NS3: E12K; NS4A: L55S, M56L; NS5: I392T, N528T, A679T" } } } ] }, { - "name": "NODE_0000323", + "name": "NODE_0000342", "node_attrs": { - "div": 0.08501633000000001, + "div": 0.0832, "clade_membership": { "value": "1I_K.1.2" } @@ -45180,113 +37364,39 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1342G", - "C1479A", - "C2068A", - "T2494C", - "C4276T", - "G4489A", - "A6142G", - "A7969G", - "T8362C" - ], - "E": [ - "T182K" + "C2068A" ] - }, - "labels": { - "aa": "E: T182K" } }, "children": [ { - "name": "MN933664.1|2017-08-15", + "name": "MW946238.1|2014", "node_attrs": { - "div": 0.08777819000000002, - "country": { - "value": "China" - }, + "div": 0.0838, "clade_membership": { "value": "1I_K.1.2" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { "mutations": { "nuc": [ - "A1160C", - "G1252T", - "G1260A", - "T2230A", - "G2231C", - "A2233C", - "A2235T", - "A2236G", - "A2719G", - "G2965A", - "A3076G", - "T3088C", - "A3146T", - "G3262A", - "G3431T", - "T3597C", - "C3599T", - "A3730T", - "A4000T", - "G4524A", - "G4528T", - "T4532G", - "G4533C", - "G4534C", - "C6429T", - "A7528T", - "C7810T", - "T7849C", - "C8734T", - "G8902C", - "C9020T", - "C9080T", - "C9125T", - "A9148C", - "C9157T", - "G9248A" - ], - "E": [ - "T76P", - "G109E", - "G433R", - "K434M" - ], - "NS1": [ - "I243F", - "V338F" - ], - "NS2A": [ - "F41S", - "L42F" - ], - "NS3": [ - "G2E", - "W5A" - ], - "NS4A": [ - "T18M" - ], - "NS5": [ - "Q443H", - "L503F", - "L518F", - "E559K" + "G3958A", + "G4630T", + "T6673C", + "A7357G", + "T8470C", + "C10208T" ] - }, - "labels": { - "aa": "E: T76P, G109E, G433R, K434M; NS1: I243F, V338F; NS2A: F41S, L42F; NS3: G2E, W5A; NS4A: T18M; NS5: Q443H, L503F, L518F, E559K" } } }, { - "name": "NODE_0000324", + "name": "NODE_0000343", "node_attrs": { - "div": 0.10168163000000002, + "div": 0.085, "clade_membership": { "value": "1I_K.1.2" } @@ -45294,212 +37404,77 @@ "branch_attrs": { "mutations": { "nuc": [ - "C230T", - "G286A", - "T304C", - "A318G", - "T328C", - "G352A", - "G363A", - "C368T", - "G384A", - "C448T", - "T505C", - 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"T7517C", - "C7648T", - "G7960A", - "T8398C", - "C8434T", - "A8524G", - "T8539C", - "A8542G", - "A8674G", - "G8680A", - "G8681A", - "C8682T", - "G8706A", - "T8719C", - "G8740A", - "T8752C", - "C8797T", - "A8810G", - "C8815T", - "C8878T", - "A8962G", - "T8965C", - "T9028C", - "C9055T", - "T9166A", - "A9181C", - "A9225G", - "G9269T", - "C9281T", - "A9298G", - "T9334C", - "T9349A", - "T9391C", - "C9394T", - "T9466C", - "G9487A", - "A9491G", - "A9535G", - "T9553C", - "T9595A", - "A9604G", - "C9619T" - ], - "C": [ - "N75S", - "S90N", - "R97K" - ], - "M": [ - "V29A" - ], - "NS1": [ - "H111Y" - ], - "NS2A": [ - "H143Y", - "K218R" - ], - "NS5": [ - "A370I", - "R378K", - "I413V", - "K551R", - "A566S", - "K640E" + "A1342G", + "C1479A", + "T2494C", + "C2824T", + "G2965A", + "A3076G", + "T3088C", + "G3431T", + "C4276T", + "G4489A", + "A6142G", + "A7528T", + "A7969G", + "T8362C", + "C8734T", + "G9248A" ] - }, - "labels": { - "aa": "C: N75S, S90N, R97K; M: V29A; NS1: H111Y; NS2A: H143Y, K218R; NS5: A370I, R378K, I413V, K551R, A566S, K640E" } }, "children": [ { - "name": "MN639764.1|2018-10", + "name": "MN933664.1|2017-08-15", "node_attrs": { - "div": 0.10187656000000002, - "country": { - "value": "China" - }, + "div": 0.0878, "clade_membership": { "value": "1I_K.1.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { "mutations": { "nuc": [ - "T556C", - "C1091T", - "T5305C", - "A5307T", - "C5310T" - ], - "E": [ - "P53S" - ], - "NS3": [ - "H263L", - "A264V" + "A1160C", + "G1252T", + "G1260A", + "T2230A", + "G2231C", + "A2233C", + "A2235T", + "A2236G", + "A3146T", + "G3262A", + "T3597C", + "C3599T", + "A3730T", + "A4000T", + "G4524A", + "G4528T", + "T4532G", + "G4533C", + "G4534C", + "C6429T", + "T6499C", + "C7810T", + "T7849C", + "G8902C", + "C9020T", + "C9080T", + "C9125T", + "A9148C", + "C9157T" ] - }, - "labels": { - "aa": "E: P53S; NS3: H263L, A264V" } } }, { - "name": "MN639766.1|2018-10", + "name": "NODE_0000344", "node_attrs": { - "div": 0.10227288000000002, - "country": { - "value": "China" - }, + "div": 0.0868, "clade_membership": { "value": "1I_K.1.2" } @@ -45507,18 +37482,364 @@ "branch_attrs": { "mutations": { "nuc": [ - "G4210C", - "T4211G", - "G4792A" - ], - "NS2B": [ - "L28V" + "C3739T", + "C3749T", + "C3778T", + "G3823A", + "C3874T", + "C3895T", + "C3920T", + "C3956T", + "C4013T", + "G4060A", + "T7186C", + "C7279T", + "G7315A", + "A9596G" + ] + } + }, + "children": [ + { + "name": "NODE_0000345", + "node_attrs": { + "div": 0.0925, + "clade_membership": { + "value": "1I_K.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A3622T", + "G3676A", + "A3790C", + "T3797C", + "G3815A", + "C3908T", + "T3929A", + "T4003C", + "C4024T", + "A4036G", + "C4090T", + "T4132C", + "A4150G", + "T4186C", + "T4223C", + "G4225A", + "G4937T", + "T6398C", + "G6400A", + "T6463C", + "C6526T", + "A6550G", + "G6603A", + "T6608C", + "G6610A", + "A6676G", + "G6679A", + "C6707T", + "C6728T", + "G6820A", + "A6905G", + "A6925G", + "C6991T", + "A7009G", + "T7048C", + "C7114T", + "T7138C", + "A7162G", + "G7268A", + "A8879C", + "T8983C" + ] + } + }, + "children": [ + { + "name": "MK166998.1|2017-10-29", + "node_attrs": { + "div": 0.0939, + "clade_membership": { + "value": "1I_K.1.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G4214A", + "G4828A", + "T5557C", + "T5563C", + "C5590T", + "T5599C", + "T5632C", + "A6298G" + ] + } + } + }, + { + "name": "MK166996.1|2017-11-04", + "node_attrs": { + "div": 0.093, + "clade_membership": { + "value": "1I_K.1.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T4187C", + "G7960A", + "T8227C", + "A8316G" + ] + } + } + } ] }, - "labels": { - "aa": "NS2B: L28V" + { + "name": "NODE_0000346", + "node_attrs": { + "div": 0.0988, + "clade_membership": { + "value": "1I_K.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C230T", + "G286A", + "T304C", + "A318G", + "T328C", + "G352A", + "G363A", + "C368T", + "G384A", + "C448T", + "T505C", + "T522C", + "T556C", + "A1690G", + "C2110T", + "G2719A", + "A2722G", + "C2731T", + "C2750T", + "T2818C", + "C2827T", + "T2857C", + "T2890C", + "C2935T", + "C2938T", + "A2965G", + "T3001C", + "G3076A", + "C3079T", + "C3088T", + "T3103C", + "C3202T", + "G3211A", + "G3271A", + "A3334G", + "T3367C", + "A3421G", + "T3431G", + "G3448A", + "T3512C", + "A3535G", + "A3592G", + "C3617T", + "T3628C", + "C3664T", + "T3703C", + "A3730G", + "C3754T", + "C3892T", + "C3902T", + "T3916C", + "T3964C", + "C4012T", + "C4058T", + "T4061C", + "T4069C", + "A4128G", + "C4211T", + "A4213G", + "T4216C", + "G4792A", + "G4846A", + "C4882T", + "C4900T", + "T4906C", + "C4915T", + "G4951A", + "G4981A", + "C4993T", + "G5101A", + "A5116G", + "C5275T", + "T5305C", + "A5307T", + "C5310T", + "T6239C", + "T6499C", + "C7177T", + "C7183T", + "G7324A", + "T7331C", + "T7355C", + "A7405G", + "C7441T", + "A7483G", + "C7501T", + "T7517C", + "T7528A", + "C7648T", + "G7960A", + "T8398C", + "C8434T", + "A8524G", + "T8539C", + "A8542G", + "A8674G", + "G8680A", + "G8681A", + "C8682T", + "G8706A", + "T8719C", + "T8734C", + "G8740A", + "T8752C", + "A8810G", + "C8815T", + "C8878T", + "A8962G", + "T8965C", + "T9028C", + "T9166A" + ] + } + }, + "children": [ + { + "name": "MN639765.1|2018-10", + "node_attrs": { + "div": 0.0988, + "clade_membership": { + "value": "1I_K.1.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": {} + } + }, + { + "name": "NODE_0000347", + "node_attrs": { + "div": 0.102, + "clade_membership": { + "value": "1I_K.1.2" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1690A", + "A1693G", + "G1723A", + "G1738A", + "A1909G", + "C1996T", + "T2050C", + "C5131T", + "C8797T", + "C9055T", + "A9181C", + "A9225G", + "A9248G", + "G9269T", + "C9281T", + "A9298G", + "T9334C", + "T9349A", + "T9391C", + "C9394T", + "T9466C", + "G9487A", + "A9491G", + "A9535G", + "T9553C", + "T9595A", + "G9596A", + "A9604G", + "C9619T" + ] + } + }, + "children": [ + { + "name": "MN639764.1|2018-10", + "node_attrs": { + "div": 0.102, + "clade_membership": { + "value": "1I_K.1.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C1091T", + "A4792G" + ] + } + } + }, + { + "name": "MN639766.1|2018-10", + "node_attrs": { + "div": 0.102, + "clade_membership": { + "value": "1I_K.1.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C556T", + "G4210C", + "T4211G", + "C5305T", + "T5307A", + "T5310C" + ] + } + } + } + ] + } + ] } - } + ] } ] } diff --git a/data/community/v-gen-lab/dengue/denv2/CHANGELOG.md b/data/community/v-gen-lab/dengue/denv2/CHANGELOG.md index c773ee6d..1ae0b6ed 100644 --- a/data/community/v-gen-lab/dengue/denv2/CHANGELOG.md +++ b/data/community/v-gen-lab/dengue/denv2/CHANGELOG.md @@ -1,3 +1,7 @@ +## Unreleased + +- Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages. + ## 2024-08-31T20:44:06Z Initial release of a DENV-2 dataset for Lineage classification! diff --git a/data/community/v-gen-lab/dengue/denv2/README.md b/data/community/v-gen-lab/dengue/denv2/README.md index d0dd6bbd..4fbf3b30 100644 --- a/data/community/v-gen-lab/dengue/denv2/README.md +++ b/data/community/v-gen-lab/dengue/denv2/README.md @@ -18,9 +18,9 @@ This system is built on experience developing lineage systems for other viruses Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't necessarily always work like that—some minor lineages are very widespread, and some major lineages are geographically limited. -The source code is available at [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade). +The source code is available at [V-GEN-Lab/dengue-lineages-workflow](https://github.com/V-GEN-Lab/dengue-lineages-workflow). -For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues). +For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-workflow/issues). ## Maintainers and Contacts: diff --git a/data/community/v-gen-lab/dengue/denv2/tree.json b/data/community/v-gen-lab/dengue/denv2/tree.json index 5c59698d..416ac20b 100644 --- a/data/community/v-gen-lab/dengue/denv2/tree.json +++ b/data/community/v-gen-lab/dengue/denv2/tree.json @@ -2,7 +2,7 @@ "version": "v2", "meta": { "title": "Dengue Lineages of DENV-2", - "updated": "2024-08-16", + "updated": "2024-09-10", "build_url": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade", "data_provenance": [ { @@ -24,86 +24,8 @@ "color_by": "country" }, "genome_annotations": { - "2K": { - "end": 6825, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 6757, - "strand": "+", - "type": "CDS" - }, - "C": { - "end": 438, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 97, - "strand": "+", - "type": "CDS" - }, - "E": { - "end": 2421, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 937, - "strand": "+", - "type": "CDS" - }, - "M": { - "end": 936, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 439, - "strand": "+", - "type": "CDS" - }, - "NS1": { - "end": 3477, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 2422, - "strand": "+", - "type": "CDS" - }, - "NS2A": { - "end": 4131, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 3478, - "strand": "+", - "type": "CDS" - }, - "NS2B": { - "end": 4521, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 4132, - "strand": "+", - "type": "CDS" - }, - "NS3": { - "end": 6375, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 4522, - "strand": "+", - "type": "CDS" - }, - "NS4A": { - "end": 6756, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 6376, - "strand": "+", - "type": "CDS" - }, - "NS4B": { - "end": 7569, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 6826, - "strand": "+", - "type": "CDS" - }, - "NS5": { - "end": 10269, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", - "start": 7570, - "strand": "+", - "type": "CDS" - }, "nuc": { "end": 10723, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv2.gb", "start": 1, "strand": "+", "type": "source" @@ -136,197 +58,185 @@ { "key": "country", "demes": { - "Thailand": { - "latitude": 14.8971921, - "longitude": 100.83273 - }, - "Burkina Faso": { - "latitude": 12.5, - "longitude": -1.66667 - }, - "France": { - "latitude": 46.603354, - "longitude": 1.8883335 - }, - "Palau": { - "latitude": 7.33978, - "longitude": 134.47326 - }, - "Bhutan": { - "latitude": 27.5142, - "longitude": 90.4336 - }, "Peru": { - "latitude": -10.0, - "longitude": -75.25 + "latitude": -9.650468, + "longitude": -75.328211 }, - "Australia": { - "latitude": -24.7761085, - "longitude": 134.755 + "Nicaragua": { + "latitude": 12.6090157, + "longitude": -85.2936911 }, - "Cuba": { - "latitude": 22.0, - "longitude": -79.5 + "Nepal": { + "latitude": 28.0, + "longitude": 84.0 }, - "USA": { - "latitude": 39.7837304, - "longitude": -100.4458824 + "Brunei": { + "latitude": 4.5353, + "longitude": 114.7277 }, - "Tanzania": { - "latitude": -6.0, - "longitude": 35.0 + "Belize": { + "latitude": 16.8259793, + "longitude": -88.7600927 }, "Venezuela": { - "latitude": 8.0, - "longitude": -66.0 - }, - "Puerto Rico": { - "latitude": 18.2459121, - "longitude": -66.4164147 - }, - "Martinique": { - "latitude": 14.6415, - "longitude": -61.0242 - }, - "Ecuador": { - "latitude": -1.3397667, - "longitude": -79.3666964 + "latitude": 7.838891, + "longitude": -65.916409 }, - "Singapore": { - "latitude": 1.2904527, - "longitude": 103.852038 + "Cambodia": { + "latitude": 13.0, + "longitude": 105.0 }, "China": { - "latitude": 35.000074, - "longitude": 104.999927 - }, - "Myanmar": { - "latitude": 21.0, - "longitude": 96.0 - }, - "Nepal": { - "latitude": 28.0, - "longitude": 84.0 - }, - "Jamaica": { - "latitude": 18.16667, - "longitude": -77.25 - }, - "Brazil": { - "latitude": -10.3333332, - "longitude": -53.1999999 + "latitude": 33.394333, + "longitude": 104.689839 }, - "Haiti": { - "latitude": 19.1399952, - "longitude": -72.3570971 + "Malaysia": { + "latitude": 4.264153, + "longitude": 102.222436 }, - "India": { - "latitude": 22.3511148, - "longitude": 78.6677428 + "Singapore": { + "latitude": 1.344189, + "longitude": 103.867546 }, - "Laos": { - "latitude": 20.0171109, - "longitude": 103.378253 + "Saudi Arabia": { + "latitude": 25.0, + "longitude": 45.0 }, "Kenya": { - "latitude": 1.0, - "longitude": 38.0 - }, - "Sri Lanka": { - "latitude": 7.75, - "longitude": 80.75 + "latitude": 0.0236, + "longitude": 37.9062 }, - "Switzerland": { - "latitude": 47.00016, - "longitude": 8.01427 + "India": { + "latitude": 21.077353, + "longitude": 78.723951 }, - "Bangladesh": { - "latitude": 24.4768783, - "longitude": 90.2932426 + "Thailand": { + "latitude": 14.8971921, + "longitude": 100.83273 }, "Colombia": { "latitude": 2.893108, "longitude": -73.7845142 }, - "Malaysia": { - "latitude": 2.3923759, - "longitude": 112.8471939 + "Ecuador": { + "latitude": -1.0541, + "longitude": -78.1489 }, - "Indonesia": { - "latitude": -5.0, - "longitude": 120.0 + "Sri Lanka": { + "latitude": 7.8731, + "longitude": 80.7718 }, - "Spain": { - "latitude": 40.0028028, - "longitude": -4.0031039 + "Burkina Faso": { + "latitude": 12.78998, + "longitude": -1.683734 }, - "Vietnam": { - "latitude": 16.16667, - "longitude": 107.83333 + "Myanmar": { + "latitude": 20.600856, + "longitude": 96.287616 }, - "Brunei": { - "latitude": 4.5, - "longitude": 114.66667 + "Haiti": { + "latitude": 19.1399952, + "longitude": -72.3570972 }, - "Saudi Arabia": { - "latitude": 25.0, - "longitude": 45.0 + "Australia": { + "latitude": -24.7761085, + "longitude": 134.755 }, - "Cambodia": { - "latitude": 13.0, - "longitude": 105.0 + "Senegal": { + "latitude": 14.5, + "longitude": -14.25 }, - "Nicaragua": { - "latitude": 13.0, - "longitude": -85.0 + "Paraguay": { + "latitude": -23.3165935, + "longitude": -58.1693445 }, - "Taiwan": { - "latitude": 23.6978, - "longitude": 120.9605 + "Spain": { + "latitude": 40.4637, + "longitude": -3.7492 }, - "Philippines": { - "latitude": 12.8797, - "longitude": 121.774 + "Bangladesh": { + "latitude": 24.506442, + "longitude": 90.041454 + }, + "Taiwan": { + "latitude": 23.8169, + "longitude": 121.031365 }, "Papua New Guinea": { - "latitude": -6.0, - "longitude": 147.0 + "latitude": -5.6816069, + "longitude": 144.2489081 + }, + "Philippines": { + "latitude": 11.383086, + "longitude": 123.521862 }, "Cameroon": { - "latitude": 6.0, - "longitude": 12.5 + "latitude": 4.6125522, + "longitude": 13.1535811 + }, + "Palau": { + "latitude": 5.3783537, + "longitude": 132.9102573 + }, + "France": { + "latitude": 46.2276, + "longitude": 2.2137 }, "Nigeria": { "latitude": 10.0, "longitude": 8.0 }, - "Reunion": { - "latitude": -21.1151, - "longitude": 55.5364 + "Laos": { + "latitude": 20.0171109, + "longitude": 103.378253 }, - "French Guiana": { - "latitude": 4.93333, - "longitude": -52.33333 + "Switzerland": { + "latitude": 46.8182, + "longitude": 8.2275 }, - "Uganda": { - "latitude": 1.5333554, - "longitude": 32.2166578 + "Puerto Rico": { + "latitude": 18.2247706, + "longitude": -66.4858295 }, - "Dominican Republic": { - "latitude": 18.50012, - "longitude": -69.98857 + "Pakistan": { + "latitude": 30.0, + "longitude": 70.0 + }, + "Bhutan": { + "latitude": 27.549511, + "longitude": 90.5119273 + }, + "Cuba": { + "latitude": 23.0131338, + "longitude": -80.8328748 + }, + "Jamaica": { + "latitude": 18.1096, + "longitude": -77.2975 + }, + "Tanzania": { + "latitude": -6.5247123, + "longitude": 35.7878438 + }, + "Indonesia": { + "latitude": -0.897599, + "longitude": 114.181602 }, "Mexico": { "latitude": 19.4325301, "longitude": -99.1332101 }, - "Pakistan": { - "latitude": 30.0, - "longitude": 70.0 + "Brazil": { + "latitude": -10.3333332, + "longitude": -53.1999999 }, - "Senegal": { - "latitude": 14.5, - "longitude": -14.25 + "USA": { + "latitude": 38.916963, + "longitude": -98.891372 + }, + "Dominican Republic": { + "latitude": 19.0974031, + "longitude": -70.3028026 } } } @@ -349,8 +259,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "G44A", - "C54T", "G120A", "A122G", "C126A", @@ -1602,7 +1510,6 @@ "T7411A", "T7416A", "C7419G", - "G7422A", "C7425T", "C7428A", "C7431A", @@ -2073,378 +1980,14 @@ "C10256A", "T10263A", "G10272A" - ], - "2K": [ - "V17L" - ], - "C": [ - "K9R", - "N10K", - "T11M", - "R41K", - "A63I", - "N79K", - "V80I", - "R82K", - "R85K", - "R99K", - "R100K", - "S101T", - "M104I", - "I105L", - "V112M" - ], - "E": [ - "M6I", - "S7A", - "N83I", - "V91I", - "M96I", - "R120T", - "V129I", - "I162V", - "A173T", - 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A19K, T20I, Q21E, Q22*, P23H, S25T, R33H, F47L, V48I, V61M, I96M, F112L, V115I, A116G, A137T, L155I, D156E, L190M, L196I, R211K, T244I, N245S, T246G; NS5: N4M, R16K, A19G, K22R, S23R, Q34K, D51N, M70L, T72K, V78I, I135T, V156I, L167I, N173G, N174X, T176N, A196K, Y201F, A204T, R246K, Y247H, P254Q, I265M, I271K, D275E, Q286E, E289K, T290K, S291T, V321M, R326K, V335I, I376M, E379K, K387R, T390M, R401N, L409M, I412V, D415E, R423K, S429E, K437R, N440K, D521E, V522I, S523R, A529I, L544E, V553I, N555E, H556Q, E558K, R586K, V628L, S631N, Q633X, H634K, T638Q, V643M, Q644H, N645T, A648K, R649K, V650K, S656R, L670V, S676K, I687V, P696A, R698K, L716I, V723K, S747A, R749K, S757A, K800N, T811E, P829C, E831K, Q864K, A865I, N868K, N876K, R890K, R891K, E894K, E895K, A896E" } }, "children": [ { "name": "KX274130.1|2015", "node_attrs": { - "div": 0.123481, - "country": { - "value": "Australia" - }, + "div": 0.123, "clade_membership": { "value": "Outgroup" } @@ -3134,7 +2677,7 @@ "A7335G", "T7356C", "A7360G", - "A7422C", + "G7422C", "T7449C", "A7452T", "T7513C", @@ -3382,286 +2925,9 @@ "A10253C", "T10262C", "A10271G" - ], - "C": [ - "K10Q", - "M11L", - "I63M", - "K67T", - "T71A", - "K76R", - "K86R", - "T101S", - "G103A", - "I104T", - "I106L", - "M107L", - "I109V", - "M112I" - ], - "E": [ - "I4V", - "I46T", - "Q52L", - "I83P", - "K93R", - "I96L", - "N124Y", - "I139V", - "V140A", - "I141V", - "A150S", - "K160Q", - "E161D", - "E174A", - "K176E", - "T180S", - "T182S", - "N203D", - "A224S", - "I232V", - "T262S", - "I365T", - "M379L", - "K430N", - "M443V", - "M477I", - "I481M", - "I484L", - "I492V" - ], - "M": [ - "S15A", - "M31V", - "I49V", - "N59S", - "T82S", - "T83S", - "V96A", - "I135V", - "I139A", - "M140I", - "K142M", - "T143A", - "K147N", - "V152A", - "M156V" - ], - "NS1": [ - "N10T", - "I27V", - "I54V", - "E83D", - "M97L", - "E99Q", - "K101R", - "A121S", - "T126S", - "I128T", - "N145D", - "I162L", - "T164S", - "K170R", - "I177T", - "K191E", - "D208G", - "R209S", - "I218L", - "K224T", - "K292N", - "I318M", - "Y323F" - ], - "NS2A": [ - "M22V", - "I35M", - "I36T", - "V41L", - "I42L", - "I44V", - "M48V", - "V58L", - "A62S", - "T65A", - "K82R", - "V89L", - "G90A", - "M102L", - "T104A", - "S114C", - "N115D", - "I116V", - "E118G", - "*127C", - "I131L", - "V133L", - "M137T", - "K139E", - "M140L", - "K142R", - "M149L", - "M150L", - "A151S", - "M152L", - "I153T", - "I159T", - "I161M", - "*162W", - "K163G", - "R168T", - "V174L", - "I177M", - "K186R", - "I192V", - "T197S", - "K199Y", - "L208F", - "T214A" - ], - "NS2B": [ - "M8V", - "K23R", - "T29A", - "V40L", - "A56S", - "K62N", - "E64D", - "K75N", - "T77A", - "I78V", - "N88D", - "K93N", - "V105A", - "I109M", - "I116A", - "L123F", - "K127R" - ], - "NS3": [ - "R9S", - "I13T", - "A56S", - "Y60C", - "I65L", - "K84R", - "E86D", - "K90T", - "N119D", - "M147I", - "I156M", - "E173D", - "K175I", - "K186R", - "K355E", - "Q451P", - "R507A", - "E510G", - "M516T", - "A529S", - "N555Y", - "N556S", - "M567V", - "M577L", - "K592R", 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"labels": { - "aa": "C: K10Q, M11L, I63M, K67T, T71A, K76R, K86R, T101S, G103A, I104T, I106L, M107L, I109V, M112I; E: I4V, I46T, Q52L, I83P, K93R, I96L, N124Y, I139V, V140A, I141V, A150S, K160Q, E161D, E174A, K176E, T180S, T182S, N203D, A224S, I232V, T262S, I365T, M379L, K430N, M443V, M477I, I481M, I484L, I492V; M: S15A, M31V, I49V, N59S, T82S, T83S, V96A, I135V, I139A, M140I, K142M, T143A, K147N, V152A, M156V; NS1: N10T, I27V, I54V, E83D, M97L, E99Q, K101R, A121S, T126S, I128T, N145D, I162L, T164S, K170R, I177T, K191E, D208G, R209S, I218L, K224T, K292N, I318M, Y323F; NS2A: M22V, I35M, I36T, V41L, I42L, I44V, M48V, V58L, A62S, T65A, K82R, V89L, G90A, M102L, T104A, S114C, N115D, I116V, E118G, *127C, I131L, V133L, M137T, K139E, M140L, K142R, M149L, M150L, A151S, M152L, I153T, I159T, I161M, *162W, K163G, R168T, V174L, I177M, K186R, I192V, T197S, K199Y, L208F, T214A; NS2B: M8V, K23R, T29A, V40L, A56S, K62N, E64D, K75N, T77A, I78V, N88D, K93N, V105A, I109M, I116A, L123F, K127R; NS3: R9S, 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- "C": [ - "K10N", - "M11T", - "K41R", - "I63A", - "K79N", - "I80V", - "K82R", - "K85R", - "K99R", - "K100R", - "M112V" - ], - "E": [ - "A7S", - "I91V", - "I96M", - "I129V", - "T173A", - "K176T", - "T273S", - "E293Q", - "E329D", - "I358V", - "K363S", - "M379I", - "M389L", - "K430T", - "M443I", - "N445G", - "M475L", - "M477V", - "I481L", - "I492M" - ], - "M": [ - "I24L", - "N29D", - "E47D", - "Y55F", - "T70S", - "N125T", - "Y133F", - "M140L", - "K142Y", - "K147T", - "N148H", - "M156I" - ], - "NS1": [ - "I27T", - "A40S", - "A44S", - "K47Q", - "I66L", - "T80S", - "V86L", - "E99A", - "A103S", - "K112R", - "S117T", - "V124L", - "I128L", - "L178F", - "K191N", - "I194V", - "K205R", - "R209T", - "K224Y", - "G248A", - "T265A", - "Y279F", - "I286V", - "E290D", - "K292G", - "I318L", - "K324R" - ], - "NS2A": [ - "I15M", - "M23L", - "K24R", - "S25T", - "I27V", - "I29T", - "T32A", - "G34L", - "I35L", - "I36V", - "I37A", - "T39S", - "I42T", - "Y50F", - "T80A", - "I83V", - "V89A", - "M92L", - "I93L", 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"I155L", - "M190L", - "I196L", - "I244T", - "G246A" - ], - "NS5": [ - "M4T", - "K16R", - "G19A", - "R23S", - "K34Q", - "N51D", - "K72T", - "I78V", - "I156V", - "I167L", - "X174S", - "N176T", - "I180V", - "K193R", - "K196A", - "T204A", - "K246R", - "Q254P", - "M265I", - "K271T", - "E275D", - "E286Q", - "K289E", - "K290T", - "T291S", - "M321V", - "K326R", - "M376I", - "K379E", - "M390T", - "M409L", - "E415D", - "K423R", - "K440N", - "E521D", - "R523S", - "I529A", - "E544S", - "E555D", - "K558E", - "K586R", - "N631S", - "X633Q", - "K634H", - "I637T", - "M643V", - "T645A", - "K648A", - "K649R", - "K650E", - "R656T", - "V670L", - "K676R", - "A696P", - "I716L", - "K723T", - "A747S", - "K749R", - "A757S", - "N800S", - "E811A", - "C829P", - "K831E", - "K864Q", - "I865T", - "K868N", - "K890R", - "K891R", - "K894E", - "K895E", - "E896A" ] - }, - "labels": { - "aa": "C: K10N, M11T, K41R, I63A, K79N, I80V, K82R, K85R, K99R, K100R, M112V; E: A7S, I91V, I96M, I129V, T173A, K176T, T273S, E293Q, E329D, I358V, K363S, M379I, M389L, K430T, M443I, N445G, M475L, M477V, I481L, I492M; M: I24L, N29D, E47D, Y55F, T70S, N125T, Y133F, M140L, K142Y, K147T, N148H, M156I; NS1: I27T, A40S, A44S, K47Q, I66L, T80S, V86L, E99A, A103S, K112R, S117T, V124L, I128L, L178F, K191N, I194V, K205R, R209T, K224Y, G248A, T265A, Y279F, I286V, E290D, K292G, I318L, K324R; NS2A: I15M, M23L, K24R, S25T, I27V, I29T, T32A, G34L, I35L, I36V, I37A, T39S, I42T, Y50F, T80A, I83V, V89A, M92L, I93L, I111L, A112S, I123L, *127L, M137V, K139N, M149I, I153L, I159M, I161L, *162Q, K163N, R168S, T173A, I177V, A178S, F181L, T184S, K186Q, V194L, Y207F, A212S, K213R, K215N, I217T; NS2B: M8I, I59V, K62E, E64Q, I74L, K75S, K93Q, I109L, Y110F, M112V, A113S, V120A; NS3: R9S, I13V, E20D, Y60H, M115L, R122T, A131S, M147V, I156T, K157R, R171S, E172V, E174D, K175N, A301S, K322R, T373A, T392S, I395V, N399T, Q451H, R507S, M516V, E535D, N555I, E565D, M567I, K594R, Q605L; NS4A: I2L, Y16F, E36A, K42N, I45L, K76R, M83L, G86C; NS4B: Y5F, N17S, K19T, I20T, E21Q, *22Q, H23P, H33R, L47F, M61V, M96I, I115V, G116A, T137A, I155L, M190L, I196L, I244T, G246A; NS5: M4T, K16R, G19A, R23S, K34Q, N51D, K72T, I78V, I156V, I167L, X174S, N176T, I180V, K193R, K196A, T204A, K246R, Q254P, M265I, K271T, E275D, E286Q, K289E, K290T, T291S, M321V, K326R, M376I, K379E, M390T, M409L, E415D, K423R, K440N, E521D, R523S, I529A, E544S, E555D, K558E, K586R, N631S, X633Q, K634H, I637T, M643V, T645A, K648A, K649R, K650E, R656T, V670L, K676R, A696P, I716L, K723T, A747S, K749R, A757S, N800S, E811A, C829P, K831E, K864Q, I865T, K868N, K890R, K891R, K894E, K895E, E896A" } }, "children": [ { "name": "NODE_0000002", "node_attrs": { - "div": 0.1843554, + "div": 0.184, "clade_membership": { "value": "2VI" } @@ -4981,6 +3971,7 @@ "A1644G", "A1695G", "A1710C", + "C1746T", "C1764T", "G1770A", "A1809G", @@ -5252,6 +4243,7 @@ "A7254G", "A7338G", "C7344T", + "C7353T", "C7362A", "T7435C", "A7482C", @@ -5380,94 +4372,9 @@ "A10195G", "C10224A", "A10251G" - ], - "C": [ - "V26I", - "N79S", - "I104L", - "L108I" - ], - "E": [ - "Y59F", - "I83V", - "K122L", - "T236M", - "I379V", - "I432V" - ], - "M": [ - "R16K", - "H119Q", - "I135L" - ], - "NS1": [ - "E37D", - "R105K", - "I123V", - "H129Q", - "T146S", - "I177M", - "I212M", - "D278E" - ], - "NS2A": [ - "I33L", - "R51K", - "T63A", - "I108V", - "I120V", - "L127I", - "N139S", - "N163H", - "V174A", - "T214P" - ], - "NS2B": [ - "D58E", - "A126T" - ], - "NS3": [ - "A160T", - "K213R", - "R248K", - "D353N", - "K381R", - "K568R", - "I581V" - ], - "NS4A": [ - "N5S", - "S59G", - "I78V" - ], - "NS4B": [ - "S17G" - ], - "NS5": [ - "L70M", - "T72A", - "K139R", - "S269C", - "L274M", - "K375R", - "K383N", - "T390K", - "M393I", - "E397A", - "T400X", - "D436E", - "K524R", - "E560K", - "T637S", - "N730S", - "E820D", - "E835D", - "S872A", - "K876E" ] }, "labels": { - "aa": "C: V26I, N79S, I104L, L108I; E: Y59F, I83V, K122L, T236M, I379V, I432V; M: R16K, H119Q, I135L; NS1: E37D, R105K, I123V, H129Q, T146S, I177M, I212M, D278E; NS2A: I33L, R51K, T63A, I108V, I120V, L127I, N139S, N163H, V174A, T214P; NS2B: D58E, A126T; NS3: A160T, K213R, R248K, D353N, K381R, K568R, I581V; NS4A: N5S, S59G, I78V; NS4B: S17G; NS5: L70M, T72A, K139R, S269C, L274M, K375R, K383N, T390K, M393I, E397A, T400X, D436E, K524R, E560K, T637S, N730S, E820D, E835D, S872A, K876E", "lineage": "2VI" } }, @@ -5475,7 +4382,7 @@ { "name": "NODE_0000003", "node_attrs": { - "div": 0.2378428, + "div": 0.238, "clade_membership": { "value": "2VI" } @@ -5551,7 +4458,7 @@ "T1693C", "A1698G", "C1728T", - "C1746A", + "T1746A", "C1833T", "A1875T", "A1878G", @@ -5831,8 +4738,9 @@ "A7311T", "G7314A", "C7350T", - "C7353A", + "T7353A", "T7392C", + "G7422A", "G7437A", "A7446G", "T7449C", @@ -5975,86 +4883,19 @@ "A10230G", "G10248A", "C10263T" - ], - "C": [ - "R41K", - "A102T" - ], - "E": [ - "I113V", - "D329E", - "S331A", - "A446V", - "L481I" - ], - "M": [ - "S70A", - "R151K", - "V152I" - ], - "NS1": [ - "S80Y", - "T109I", - "T117S", - "R172K", - "M177T", - "M275L", - "F279L", - "E326D", - "K339R" - ], - "NS2A": [ - "V27M", - "M48L", - "I116M", - "A146S", - "M159I", - "T170A", - "V177A", - "Q186H" - ], - "NS3": [ - "K15R", - "K73R", - "K355E" - ], - "NS4A": [ - "M10V" - ], - "NS4B": [ - "K11R", - "I18G", - "P23L", - "T25A" - ], - "NS5": [ - "I5T", - "R98K", - "M234T", - "I240L", - "T271V", - "F399X", - "X400C", - "R676K", - "T679V", - "S800T", - "P829F" ] - }, - "labels": { - "aa": "C: R41K, A102T; E: I113V, D329E, S331A, A446V, L481I; M: S70A, R151K, V152I; NS1: S80Y, T109I, T117S, R172K, M177T, M275L, F279L, E326D, K339R; NS2A: V27M, M48L, I116M, A146S, M159I, T170A, V177A, Q186H; NS3: K15R, K73R, K355E; NS4A: M10V; NS4B: K11R, I18G, P23L, T25A; NS5: I5T, R98K, M234T, I240L, T271V, F399X, X400C, R676K, T679V, S800T, P829F" } }, "children": [ { "name": "EF105379.1|1970", "node_attrs": { - "div": 0.2607199, - "country": { - "value": "Malaysia" - }, + "div": 0.261, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Malaysia" } }, "branch_attrs": { @@ -6272,50 +5113,19 @@ "C10179T", "G10197A", "C10236T" - ], - "2K": [ - "V11I" - ], - "E": [ - "N203K" - ], - "NS1": [ - "R112K", - "K272R" - ], - "NS2A": [ - "I159T" - ], - "NS3": [ - "G14E", - "K112I", - "V172M", - "K418R" - ], - "NS4A": [ - "A36T" - ], - "NS5": [ - "Y90F", - "I276V", - "M552K", - "D555N" ] - }, - "labels": { - "aa": "2K: V11I; E: N203K; NS1: R112K, K272R; NS2A: I159T; NS3: G14E, K112I, V172M, K418R; NS4A: A36T; NS5: Y90F, I276V, M552K, D555N" } } }, { "name": "FJ467493.1|2008", "node_attrs": { - "div": 0.2635096, - "country": { - "value": "Malaysia" - }, + "div": 0.264, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Malaysia" } }, "branch_attrs": { @@ -6590,43 +5400,7 @@ "G10059T", "A10098G", "C10208T" - ], - "C": [ - "S79N" - ], - "E": [ - "K36R", - "I139V" - ], - "M": [ - "I156V" - ], - "NS1": [ - "K69R", - "T72A", - "I109V", - "V123I" - ], - "NS2A": [ - "A80T", - "F207L" - ], - "NS3": [ - "T122A" - ], - "NS4A": [ - "I89V" - ], - "NS5": [ - "A19T", - "D275E", - "R437K", - "R524K", - "T880I" ] - }, - "labels": { - "aa": "C: S79N; E: K36R, I139V; M: I156V; NS1: K69R, T72A, I109V, V123I; NS2A: A80T, F207L; NS3: T122A; NS4A: I89V; NS5: A19T, D275E, R437K, R524K, T880I" } } } @@ -6635,7 +5409,7 @@ { "name": "NODE_0000004", "node_attrs": { - "div": 0.2424692, + "div": 0.242, "clade_membership": { "value": "2VI" } @@ -6730,7 +5504,6 @@ "A1707G", "T1719C", "C1737A", - "C1746T", "T1765A", "C1773T", "C1775T", @@ -7034,13 +5807,11 @@ "A7311G", "A7320G", "A7332G", - "C7353T", "T7383C", "G7395A", "T7398C", "T7405C", "T7419A", - "A7422G", "C7485T", "C7512T", "T7530C", @@ -7195,96 +5966,14 @@ "A10242T", "G10255T", "G10272A" - ], - "C": [ - "L104F", - "I108V" - ], - "E": [ - "K93R", - "N124K", - "T171A", - "G177D", - "K247R", - "L277I", - "T280M", - "G330D", - "L425I", - "I462V" - ], - "M": [ - "H17N", - "D29N", - "M31I", - "I49V", - "T82S", - "I139V", - "V152A" - ], - "NS1": [ - "D92E", - "K101R", - "F178V", - "N191D" - ], - "NS2A": [ - "F18L", - "V58I", - "K82R", - "A89V", - "M102L", - "T104A", - "E118G", - "M136I", - "I149V", - "A158V", - "S168G" - ], - "NS3": [ - "V13M", - "M59V", - "V273I", - "M333V", - "S392T", - "V395T", - "I442V", - "R538K", - "R561K" - ], - "NS4A": [ - "T33S", - "A36M" - ], - "NS4B": [ - "T25I", - "I48V", - "K241R" - ], - "NS5": [ - "N383G", - "K388R", - "E444D", - "E526A", - "K560R", - "Q633L", - "S637P", - "A648V", - "T656A", - "N701S", - "T723K", - "R891S", - "A896S" ] - }, - "labels": { - "aa": "C: L104F, I108V; E: K93R, N124K, T171A, G177D, K247R, L277I, T280M, G330D, L425I, I462V; M: H17N, D29N, M31I, I49V, T82S, I139V, V152A; NS1: D92E, K101R, F178V, N191D; NS2A: F18L, V58I, K82R, A89V, M102L, T104A, E118G, M136I, I149V, A158V, S168G; NS3: V13M, M59V, V273I, M333V, S392T, V395T, I442V, R538K, R561K; NS4A: T33S, A36M; NS4B: T25I, I48V, K241R; NS5: N383G, K388R, E444D, E526A, K560R, Q633L, S637P, A648V, T656A, N701S, T723K, R891S, A896S" } }, "children": [ { "name": "NODE_0000005", "node_attrs": { - "div": 0.2483912, + "div": 0.248, "clade_membership": { "value": "2VI" } @@ -7356,38 +6045,19 @@ "C9906A", "C9939T", "A10098G" - ], - "E": [ - "N203S", - "S274L" - ], - "NS1": [ - "V178I", - "K341R" - ], - "NS4B": [ - "T20M" - ], - "NS5": [ - "R437K", - "I641T", - "S730N" ] - }, - "labels": { - "aa": "E: N203S, S274L; NS1: V178I, K341R; NS4B: T20M; NS5: R437K, I641T, S730N" } }, "children": [ { "name": "EF105386.1|1980", "node_attrs": { - "div": 0.2605615, - "country": { - "value": "Burkina Faso" - }, + "div": 0.261, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Burkina Faso" } }, "branch_attrs": { @@ -7512,46 +6182,19 @@ "T9492A", "C9715T", "C10084T" - ], - "E": [ - "S363N", - "T454A" - ], - "NS1": [ - "I162F" - ], - "NS2A": [ - "A195V", - "L196F" - ], - "NS3": [ - "G14E", - "F31L", - "T395I", - "N556S" - ], - "NS4B": [ - "L196I" - ], - "NS5": [ - "E379K", - "R388K" ] - }, - "labels": { - "aa": "E: S363N, T454A; NS1: I162F; NS2A: A195V, L196F; NS3: G14E, F31L, T395I, N556S; NS4B: L196I; NS5: E379K, R388K" } } }, { "name": "JF260983.1|2009", "node_attrs": { - "div": 0.26958160000000003, - "country": { - "value": "Spain" - }, + "div": 0.27, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Spain" } }, "branch_attrs": { @@ -7758,46 +6401,7 @@ "C10208T", "G10239A", "G10254A" - ], - "C": [ - "K67E" - ], - "E": [ - "A171S", - "A173T" - ], - "M": [ - "S22G" - ], - "NS2A": [ - "V137M", - "N215S", - "T217I" - ], - "NS2B": [ - "V76I" - ], - "NS3": [ - "I65L", - "E91D", - "K142R", - "V333M", - "M577I" - ], - "NS4B": [ - "I18F" - ], - "NS5": [ - "V180I", - "A196T", - "T290A", - "X400C", - "K570R", - "T880M" ] - }, - "labels": { - "aa": "C: K67E; E: A171S, A173T; M: S22G; NS2A: V137M, N215S, T217I; NS2B: V76I; NS3: I65L, E91D, K142R, V333M, M577I; NS4B: I18F; NS5: V180I, A196T, T290A, X400C, K570R, T880M" } } } @@ -7806,7 +6410,7 @@ { "name": "NODE_0000006", "node_attrs": { - "div": 0.24568684999999998, + "div": 0.246, "clade_membership": { "value": "2VI" } @@ -7837,29 +6441,19 @@ "A9233G", "A9315G", "A10151G" - ], - "E": [ - "T359I" - ], - "NS5": [ - "D555G", - "K861R" ] - }, - "labels": { - "aa": "E: T359I; NS5: D555G, K861R" } }, "children": [ { "name": "EF105385.1|1974", "node_attrs": { - "div": 0.26311235, - "country": { - "value": "Senegal" - }, + "div": 0.263, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Senegal" } }, "branch_attrs": { @@ -8035,54 +6629,19 @@ "C10116T", "C10117T", "A10161G" - ], - "C": [ - "T11S" - ], - "E": [ - "N153K", - "D177G", - "F193S", - "N230S", - "D329E", - "E360G" - ], - "NS1": [ - "L13M", - "K69R", - "N145S", - "M177T", - "Y224H", - "Y256H" - ], - "NS2A": [ - "K166R" - ], - "NS4B": [ - "I18T", - "I25T" - ], - "NS5": [ - "A196T", - "A250V", - "M530I", - "A645T" ] - }, - "labels": { - "aa": "C: T11S; E: N153K, D177G, F193S, N230S, D329E, E360G; NS1: L13M, K69R, N145S, M177T, Y224H, Y256H; NS2A: K166R; NS4B: I18T, I25T; NS5: A196T, A250V, M530I, A645T" } } }, { "name": "EF105388.1|1966", "node_attrs": { - "div": 0.26152325, - "country": { - "value": "Nigeria" - }, + "div": 0.262, "clade_membership": { "value": "2VI" + }, + "country": { + "value": "Nigeria" } }, "branch_attrs": { @@ -8241,49 +6800,7 @@ "G10089A", "T10126C", "C10212T" - ], - "E": [ - "V83A", - "N194D", - "G228E", - "M280V", - "I320V", - "F448L" - ], - "M": [ - "V49I" - ], - "NS1": [ - "Y261H" - ], - "NS2A": [ - "A174V", - "A195V", - "T197I", - "T217I" - ], - "NS3": [ - "L115F", - "K170T", - "I365T" - ], - "NS4A": [ - "S5N" - ], - "NS4B": [ - "P23S", - "V48I" - ], - "NS5": [ - "T4N", - "T135I", - "K301R", - "R524K", - "A656S" ] - }, - "labels": { - "aa": "E: V83A, N194D, G228E, M280V, I320V, F448L; M: V49I; NS1: Y261H; NS2A: A174V, A195V, T197I, T217I; NS3: L115F, K170T, I365T; NS4A: S5N; NS4B: P23S, V48I; NS5: T4N, T135I, K301R, R524K, A656S" } } } @@ -8296,7 +6813,7 @@ { "name": "NODE_0000007", "node_attrs": { - "div": 0.2023241, + "div": 0.202, "clade_membership": { "value": "unassigned" } @@ -8960,118 +7477,14 @@ "C10212T", "C10221A", "G10239A" - ], - "2K": [ - "L17V" - ], - "C": [ - "I104M", - "L105I" - ], - "E": [ - "I83N", - "I181V", - "K345R", - "I365V", - "T478S" - ], - "M": [ - "H17Q", - "S81T" - ], - "NS1": [ - "I123M", - "T141A", - "I162V", - "I177V", - "V188I", - "R205A", - "Y224H", - "R227K", - "L247F", - "Y261H" - ], - "NS2A": [ - "I38V", - "I57M", - "E67D", - "M68I", - "N115S", - "I131M", - "M152I", - "I155V", - "M159V", - "T189A", - "N215S", - "T217K" - ], - "NS2B": [ - "K55R", - "V76I", - "A126V" - ], - "NS3": [ - "R28K", - "F31L", - "S164A", - "V172I", - "I351V", - "R366K", - "K549R", - "S552A", - "M577V", - "T600I" - ], - "NS4A": [ - "T21A", - "S59T", - "G93I" - ], - "NS4B": [ - "T19A", - "T25S", - "E156D", - "I201M", - "K211R", - "A246T" - ], - "NS5": [ - "T4N", - "R22K", - "G173N", - "S174N", - "F201Y", - "I335V", - "R387K", - "N401K", - "V412I", - "E429S", - "R437K", - "I522V", - "S544L", - "D555N", - "Q556H", - "L628I", - "T637A", - "Q638S", - "H644Q", - "A645D", - "E650V", - "T656S", - "K698R", - "A811T", - "K876N" ] - }, - "labels": { - "aa": "2K: L17V; C: I104M, L105I; E: I83N, I181V, K345R, I365V, T478S; M: H17Q, S81T; NS1: I123M, T141A, I162V, I177V, V188I, R205A, Y224H, R227K, L247F, Y261H; NS2A: I38V, I57M, E67D, M68I, N115S, I131M, M152I, I155V, M159V, T189A, N215S, T217K; NS2B: K55R, V76I, A126V; NS3: R28K, F31L, S164A, V172I, I351V, R366K, K549R, S552A, M577V, T600I; NS4A: T21A, S59T, G93I; NS4B: T19A, T25S, E156D, I201M, K211R, A246T; NS5: T4N, R22K, G173N, S174N, F201Y, I335V, R387K, N401K, V412I, E429S, R437K, I522V, S544L, D555N, Q556H, L628I, T637A, Q638S, H644Q, A645D, E650V, T656S, K698R, A811T, K876N" } }, "children": [ { "name": "NODE_0000008", "node_attrs": { - "div": 0.2325936, + "div": 0.233, "clade_membership": { "value": "2I" } @@ -9282,6 +7695,7 @@ "C7287T", "C7393T", "C7410T", + "G7422A", "A7426G", "T7491A", "T7497C", @@ -9387,52 +7801,9 @@ "T10188C", "C10263T", "C10264T" - ], - "2K": [ - "V11I" - ], - "E": [ - "E71D", - "S81T", - "V129I", - "I139V", - "N203D", - "V308I", - "N390D" - ], - "M": [ - "E28K", - "M31T", - "V161I" - ], - "NS1": [ - "A99V", - "K170R", - "I242V", - "Y256N", - "N347S" - ], - "NS3": [ - "K186R" - ], - "NS4A": [ - "R39K" - ], - "NS4B": [ - "S17N", - "M201V" - ], - "NS5": [ - "T135V", - "A196T", - "D521E", - "L544I", - "E558A", - "Q819L" ] }, "labels": { - "aa": "2K: V11I; E: E71D, S81T, V129I, I139V, N203D, V308I, N390D; M: E28K, M31T, V161I; NS1: A99V, K170R, I242V, Y256N, N347S; NS3: K186R; NS4A: R39K; NS4B: S17N, M201V; NS5: T135V, A196T, D521E, L544I, E558A, Q819L", "lineage": "2I" } }, @@ -9440,12 +7811,12 @@ { "name": "GQ398257.1|1977", "node_attrs": { - "div": 0.23696029000000002, - "country": { - "value": "Indonesia" - }, + "div": 0.237, "clade_membership": { "value": "2I" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -9502,32 +7873,14 @@ "C9512T", "G10013A", "C10143A" - ], - "NS1": [ - "P73S" - ], - "NS3": [ - "T120A", - "R187K", - "N345S" - ], - "NS4B": [ - "T108I" - ], - "NS5": [ - "A648V", - "R815K" ] - }, - "labels": { - "aa": "NS1: P73S; NS3: T120A, R187K, N345S; NS4B: T108I; NS5: A648V, R815K" } } }, { "name": "NODE_0000009", "node_attrs": { - "div": 0.2458448, + "div": 0.246, "clade_membership": { "value": "2I" } @@ -9649,26 +8002,14 @@ "A6438C", "C6885T", "A9333G" - ], - "NS2B": [ - "E62D" - ], - "NS3": [ - "I140V", - "V273I", - "A367T", - "K381R" ] - }, - "labels": { - "aa": "NS2B: E62D; NS3: I140V, V273I, A367T, K381R" } }, "children": [ { "name": "NODE_0000010", "node_attrs": { - "div": 0.25316196, + "div": 0.253, "clade_membership": { "value": "2I" } @@ -9751,45 +8092,19 @@ "G9111A", "G9383T", "T9384C" - ], - "NS1": [ - "D290E" - ], - "NS2A": [ - "I171T" - ], - "NS2B": [ - "A57T" - ], - "NS3": [ - "K117R", - "K466R", - "R549K", - "I567T", - "K568R" - ], - "NS4B": [ - "N17H" - ], - "NS5": [ - "S429N", - "G605V" ] - }, - "labels": { - "aa": "NS1: D290E; NS2A: I171T; NS2B: A57T; NS3: K117R, K466R, R549K, I567T, K568R; NS4B: N17H; NS5: S429N, G605V" } }, "children": [ { "name": "JX966379.1|1994", "node_attrs": { - "div": 0.26676236000000003, - "country": { - "value": "Mexico" - }, + "div": 0.267, "clade_membership": { "value": "2I" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { @@ -9923,52 +8238,19 @@ "A10116G", "T10122C", "T10155C" - ], - "C": [ - "R90K" - ], - "E": [ - "T55S" - ], - "M": [ - "E89G" - ], - "NS1": [ - "F247Y" - ], - "NS2A": [ - "T25S", - "F81Y" - ], - "NS2B": [ - "I114T" - ], - "NS3": [ - "T367A", - "A373T", - "A552S" - ], - "NS5": [ - "N174D", - "I228V", - "T290A", - "K469R" ] - }, - "labels": { - "aa": "C: R90K; E: T55S; M: E89G; NS1: F247Y; NS2A: T25S, F81Y; NS2B: I114T; NS3: T367A, A373T, A552S; NS5: N174D, I228V, T290A, K469R" } } }, { "name": "MW946575.1|1996", "node_attrs": { - "div": 0.26845556000000004, - "country": { - "value": "Peru" - }, + "div": 0.268, "clade_membership": { "value": "2I" + }, + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -10120,39 +8402,7 @@ "C10236T", "A10242G", "C10256T" - ], - "E": [ - "V382A" - ], - "NS1": [ - "P73S", - "V177A", - "F247I" - ], - "NS2A": [ - "V41L", - "S212T" - ], - "NS3": [ - "K15R", - "S158G", - "S171G" - ], - "NS4B": [ - "L113M" - ], - "NS5": [ - "I5M", - "S15N", - "V335I", - "I628V", - "A648V", - "R676K", - "A896V" ] - }, - "labels": { - "aa": "E: V382A; NS1: P73S, V177A, F247I; NS2A: V41L, S212T; NS3: K15R, S158G, S171G; NS4B: L113M; NS5: I5M, S15N, V335I, I628V, A648V, R676K, A896V" } } } @@ -10161,7 +8411,7 @@ { "name": "NODE_0000011", "node_attrs": { - "div": 0.25205572, + "div": 0.252, "clade_membership": { "value": "2I" } @@ -10226,36 +8476,19 @@ "A9325G", "C9465T", "C9774T" - ], - "E": [ - "E126K", - "I308V" - ], - "NS5": [ - "V135I", - "V180I", - "R193K", - "S429G", - "I544L", - "M552R", - "A558E", - "R586G" ] - }, - "labels": { - "aa": "E: E126K, I308V; NS5: V135I, V180I, R193K, S429G, I544L, M552R, A558E, R586G" } }, "children": [ { "name": "JQ922552.1|1960", "node_attrs": { - "div": 0.29464582, - "country": { - "value": "India" - }, + "div": 0.295, "clade_membership": { "value": "2I" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -10661,150 +8894,14 @@ "A9982G", "T10025A", "C10173T" - ], - "C": [ - "N2I" - ], - "E": [ - "N124I", - "D390N", - "F402L", - "I459T" - ], - "M": [ - "H11P", - "K28E", - "T31V", - "T35A", - "L44R", - "K52N", - "F55L", - "K57N", - "H86L", - "R91I", - "T125I", - "T147S" - ], - "NS1": [ - "K33M", - "K120Q", - "A121P", - "T126P", - "N130H", - "A149T", - "N151D", - "N166K", - "N234M", - "N256H", - "Y260I", - "H261P", - "T301S" - ], - "NS2A": [ - "F50G", - "V174L", - "L181F" - ], - "NS2B": [ - "G102E", - "V112I" - ], - "NS3": [ - "R187X", - "V550G", - "A551P", - "N570S", - "I572F", - "T583P", - "K584S", - "E585G", - "K590E" - ], - "NS4A": [ - "D23N", - "K39R" - ], - "NS4B": [ - "A19V", - "V43A", - "V63M", - "L112F", - "I121K", - "A233S", - "G234S", - "L235Q", - "L236V", - "F237S", - "M240N", - "K241N", - "N242K", - "T243G", - "T244G", - "S245-", - "T246-" - ], - "NS5": [ - "N4A", - "I5Q", - "S15R", - "R16Q", - "A19Q", - "G21S", - "Q26N", - "I27T", - "K30R", - "Q34M", - "T39S", - "L40E", - "I45L", - "D51T", - "H52K", - "S59T", - "T72K", - "V78I", - "G92A", - "N96K", - "R98T", - "L103Y", - "S117A", - "R125K", - "Q127H", - "V130K", - "I135T", - "T395P", - "E416A", - "N417T", - "S523R", - "T535S", - "G559V", - "F569X", - "K570I", - "Q574P", - "G586V", - "D597G", - "M615L", - "A617G", - "Q618P", - "L619R", - "I632H", - "H634L", - "L635Q", - "S638T", - "I641X", - "M804V", - "T805A", - "L819Q" ] - }, - "labels": { - "aa": "C: N2I; E: N124I, D390N, F402L, I459T; M: H11P, K28E, T31V, T35A, L44R, K52N, F55L, K57N, H86L, R91I, T125I, T147S; NS1: K33M, K120Q, A121P, T126P, N130H, A149T, N151D, N166K, N234M, N256H, Y260I, H261P, T301S; NS2A: F50G, V174L, L181F; NS2B: G102E, V112I; NS3: R187X, V550G, A551P, N570S, I572F, T583P, K584S, E585G, K590E; NS4A: D23N, K39R; NS4B: A19V, V43A, V63M, L112F, I121K, A233S, G234S, L235Q, L236V, F237S, M240N, K241N, N242K, T243G, T244G, S245-, T246-; NS5: N4A, I5Q, S15R, R16Q, A19Q, G21S, Q26N, I27T, K30R, Q34M, T39S, L40E, I45L, D51T, H52K, S59T, T72K, V78I, G92A, N96K, R98T, L103Y, S117A, R125K, Q127H, V130K, I135T, T395P, E416A, N417T, S523R, T535S, G559V, F569X, K570I, Q574P, G586V, D597G, M615L, A617G, Q618P, L619R, I632H, H634L, L635Q, S638T, I641X, M804V, T805A, L819Q" } } }, { "name": "NODE_0000012", "node_attrs": { - "div": 0.25687766, + "div": 0.257, "clade_membership": { "value": "2I" } @@ -10851,56 +8948,19 @@ "G10088A", "G10138C", "A10141C" - ], - "M": [ - "L23F", - "T31H", - "N32D" - ], - "NS1": [ - "S233G", - "H261Y" - ], - "NS2A": [ - "L111F" - ], - "NS3": [ - "F533L", - "V534L", - "D535E", - "M537I", - "R539G", - "D541P", - "L542I", - "W545Y", - "A547G", - "R549X", - "A552G", - "R560S", - "W562L" - ], - "NS5": [ - "K562R", - "I641N", - "G840E", - "A857P", - "T858P" ] - }, - "labels": { - "aa": "M: L23F, T31H, N32D; NS1: S233G, H261Y; NS2A: L111F; NS3: F533L, V534L, D535E, M537I, R539G, D541P, L542I, W545Y, A547G, R549X, A552G, R560S, W562L; NS5: K562R, I641N, G840E, A857P, T858P" } }, "children": [ { "name": "JQ922550.1|1971", "node_attrs": { - "div": 0.27936626000000003, - "country": { - "value": "India" - }, + "div": 0.279, "clade_membership": { "value": "2I" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -11121,133 +9181,19 @@ "G10255T", "A10257T", "G10261T" - ], - "C": [ - "N3S", - "K6R", - "A102V" - ], - "E": [ - "M340K", - "F373L", - "T404N" - ], - "M": [ - "F1S", - "E9G", - "S15I", - "R16G", - "E18Q", - "G20R", - "S22X", - "F23S", - "L24F", - "D29K", - "D40A", - "L41F", - "L44F", - "D47N" - ], - "NS1": [ - "V5G", - "W8G", - "N10Q", - "L13P", - "V99A", - "L321P", - "R322K" - ], - "NS2A": [ - "F111S", - "R213G", - "K217R" - ], - "NS2B": [ - "A57T" - ], - "NS3": [ - "P12L", - "K117R", - "F564V", - "D565G", - "G566R", - "I567T", - "K568Q", - "E587K", - "R588G" - ], - "NS4B": [ - "A218L", - "V219I", - "S220Q", - "F225L", - "L235P", - "K241E", - "S245G", - "T246P" - ], - "NS5": [ - "G1R", - "I5X", - "T8M", - "G10X", - "E11X", - "K12R", - "K139R", - "T271I", - "T363I", - "T377M", - "K437R", - "E545G", - "D546A", - "R552S", - "I553V", - "T554P", - "H561P", - "L571M", - "T572A", - "K576R", - "R579G", - "R582G", - "I628F", - "S631N", - "R654K", - "L655V", - "A659P", - "L748F", - "R749G", - "M765I", - "Y766N", - "H768R", - "R769I", - "R770P", - "A778V", - "A782V", - "S800N", - "S855P", - "R856Q", - "Q864E", - "T880I", - "M883L", - "R891I", - "A896S", - "V898F" ] - }, - "labels": { - "aa": "C: N3S, K6R, A102V; E: M340K, F373L, T404N; M: F1S, E9G, S15I, R16G, E18Q, G20R, S22X, F23S, L24F, D29K, D40A, L41F, L44F, D47N; NS1: V5G, W8G, N10Q, L13P, V99A, L321P, R322K; NS2A: F111S, R213G, K217R; NS2B: A57T; NS3: P12L, K117R, F564V, D565G, G566R, I567T, K568Q, E587K, R588G; NS4B: A218L, V219I, S220Q, F225L, L235P, K241E, S245G, T246P; NS5: G1R, I5X, T8M, G10X, E11X, K12R, K139R, T271I, T363I, T377M, K437R, E545G, D546A, R552S, I553V, T554P, H561P, L571M, T572A, K576R, R579G, R582G, I628F, S631N, R654K, L655V, A659P, L748F, R749G, M765I, Y766N, H768R, R769I, R770P, A778V, A782V, S800N, S855P, R856Q, Q864E, T880I, M883L, R891I, A896S, V898F" } } }, { "name": "JQ922553.1|1980", "node_attrs": { - "div": 0.28887586, - "country": { - "value": "India" - }, + "div": 0.289, "clade_membership": { "value": "2I" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -11575,169 +9521,7 @@ "A10205C", "A10207G", "A10214T" - ], - "C": [ - "R85K" - ], - "E": [ - "F43L", - "G112A", - "N124S", - "H149Y", - "F402L" - ], - "M": [ - "G8V", - "H11P", - "V14F", - "L36F", - "A120V", - "A160G", - "I161V", - "T166R" - ], - "NS1": [ - "P73L", - "T146A", - "G161E", - "T164K", - "N166K", - "L169P", - "R170T", - "R172K", - "K174W", - "Q175R", - "D176K", - "L237Q", - "D327A", - "G332W", - "E334D", - "E343K" - ], - "NS2A": [ - "G11R", - "E21K", - "R24M", - "V27L", - "G46R", - "R51K", - "I68M", - "G69R", - "A79P", - "A89T", - "K166R", - "L181F", - "Q186R" - ], - "NS3": [ - "K26Q", - "L31F", - "H47P", - "N175Y", - "I178V", - "E179X", - "R186K", - "L193F", - "K199R", - "T200Q", - "L204F", - "T358I", - "I365L", - "N369K", - "D370Y", - "K590E" - ], - "NS4A": [ - "D23G", - "D26A", - "N27S", - "A29M", - "K39R", - "I116T" - ], - "NS4B": [ - "P23S", - "E24C", - "S25K", - "N26K", - "D31Y", - "R33G", - "S36L", - "A37P", - "T39K", - "V43G", - "A44G", - "L112F", - "A129P" - ], - "NS5": [ - "V66D", - "Y89F", - "Y90F", - "G102A", - "K105I", - "P115L", - "W121R", - "L126S", - "D131V", - "V132X", - "L143S", - "C145R", - "T196A", - "A304G", - "Y305S", - "T400I", - "I553K", - "E558G", - "I568F", - "F569L", - "L571X", - "Y573X", - "V589L", - "R596K", - "G602E", - "N610T", - "F612L", - "M615L", - "Q618P", - "L619P", - "E626K", - "I628V", - "S631G", - "I632H", - "L635R", - "R652G", - "M658L", - "S757F", - "M761R", - "A776P", - "P784R", - "S785T", - "T793K", - "S796P", - "E802D", - "D808V", - "R815K", - "V816L", - "I818F", - "L819Q", - "E831G", - "S832F", - "Y838F", - "R842G", - "E843K", - "C847G", - "I863F", - "T865P", - "I874L", - "G875C", - "Y879S", - "T880A", - "Y882F" ] - }, - "labels": { - "aa": "C: R85K; E: F43L, G112A, N124S, H149Y, F402L; M: G8V, H11P, V14F, L36F, A120V, A160G, I161V, T166R; NS1: P73L, T146A, G161E, T164K, N166K, L169P, R170T, R172K, K174W, Q175R, D176K, L237Q, D327A, G332W, E334D, E343K; NS2A: G11R, E21K, R24M, V27L, G46R, R51K, I68M, G69R, A79P, A89T, K166R, L181F, Q186R; NS3: K26Q, L31F, H47P, N175Y, I178V, E179X, R186K, L193F, K199R, T200Q, L204F, T358I, I365L, N369K, D370Y, K590E; NS4A: D23G, D26A, N27S, A29M, K39R, I116T; NS4B: P23S, E24C, S25K, N26K, D31Y, R33G, S36L, A37P, T39K, V43G, A44G, L112F, A129P; NS5: V66D, Y89F, Y90F, G102A, K105I, P115L, W121R, L126S, D131V, V132X, L143S, C145R, T196A, A304G, Y305S, T400I, I553K, E558G, I568F, F569L, L571X, Y573X, V589L, R596K, G602E, N610T, F612L, M615L, Q618P, L619P, E626K, I628V, S631G, I632H, L635R, R652G, M658L, S757F, M761R, A776P, P784R, S785T, T793K, S796P, E802D, D808V, R815K, V816L, I818F, L819Q, E831G, S832F, Y838F, R842G, E843K, C847G, I863F, T865P, I874L, G875C, Y879S, T880A, Y882F" } } } @@ -11752,7 +9536,7 @@ { "name": "NODE_0000013", "node_attrs": { - "div": 0.2256006, + "div": 0.226, "clade_membership": { "value": "unassigned" } @@ -11893,7 +9677,6 @@ "C7404T", "C7411T", "A7416G", - "A7422G", "G7428C", "C7461T", "G7559A", @@ -11976,53 +9759,14 @@ "G10128A", "C10179T", "T10191A" - ], - "E": [ - "V162I", - "I484V" - ], - "M": [ - "M31V", - "F55L", - "K57R" - ], - "NS1": [ - "V21I", - "R112K", - "L128P" - ], - "NS2A": [ - "I12V", - "S115T", - "M136I" - ], - "NS4B": [ - "M201I", - "S245N" - ], - "NS5": [ - "V180I", - "R193K", - "K401R", - "I553V", - "I628V", - "A637V", - "S638T", - "D645N", - "R676S", - "T723V", - "S800R" ] - }, - "labels": { - "aa": "E: V162I, I484V; M: M31V, F55L, K57R; NS1: V21I, R112K, L128P; NS2A: I12V, S115T, M136I; NS4B: M201I, S245N; NS5: V180I, R193K, K401R, I553V, I628V, A637V, S638T, D645N, R676S, T723V, S800R" } }, "children": [ { "name": "NODE_0000014", "node_attrs": { - "div": 0.23101503, + "div": 0.231, "clade_membership": { "value": "unassigned" } @@ -12077,28 +9821,14 @@ "T9261A", "C9465T", "G9968A" - ], - "M": [ - "V152A" - ], - "NS1": [ - "P128S" - ], - "NS5": [ - "L70M", - "T271I", - "R800K" ] - }, - "labels": { - "aa": "M: V152A; NS1: P128S; NS5: L70M, T271I, R800K" } }, "children": [ { "name": "NODE_0000015", "node_attrs": { - "div": 0.23562296000000002, + "div": 0.236, "clade_membership": { "value": "unassigned" } @@ -12150,20 +9880,14 @@ "T9525C", "T9591C", "C9859T" - ], - "NS3": [ - "T120A" ] - }, - "labels": { - "aa": "NS3: T120A" } }, "children": [ { "name": "NODE_0000016", "node_attrs": { - "div": 0.26414846000000003, + "div": 0.264, "clade_membership": { "value": "2IV" } @@ -12426,47 +10150,9 @@ "C9963T", "C10032T", "A10050G" - ], - "E": [ - "V129I", - "I322V", - "I378V", - "M492V" - ], - "M": [ - "I135L" - ], - "NS1": [ - "E51Q", - "Q98H", - "K112R", - "M123I", - "V177A", - "N347S" - ], - "NS2A": [ - "N139K", - "K142R" - ], - "NS2B": [ - "R55K", - "K60R" - ], - "NS3": [ - "S158N", - "A160S", - "V273I", - "R549K", - "K568R" - ], - "NS5": [ - "R246K", - "I271V", - "V335I" ] }, "labels": { - "aa": "E: V129I, I322V, I378V, M492V; M: I135L; NS1: E51Q, Q98H, K112R, M123I, V177A, N347S; NS2A: N139K, K142R; NS2B: R55K, K60R; NS3: S158N, A160S, V273I, R549K, K568R; NS5: R246K, I271V, V335I", "lineage": "2IV" } }, @@ -12474,7 +10160,7 @@ { "name": "NODE_0000017", "node_attrs": { - "div": 0.26629081000000004, + "div": 0.266, "clade_membership": { "value": "2IV" } @@ -12502,31 +10188,19 @@ "A8049G", "T8853C", "T8856C" - ], - "NS1": [ - "N145S" - ], - "NS4B": [ - "A19T" - ], - "NS5": [ - "I27M" ] - }, - "labels": { - "aa": "NS1: N145S; NS4B: A19T; NS5: I27M" } }, "children": [ { "name": "OK605760.1|1988", "node_attrs": { - "div": 0.26891963, - "country": { - "value": "Philippines" - }, + "div": 0.269, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -12561,36 +10235,19 @@ "A8867G", "A9502G", "C10263T" - ], - "E": [ - "V484F" - ], - "NS1": [ - "L307I" - ], - "NS3": [ - "V13A" - ], - "NS5": [ - "Q177H", - "E433G", - "N645D" ] - }, - "labels": { - "aa": "E: V484F; NS1: L307I; NS3: V13A; NS5: Q177H, E433G, N645D" } } }, { "name": "OK469347.1|1988", "node_attrs": { - "div": 0.26880148000000004, - "country": { - "value": "Palau" - }, + "div": 0.269, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Palau" } }, "branch_attrs": { @@ -12620,16 +10277,7 @@ "A9282G", "T9561C", "G10071A" - ], - "M": [ - "I49T" - ], - "NS5": [ - "I284M" ] - }, - "labels": { - "aa": "M: I49T; NS5: I284M" } } } @@ -12638,7 +10286,7 @@ { "name": "NODE_0000018", "node_attrs": { - "div": 0.26515179000000005, + "div": 0.265, "clade_membership": { "value": "2IV" } @@ -12665,28 +10313,19 @@ "C9777T", "G9819A", "C10113T" - ], - "NS2B": [ - "T77I" - ], - "NS5": [ - "V637A" ] - }, - "labels": { - "aa": "NS2B: T77I; NS5: V637A" } }, "children": [ { "name": "KF744400.1|2000", "node_attrs": { - "div": 0.27886709000000004, - "country": { - "value": "Philippines" - }, + "div": 0.279, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -12823,50 +10462,14 @@ "G9511A", "T9600C", "C10110T" - ], - "E": [ - "Q52E", - "I170T", - "E269D" - ], - "M": [ - "D29N" - ], - "NS1": [ - "S181P", - "S222N", - "M275L", - "R324K" - ], - "NS2A": [ - "T29M", - "A158S" - ], - "NS2B": [ - "I76V", - "I78V", - "T94I" - ], - "NS4B": [ - "V152A" - ], - "NS5": [ - "R263C", - "T311A", - "H513Y", - "V628I", - "A648T" ] - }, - "labels": { - "aa": "E: Q52E, I170T, E269D; M: D29N; NS1: S181P, S222N, M275L, R324K; NS2A: T29M, A158S; NS2B: I76V, I78V, T94I; NS4B: V152A; NS5: R263C, T311A, H513Y, V628I, A648T" } } }, { "name": "NODE_0000019", "node_attrs": { - "div": 0.2804434900000001, + "div": 0.28, "clade_membership": { "value": "2IV" } @@ -13005,45 +10608,19 @@ "A9831G", "T9843C", "T9859C" - ], - "C": [ - "A63V" - ], - "E": [ - "Q52H" - ], - "M": [ - "H148N" - ], - "NS2A": [ - "K139N", - "R142K" - ], - "NS2B": [ - "D63E" - ], - "NS4A": [ - "R76K", - "I93V" - ], - "NS4B": [ - "L13F" ] - }, - "labels": { - "aa": "C: A63V; E: Q52H; M: H148N; NS2A: K139N, R142K; NS2B: D63E; NS4A: R76K, I93V; NS4B: L13F" } }, "children": [ { "name": "KF744407.1|1996", "node_attrs": { - "div": 0.29017325000000005, - "country": { - "value": "Philippines" - }, + "div": 0.29, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -13139,31 +10716,14 @@ "G9915A", "A9943C", "C9951T" - ], - "E": [ - "E71A", - "I129V", - "V492M" - ], - "NS1": [ - "V6A", - "K170R" - ], - "NS5": [ - "V71I", - "A648T", - "R698K" ] - }, - "labels": { - "aa": "E: E71A, I129V, V492M; NS1: V6A, K170R; NS5: V71I, A648T, R698K" } } }, { "name": "NODE_0000020", "node_attrs": { - "div": 0.28550249000000005, + "div": 0.286, "clade_membership": { "value": "2IV" } @@ -13205,31 +10765,19 @@ "C8322A", "A8343C", "C8358T" - ], - "E": [ - "I164V" - ], - "NS1": [ - "S347N" - ], - "NS5": [ - "K246R" ] - }, - "labels": { - "aa": "E: I164V; NS1: S347N; NS5: K246R" } }, "children": [ { "name": "KF744402.1|2000", "node_attrs": { - "div": 0.29533611000000004, - "country": { - "value": "Philippines" - }, + "div": 0.295, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -13328,47 +10876,19 @@ "C9610T", "G9780A", "T10113C" - ], - "C": [ - "I78V" - ], - "E": [ - "V480I" - ], - "NS1": [ - "K9R", - "K120R", - "R172K", - "K174R", - "A177V" - ], - "NS2A": [ - "A32T", - "D67N" - ], - "NS2B": [ - "M28I", - "K55R" - ], - "NS3": [ - "E169G", - "C485H" ] - }, - "labels": { - "aa": "C: I78V; E: V480I; NS1: K9R, K120R, R172K, K174R, A177V; NS2A: A32T, D67N; NS2B: M28I, K55R; NS3: E169G, C485H" } } }, { "name": "KF744399.1|1998", "node_attrs": { - "div": 0.30480549000000007, - "country": { - "value": "Philippines" - }, + "div": 0.305, "clade_membership": { "value": "2IV" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -13571,36 +11091,7 @@ "C9859T", "C9970A", "C10264T" - ], - "E": [ - "H149N", - "D192G", - "N390S", - "I462V", - "V492M" - ], - "NS1": [ - "T117A", - "S128L", - "E281K" - ], - "NS2A": [ - "N139K", - "K142R" - ], - "NS3": [ - "I65L", - "A120T" - ], - "NS5": [ - "V271I", - "D521E", - "I641N", - "H801N" ] - }, - "labels": { - "aa": "E: H149N, D192G, N390S, I462V, V492M; NS1: T117A, S128L, E281K; NS2A: N139K, K142R; NS3: I65L, A120T; NS5: V271I, D521E, I641N, H801N" } } } @@ -13615,7 +11106,7 @@ { "name": "NODE_0000021", "node_attrs": { - "div": 0.25125866, + "div": 0.251, "clade_membership": { "value": "2V" } @@ -13787,41 +11278,9 @@ "C10126T", "A10162G", "G10254A" - ], - "C": [ - "R9K", - "T101S" - ], - "E": [ - "V484I" - ], - "NS1": [ - "R172K", - "S222N", - "F247L", - "T264I", - "E281D" - ], - "NS2A": [ - "I5V", - "A189T" - ], - "NS3": [ - "V13M", - "K186R", - "M333I" - ], - "NS4B": [ - "I48V" - ], - "NS5": [ - "T135I", - "V687I", - "T865A" ] }, "labels": { - "aa": "C: R9K, T101S; E: V484I; NS1: R172K, S222N, F247L, T264I, E281D; NS2A: I5V, A189T; NS3: V13M, K186R, M333I; NS4B: I48V; NS5: T135I, V687I, T865A", "lineage": "2V" } }, @@ -13829,12 +11288,12 @@ { "name": "GQ868591.1|1964", "node_attrs": { - "div": 0.25767470000000003, - "country": { - "value": "Thailand" - }, + "div": 0.258, "clade_membership": { "value": "2V" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -13904,45 +11363,14 @@ "C9966T", "G10200A", "C10263T" - ], - "E": [ - "I6M", - "T120R", - "S478T" - ], - "M": [ - "T83M", - "A120V", - "I135M", - "A162T" - ], - "NS1": [ - "A265T" - ], - "NS2A": [ - "I136M" - ], - "NS3": [ - "I567V" - ], - "NS4B": [ - "L112F" - ], - "NS5": [ - "H247Y", - "T414A", - "V637I" ] - }, - "labels": { - "aa": "E: I6M, T120R, S478T; M: T83M, A120V, I135M, A162T; NS1: A265T; NS2A: I136M; NS3: I567V; NS4B: L112F; NS5: H247Y, T414A, V637I" } } }, { "name": "NODE_0000022", "node_attrs": { - "div": 0.25397432000000003, + "div": 0.254, "clade_membership": { "value": "2V" } @@ -13983,31 +11411,19 @@ "C9384T", "T9715C", "T10053C" - ], - "E": [ - "I164V" - ], - "NS1": [ - "V177A" - ], - "NS3": [ - "R549K" ] - }, - "labels": { - "aa": "E: I164V; NS1: V177A; NS3: R549K" } }, "children": [ { "name": "OK469345.1|1985", "node_attrs": { - "div": 0.27080882, - "country": { - "value": "Myanmar" - }, + "div": 0.271, "clade_membership": { "value": "2V" + }, + "country": { + "value": "Myanmar" } }, "branch_attrs": { @@ -14176,46 +11592,14 @@ "G10162A", "A10167G", "A10239G" - ], - "E": [ - "N203D" - ], - "M": [ - "T81A" - ], - "NS1": [ - "T117A", - "L247F" - ], - "NS2A": [ - "I152M" - ], - "NS2B": [ - "V59I" - ], - "NS3": [ - "V534I" - ], - "NS4A": [ - "R39K" - ], - "NS5": [ - "V164I", - "V637A", - "A648V", - "M765I", - "A865T" ] - }, - "labels": { - "aa": "E: N203D; M: T81A; NS1: T117A, L247F; NS2A: I152M; NS2B: V59I; NS3: V534I; NS4A: R39K; NS5: V164I, V637A, A648V, M765I, A865T" } } }, { "name": "NODE_0000023", "node_attrs": { - "div": 0.27098572000000004, + "div": 0.271, "clade_membership": { "value": "2V" } @@ -14386,46 +11770,14 @@ "A9918G", "C10143A", "C10185T" - ], - "E": [ - "N83K", - "V129I", - "I141V", - "H346Y" - ], - "NS1": [ - "H50Q", - "S80A" - ], - "NS2A": [ - "R51K", - "M57V" - ], - "NS2B": [ - "A57T" - ], - "NS4A": [ - "A21T" - ], - "NS5": [ - "A196T", - "V335L", - "M337T", - "S631N" ] - }, - "labels": { - "aa": "E: N83K, V129I, I141V, H346Y; NS1: H50Q, S80A; NS2A: R51K, M57V; NS2B: A57T; NS4A: A21T; NS5: A196T, V335L, M337T, S631N" } }, "children": [ { "name": "DQ181803.1|1985", "node_attrs": { - "div": 0.27377718000000006, - "country": { - "value": "Thailand" - }, + "div": 0.274, "clade_membership": { "value": "2V" } @@ -14462,34 +11814,14 @@ "T9491C", "G9588A", "T10212C" - ], - "E": [ - "Q400R" - ], - "NS1": [ - "L124I" - ], - "NS2A": [ - "I136M" - ], - "NS3": [ - "K549Q" - ], - "NS5": [ - "I135F", - "E444D", - "I641T" ] - }, - "labels": { - "aa": "E: Q400R; NS1: L124I; NS2A: I136M; NS3: K549Q; NS5: I135F, E444D, I641T" } } }, { "name": "NODE_0000024", "node_attrs": { - "div": 0.27208762000000003, + "div": 0.272, "clade_membership": { "value": "2V" } @@ -14507,26 +11839,14 @@ "G4879A", "C6957T", "C9399T" - ], - "M": [ - "R16I" - ], - "NS2A": [ - "S215N" - ], - "NS3": [ - "A120T" ] - }, - "labels": { - "aa": "M: R16I; NS2A: S215N; NS3: A120T" } }, "children": [ { "name": "NODE_0000025", "node_attrs": { - "div": 0.27401215, + "div": 0.274, "clade_membership": { "value": "2V" } @@ -14554,23 +11874,14 @@ "C9453T", "C9889T", "C10011T" - ], - "NS2A": [ - "N139D" ] - }, - "labels": { - "aa": "NS2A: N139D" } }, "children": [ { "name": "MW946422.1|1994", "node_attrs": { - "div": 0.28073836, - "country": { - "value": "Thailand" - }, + "div": 0.281, "clade_membership": { "value": "2V" } @@ -14646,29 +11957,14 @@ "T9859C", "C10134T", "C10155T" - ], - "NS1": [ - "D278G" - ], - "NS2A": [ - "T63A", - "R94K", - "V155A" - ], - "NS3": [ - "V208I", - "V395A" ] - }, - "labels": { - "aa": "NS1: D278G; NS2A: T63A, R94K, V155A; NS3: V208I, V395A" } } }, { "name": "NODE_0000026", "node_attrs": { - "div": 0.27444881, + "div": 0.274, "clade_membership": { "value": "2V" } @@ -14682,20 +11978,14 @@ "G5445A", "C7185T", "C8031T" - ], - "NS3": [ - "E177D" ] - }, - "labels": { - "aa": "NS3: E177D" } }, "children": [ { "name": "NODE_0000027", "node_attrs": { - "div": 0.27961387, + "div": 0.28, "clade_membership": { "value": "2V_D" } @@ -14753,20 +12043,9 @@ "C9825T", "C9957T", "A10026G" - ], - "C": [ - "N10T" - ], - "E": [ - "M96I", - "I170V" - ], - "NS5": [ - "N440K" ] }, "labels": { - "aa": "C: N10T; E: M96I, I170V; NS5: N440K", "lineage": "2V_D" } }, @@ -14774,12 +12053,12 @@ { "name": "KY586688.1|1998", "node_attrs": { - "div": 0.28382921, - "country": { - "value": "Thailand" - }, + "div": 0.284, "clade_membership": { "value": "2V_D" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -14827,26 +12106,14 @@ "G9726A", "A9984G", "A10095G" - ], - "M": [ - "I135M" - ], - "NS1": [ - "H261Y" - ], - "NS2A": [ - "I44T" ] - }, - "labels": { - "aa": "M: I135M; NS1: H261Y; NS2A: I44T" } } }, { "name": "NODE_0000028", "node_attrs": { - "div": 0.28023104, + "div": 0.28, "clade_membership": { "value": "2V_D" } @@ -14861,25 +12128,19 @@ "A5886G", "T7999C", "T9753C" - ], - "NS2A": [ - "V5I" ] - }, - "labels": { - "aa": "NS2A: V5I" } }, "children": [ { "name": "MW946284.1|1995", "node_attrs": { - "div": 0.28092046, - "country": { - "value": "Thailand" - }, + "div": 0.281, "clade_membership": { "value": "2V_D" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -14892,20 +12153,14 @@ "A5663G", "A6546G", "C8451T" - ], - "NS3": [ - "K381R" ] - }, - "labels": { - "aa": "NS3: K381R" } } }, { "name": "NODE_0000029", "node_attrs": { - "div": 0.28023203999999996, + "div": 0.28, "clade_membership": { "value": "2V_D" } @@ -14917,12 +12172,12 @@ { "name": "KY586686.1|2000", "node_attrs": { - "div": 0.2862374, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_D" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -14989,33 +12244,14 @@ "T9508C", "T9600C", "A9663G" - ], - "C": [ - "R99H" - ], - "NS1": [ - "L66I", - "T109I" - ], - "NS3": [ - "K170R", - "R322K" - ], - "NS5": [ - "L20M", - "H513Y", - "R596K" ] - }, - "labels": { - "aa": "C: R99H; NS1: L66I, T109I; NS3: K170R, R322K; NS5: L20M, H513Y, R596K" } } }, { "name": "NODE_0000030", "node_attrs": { - "div": 0.28170814999999993, + "div": 0.282, "clade_membership": { "value": "2V_D" } @@ -15039,28 +12275,19 @@ "G6880A", "C9462T", "T9942C" - ], - "NS3": [ - "I30V" - ], - "NS4B": [ - "A19T" ] - }, - "labels": { - "aa": "NS3: I30V; NS4B: A19T" } }, "children": [ { "name": "KY586678.1|2002", "node_attrs": { - "div": 0.28761520999999995, - "country": { - "value": "Thailand" - }, + "div": 0.288, "clade_membership": { "value": "2V_D" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15119,28 +12346,19 @@ "T9957C", "C10101T", "T10117C" - ], - "NS3": [ - "V351I" - ], - "NS5": [ - "M765I" ] - }, - "labels": { - "aa": "NS3: V351I; NS5: M765I" } } }, { "name": "KC964095.1|1998", "node_attrs": { - "div": 0.29847074999999995, - "country": { - "value": "China" - }, + "div": 0.298, "clade_membership": { "value": "2V_D" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -15313,64 +12531,7 @@ "C10110T", "A10116G", "G10162A" - ], - "E": [ - "L107S", - "V151I", - "M183I", - "E202G", - "R286G" - ], - "M": [ - "C66R", - "S164P" - ], - "NS1": [ - "H26R", - "I96T", - "V162M", - "K170Q", - "L270Q", - "L273P" - ], - "NS2A": [ - "I120V", - "V133A" - ], - "NS2B": [ - "K60N" - ], - "NS3": [ - "E86G", - "V147E", - "A160T", - "D177E", - "R186K" - ], - "NS4B": [ - "R33P" - ], - "NS5": [ - "S150W", - "I271T", - "E282G", - "N322D", - "L335I", - "T337M", - "K389E", - "R430G", - "K440N", - "T584P", - "G605V", - "M684V", - "N701D", - "F713S", - "D844G", - "A865T" ] - }, - "labels": { - "aa": "E: L107S, V151I, M183I, E202G, R286G; M: C66R, S164P; NS1: H26R, I96T, V162M, K170Q, L270Q, L273P; NS2A: I120V, V133A; NS2B: K60N; NS3: E86G, V147E, A160T, D177E, R186K; NS4B: R33P; NS5: S150W, I271T, E282G, N322D, L335I, T337M, K389E, R430G, K440N, T584P, G605V, M684V, N701D, F713S, D844G, A865T" } } } @@ -15385,7 +12546,7 @@ { "name": "NODE_0000031", "node_attrs": { - "div": 0.27568655, + "div": 0.276, "clade_membership": { "value": "2V" } @@ -15406,20 +12567,14 @@ "A9501G", "A9594G", "A10080G" - ], - "NS4A": [ - "I89V" ] - }, - "labels": { - "aa": "NS4A: I89V" } }, "children": [ { "name": "NODE_0000032", "node_attrs": { - "div": 0.28030752, + "div": 0.28, "clade_membership": { "value": "2V_B" } @@ -15472,19 +12627,9 @@ "A9513G", "T9867C", "T10117C" - ], - "C": [ - "A102V" - ], - "E": [ - "I335V" - ], - "NS2A": [ - "H2Q" ] }, "labels": { - "aa": "C: A102V; E: I335V; NS2A: H2Q", "lineage": "2V_B" } }, @@ -15492,12 +12637,12 @@ { "name": "MW946460.1|1997", "node_attrs": { - "div": 0.28406042, - "country": { - "value": "Thailand" - }, + "div": 0.284, "clade_membership": { "value": "2V_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15540,27 +12685,14 @@ "C8738T", "T9399C", "T9840C" - ], - "C": [ - "V80I", - "I106T" - ], - "E": [ - "S470T" - ], - "NS5": [ - "T390I" ] - }, - "labels": { - "aa": "C: V80I, I106T; E: S470T; NS5: T390I" } } }, { "name": "NODE_0000033", "node_attrs": { - "div": 0.28049883, + "div": 0.28, "clade_membership": { "value": "2V_B" } @@ -15576,12 +12708,12 @@ { "name": "MW946551.1|1997", "node_attrs": { - "div": 0.28553270999999997, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15638,30 +12770,14 @@ "G9588A", "T9741A", "C10163T" - ], - "E": [ - "H149Q" - ], - "NS1": [ - "D278G" - ], - "NS3": [ - "A160V" - ], - "NS5": [ - "E433K", - "A865V" ] - }, - "labels": { - "aa": "E: H149Q; NS1: D278G; NS3: A160V; NS5: E433K, A865V" } } }, { "name": "NODE_0000034", "node_attrs": { - "div": 0.28049982999999995, + "div": 0.28, "clade_membership": { "value": "2V_B" } @@ -15673,12 +12789,12 @@ { "name": "MW946473.1|1999", "node_attrs": { - "div": 0.28523244, - "country": { - "value": "Thailand" - }, + "div": 0.285, "clade_membership": { "value": "2V_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15732,38 +12848,14 @@ "G9594A", "C9879T", "G10200T" - ], - "E": [ - "Y346H" - ], - "NS1": [ - "K112R" - ], - "NS2A": [ - "L92F" - ], - "NS3": [ - "V273I", - "K568R", - "I581V" - ], - "NS4B": [ - "I18V" - ], - "NS5": [ - "T290A", - "E877D" ] - }, - "labels": { - "aa": "E: Y346H; NS1: K112R; NS2A: L92F; NS3: V273I, K568R, I581V; NS4B: I18V; NS5: T290A, E877D" } } }, { "name": "NODE_0000035", "node_attrs": { - "div": 0.28246984999999997, + "div": 0.282, "clade_membership": { "value": "2V_B" } @@ -15791,25 +12883,19 @@ "T7491C", "T9006C", "C9259T" - ], - "NS3": [ - "V395A" ] - }, - "labels": { - "aa": "NS3: V395A" } }, "children": [ { "name": "KY586690.1|1999", "node_attrs": { - "div": 0.28661381999999996, - "country": { - "value": "Thailand" - }, + "div": 0.287, "clade_membership": { "value": "2V_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15857,30 +12943,19 @@ "A10025G", "G10080A", "C10117T" - ], - "NS4B": [ - "L230V" - ], - "NS5": [ - "I271T", - "I412V", - "Q819R" ] - }, - "labels": { - "aa": "NS4B: L230V; NS5: I271T, I412V, Q819R" } } }, { "name": "KY586692.1|2001", "node_attrs": { - "div": 0.28621644999999996, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -15924,22 +12999,7 @@ "A10029G", "A10104G", "C10110T" - ], - "E": [ - "V335I" - ], - "NS1": [ - "K9E", - "K41R" - ], - "NS2A": [ - "V36I", - "K51R", - "N202S" ] - }, - "labels": { - "aa": "E: V335I; NS1: K9E, K41R; NS2A: V36I, K51R, N202S" } } } @@ -15954,7 +13014,7 @@ { "name": "NODE_0000036", "node_attrs": { - "div": 0.28208814, + "div": 0.282, "clade_membership": { "value": "2V_E" } @@ -16024,27 +13084,9 @@ "G10059A", "C10101T", "T10212C" - ], - "E": [ - "I484V" - ], - "M": [ - "A152T" - ], - "NS2A": [ - "L92F", - "I136M" - ], - "NS3": [ - "K28R" - ], - "NS4B": [ - "V91A", - "T246S" ] }, "labels": { - "aa": "E: I484V; M: A152T; NS2A: L92F, I136M; NS3: K28R; NS4B: V91A, T246S", "lineage": "2V_E" } }, @@ -16052,12 +13094,12 @@ { "name": "MW946449.1|2014", "node_attrs": { - "div": 0.29403293999999996, - "country": { - "value": "Thailand" - }, + "div": 0.294, "clade_membership": { "value": "2V_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16183,41 +13225,14 @@ "A10128G", "C10208T", "A10254T" - ], - "NS1": [ - "S125F" - ], - "NS2A": [ - "T29M", - "I33T" - ], - "NS3": [ - "I333L", - "I567V" - ], - "NS4B": [ - "S25T" - ], - "NS5": [ - "I180V", - "Y201F", - "I281V", - "M393I", - "G627R", - "V637A", - "T880I", - "E895D" ] - }, - "labels": { - "aa": "NS1: S125F; NS2A: T29M, I33T; NS3: I333L, I567V; NS4B: S25T; NS5: I180V, Y201F, I281V, M393I, G627R, V637A, T880I, E895D" } } }, { "name": "NODE_0000037", "node_attrs": { - "div": 0.28243767999999997, + "div": 0.282, "clade_membership": { "value": "2V_E" } @@ -16236,7 +13251,7 @@ { "name": "NODE_0000038", "node_attrs": { - "div": 0.28342709, + "div": 0.283, "clade_membership": { "value": "2V_E" } @@ -16253,25 +13268,19 @@ "C7914T", "C8766T", "G9714A" - ], - "C": [ - "A102V" ] - }, - "labels": { - "aa": "C: A102V" } }, "children": [ { "name": "FJ639828.1|2001", "node_attrs": { - "div": 0.28596968, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16302,34 +13311,19 @@ "C8292T", "A9110G", "G9891A" - ], - "E": [ - "V358A" - ], - "NS2A": [ - "I116L" - ], - "NS3": [ - "M59T" - ], - "NS5": [ - "K514R" ] - }, - "labels": { - "aa": "E: V358A; NS2A: I116L; NS3: M59T; NS5: K514R" } } }, { "name": "FJ687436.1|2001", "node_attrs": { - "div": 0.28630914, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16365,20 +13359,7 @@ "G8952A", "A9489G", "A10056T" - ], - "E": [ - "K64R", - "G190S" - ], - "NS2A": [ - "F92L" - ], - "NS4B": [ - "V171A" ] - }, - "labels": { - "aa": "E: K64R, G190S; NS2A: F92L; NS4B: V171A" } } } @@ -16387,7 +13368,7 @@ { "name": "NODE_0000039", "node_attrs": { - "div": 0.28774926999999995, + "div": 0.288, "clade_membership": { "value": "2V_E" } @@ -16447,29 +13428,19 @@ "G9596A", "C9690T", "C9963T" - ], - "NS3": [ - "V577M" - ], - "NS5": [ - "I641T", - "S676N" ] - }, - "labels": { - "aa": "NS3: V577M; NS5: I641T, S676N" } }, "children": [ { "name": "MW946517.1|2005", "node_attrs": { - "div": 0.29001383, - "country": { - "value": "Thailand" - }, + "div": 0.29, "clade_membership": { "value": "2V_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16496,31 +13467,19 @@ "C9482T", "G9594A", "T10011C" - ], - "NS1": [ - "A177I" - ], - "NS4A": [ - "T15A" - ], - "NS5": [ - "T638I" ] - }, - "labels": { - "aa": "NS1: A177I; NS4A: T15A; NS5: T638I" } } }, { "name": "MW946595.1|2005", "node_attrs": { - "div": 0.2892257899999999, - "country": { - "value": "Thailand" - }, + "div": 0.289, "clade_membership": { "value": "2V_E" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16543,13 +13502,7 @@ "C7057T", "T7293C", "C8349T" - ], - "M": [ - "V161I" ] - }, - "labels": { - "aa": "M: V161I" } } } @@ -16568,7 +13521,7 @@ { "name": "NODE_0000040", "node_attrs": { - "div": 0.27412745000000005, + "div": 0.274, "clade_membership": { "value": "2V" } @@ -16598,20 +13551,14 @@ "C9288T", "C9492T", "T9927C" - ], - "NS5": [ - "T196A" ] - }, - "labels": { - "aa": "NS5: T196A" } }, "children": [ { "name": "NODE_0000041", "node_attrs": { - "div": 0.27522384000000005, + "div": 0.275, "clade_membership": { "value": "2V" } @@ -16630,23 +13577,14 @@ "C6876T", "T9615C", "A10251G" - ], - "NS4A": [ - "T3A" ] - }, - "labels": { - "aa": "NS4A: T3A" } }, "children": [ { "name": "KY586675.1|1995", "node_attrs": { - "div": 0.28173701000000007, - "country": { - "value": "Thailand" - }, + "div": 0.282, "clade_membership": { "value": "2V" } @@ -16722,27 +13660,14 @@ "T10023C", "C10032T", "A10056G" - ], - "NS1": [ - "T288N" - ], - "NS2A": [ - "I116V", - "V159M" - ], - "NS5": [ - "N440S" ] - }, - "labels": { - "aa": "NS1: T288N; NS2A: I116V, V159M; NS5: N440S" } } }, { "name": "NODE_0000042", "node_attrs": { - "div": 0.27859565000000003, + "div": 0.279, "clade_membership": { "value": "2V_C" } @@ -16781,13 +13706,9 @@ "C9720T", "T9735A", "T10179C" - ], - "M": [ - "I16M" ] }, "labels": { - "aa": "M: I16M", "lineage": "2V_C" } }, @@ -16795,7 +13716,7 @@ { "name": "NODE_0000043", "node_attrs": { - "div": 0.28013760000000004, + "div": 0.28, "clade_membership": { "value": "2V_C" } @@ -16819,32 +13740,19 @@ "A9243G", "A9969G", "G10251T" - ], - "NS2A": [ - "N215S" - ], - "NS4B": [ - "P23L" - ], - "NS5": [ - "Y201H", - "E894D" ] - }, - "labels": { - "aa": "NS2A: N215S; NS4B: P23L; NS5: Y201H, E894D" } }, "children": [ { "name": "MW946509.1|1998", "node_attrs": { - "div": 0.28196829000000007, - "country": { - "value": "Thailand" - }, + "div": 0.282, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16869,25 +13777,19 @@ "A8619G", "G9714A", "A10149G" - ], - "NS2A": [ - "A80T" ] - }, - "labels": { - "aa": "NS2A: A80T" } } }, { "name": "MW946590.1|1997", "node_attrs": { - "div": 0.28294253, - "country": { - "value": "Thailand" - }, + "div": 0.283, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -16921,19 +13823,7 @@ "A9210G", "C9591T", "A9595G" - ], - "C": [ - "M113T" - ], - "E": [ - "T55I" - ], - "NS5": [ - "S676G" ] - }, - "labels": { - "aa": "C: M113T; E: T55I; NS5: S676G" } } } @@ -16942,7 +13832,7 @@ { "name": "NODE_0000044", "node_attrs": { - "div": 0.28100596000000005, + "div": 0.281, "clade_membership": { "value": "2V_C" } @@ -16974,35 +13864,19 @@ "G9141A", "A9278G", "T9811C" - ], - "C": [ - "T11A" - ], - "NS2A": [ - "N139K", - "V174A" - ], - "NS4B": [ - "Q21H" - ], - "NS5": [ - "K570R" ] - }, - "labels": { - "aa": "C: T11A; NS2A: N139K, V174A; NS4B: Q21H; NS5: K570R" } }, "children": [ { "name": "MW946369.1|1994", "node_attrs": { - "div": 0.28123210000000004, - "country": { - "value": "Thailand" - }, + "div": 0.281, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -17017,7 +13891,7 @@ { "name": "NODE_0000045", "node_attrs": { - "div": 0.28206137000000003, + "div": 0.282, "clade_membership": { "value": "2V_C" } @@ -17042,12 +13916,12 @@ { "name": "MW946428.1|2001", "node_attrs": { - "div": 0.28826334000000003, - "country": { - "value": "Thailand" - }, + "div": 0.288, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -17117,38 +13991,14 @@ "C10083T", "G10086A", "A10253G" - ], - "NS1": [ - "V60A", - "T109I" - ], - "NS2A": [ - "T214A" - ], - "NS2B": [ - "R55K", - "I76V" - ], - "NS4B": [ - "I18V", - "P23L" - ], - "NS5": [ - "I271T", - "T390A", - "I641T", - "E895G" ] - }, - "labels": { - "aa": "NS1: V60A, T109I; NS2A: T214A; NS2B: R55K, I76V; NS4B: I18V, P23L; NS5: I271T, T390A, I641T, E895G" } } }, { "name": "NODE_0000046", "node_attrs": { - "div": 0.28461982, + "div": 0.285, "clade_membership": { "value": "2V_C" } @@ -17180,25 +14030,19 @@ "C8754T", "T8919C", "T9753C" - ], - "NS1": [ - "D278A" ] - }, - "labels": { - "aa": "NS1: D278A" } }, "children": [ { "name": "MW946279.1|2001", "node_attrs": { - "div": 0.28786692, - "country": { - "value": "Thailand" - }, + "div": 0.288, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -17236,28 +14080,19 @@ "G8913A", "C9280T", "T9552C" - ], - "NS1": [ - "F279L" - ], - "NS2A": [ - "L180M" ] - }, - "labels": { - "aa": "NS1: F279L; NS2A: L180M" } } }, { "name": "KY586667.1|2001", "node_attrs": { - "div": 0.2870837, - "country": { - "value": "Thailand" - }, + "div": 0.287, "clade_membership": { "value": "2V_C" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -17289,16 +14124,7 @@ "A9141G", "A9579G", "T9741C" - ], - "NS1": [ - "L134F" - ], - "NS2A": [ - "A37T" ] - }, - "labels": { - "aa": "NS1: L134F; NS2A: A37T" } } } @@ -17315,7 +14141,7 @@ { "name": "NODE_0000047", "node_attrs": { - "div": 0.2777501700000001, + "div": 0.278, "clade_membership": { "value": "2V_A" } @@ -17358,20 +14184,9 @@ "G9662A", "G10089A", "G10272A" - ], - "E": [ - "T226K" - ], - "NS4B": [ - "V175I" - ], - "NS5": [ - "S676N", - "R698K" ] }, "labels": { - "aa": "E: T226K; NS4B: V175I; NS5: S676N, R698K", "lineage": "2V_A" } }, @@ -17379,12 +14194,12 @@ { "name": "MW946420.1|1996", "node_attrs": { - "div": 0.28121539000000007, - "country": { - "value": "Thailand" - }, + "div": 0.281, "clade_membership": { "value": "2V_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -17427,23 +14242,14 @@ "C9345T", "T9384C", "C9639T" - ], - "NS1": [ - "I202M" - ], - "NS4A": [ - "N5S" ] - }, - "labels": { - "aa": "NS1: I202M; NS4A: N5S" } } }, { "name": "NODE_0000048", "node_attrs": { - "div": 0.2807465700000001, + "div": 0.281, "clade_membership": { "value": "2V_A" } @@ -17484,32 +14290,19 @@ "A9876G", "C9879T", "A10025G" - ], - "M": [ - "S15G" - ], - "NS1": [ - "V286I" - ], - "NS5": [ - "I641V", - "Q819R" ] - }, - "labels": { - "aa": "M: S15G; NS1: V286I; NS5: I641V, Q819R" } }, "children": [ { "name": "JN368476.1|2007", "node_attrs": { - "div": 0.29400237000000007, - "country": { - "value": "Cambodia" - }, + "div": 0.294, "clade_membership": { "value": "2V_A" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -17614,38 +14407,14 @@ "G9861A", "C9966T", "T10126C" - ], - "E": [ - "N203S" - ], - "NS1": [ - "I264T" - ], - "NS2A": [ - "A62T", - "N139D" - ], - "NS3": [ - "S346T" - ], - "NS4A": [ - "I93V" - ], - "NS5": [ - "I27T", - "Q286E", - "V641A" ] - }, - "labels": { - "aa": "E: N203S; NS1: I264T; NS2A: A62T, N139D; NS3: S346T; NS4A: I93V; NS5: I27T, Q286E, V641A" } } }, { "name": "NODE_0000049", "node_attrs": { - "div": 0.2833241700000001, + "div": 0.283, "clade_membership": { "value": "2V_A" } @@ -17675,34 +14444,19 @@ "C6145T", "C6597T", "A10176G" - ], - "E": [ - "G228E" - ], - "M": [ - "A152V" - ], - "NS1": [ - "H129Y" - ], - "NS2B": [ - "V112I" ] - }, - "labels": { - "aa": "E: G228E; M: A152V; NS1: H129Y; NS2B: V112I" } }, "children": [ { "name": "OQ028229.1|2017-08-03", "node_attrs": { - "div": 0.3014917700000001, - "country": { - "value": "Vietnam" - }, + "div": 0.301, "clade_membership": { "value": "2V_A" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -17873,46 +14627,14 @@ "T10063A", "G10119A", "T10126C" - ], - "E": [ - "K160Q", - "V181I" - ], - "NS1": [ - "I93T", - "V162M", - "D278N" - ], - "NS2A": [ - "A32T", - "V38A", - "A88V", - "T105S" - ], - "NS3": [ - "A249T", - "V577M", - "E585D" - ], - "NS4B": [ - "I175V" - ], - "NS5": [ - "I5M", - "I542V", - "Q644K", - "S832T" ] - }, - "labels": { - "aa": "E: K160Q, V181I; NS1: I93T, V162M, D278N; NS2A: A32T, V38A, A88V, T105S; NS3: A249T, V577M, E585D; NS4B: I175V; NS5: I5M, I542V, Q644K, S832T" } } }, { "name": "NODE_0000050", "node_attrs": { - "div": 0.2838866800000001, + "div": 0.284, "clade_membership": { "value": "2V_A" } @@ -17925,21 +14647,14 @@ "T5499C", "T6966C", "G7647A" - ], - "NS2A": [ - "T65A", - "I120V" ] - }, - "labels": { - "aa": "NS2A: T65A, I120V" } }, "children": [ { "name": "NODE_0000051", "node_attrs": { - "div": 0.2842671700000001, + "div": 0.284, "clade_membership": { "value": "2V_A" } @@ -17959,1096 +14674,7 @@ { "name": "NODE_0000052", "node_attrs": { - "div": 0.28902036000000014, - "clade_membership": { - "value": "2V_A" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C546A", - "G618A", - "T678C", - "T696C", - "A849G", - "C894T", - "T1197C", - "T1719C", - "A2262G", - "A2394G", - "G2742A", - "C2853T", - "G3129T", - "A3306G", - "G3534A", - "T3591C", - "C3720T", - "T3735C", - "A3915G", - "C3939T", - "C3984T", - "C4005T", - "G4230A", - "T4692C", - "C4848G", - "A5220G", - "C5262T", - "G5271A", - "G5283A", - "C5367T", - "A5925G", - "C5973T", - "T6015C", - "T6039C", - "T6222C", - "C6567T", - "G6945A", - "A7632G", - "C7806T", - "A8471G", - "G8589A", - "A8854G", - "C9480T", - "T9744C", - "G10017A", - "C10264T" - ], - "NS5": [ - "K301R", - "S429G" - ] - }, - "labels": { - "aa": "NS5: 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"C10208T" + ] + } + } + }, + { + "name": "MN923120.1|2019-10-02", + "node_attrs": { + "div": 0.3, + "clade_membership": { + "value": "2V_A.2" + }, + "country": { + "value": "China" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G111A", + "T384C", + "C480T", + "A729G", + "A936T", + "T942C", + "G978T", + "A1056G", + "C1347T", + "A1613G", + "T1776C", + "A2238G", + "G2286A", + "T2550A", + "T2608C", + "C2832T", + "C2898T", + "G3237A", + "G3435T", + "G3490A", + "C3666T", + "A4391G", + "G4827A", + "C4881T", + "G5007A", + "A5028G", + "T5067C", + "T5262C", + "A5283G", + "C5340T", + "T5367C", + "C5475T", + "T5496C", + "A5511G", + "A5514T", + "T5640C", + "G5682A", + "T5688C", + "C5694T", + "A5712T", + "T5859C", + "G5925A", + "C6084T", + "A6087G", + "C6189T", + "C6330T", + "C6423T", + "C6457T", + "C6556T", + "T6653C", + "T6717C", + "T6868C", + "T6969C", + "A6984G", + "T6987C", + "T7104C", + "C7266T", + "A7338G", + "T7362C", + "C7404T", + "A8086G", + "C8226T", + "C8349T", + "A8367G", + "T8381C", + "A8502G", + "G8550A", + "T8610C", + "G8952A", + "C9108T", + "T9399C", + "A9660C", + "G10025T", + "A10026G", + "T10084C" + ] + } + } + } + ] + } + ] } ] } @@ -19564,9 +16084,9 @@ ] }, { - "name": "NODE_0000062", + "name": "NODE_0000063", "node_attrs": { - "div": 0.2838876800000001, + "div": 0.284, "clade_membership": { "value": "2V_A" } @@ -19576,9 +16096,9 @@ }, "children": [ { - "name": "NODE_0000063", + "name": "NODE_0000064", "node_attrs": { - "div": 0.2847756400000001, + "div": 0.285, "clade_membership": { "value": "2V_A" } @@ -19595,23 +16115,14 @@ "G6872T", "A9222G", "A10089G" - ], - "NS4B": [ - "G16V" ] - }, - "labels": { - "aa": "NS4B: G16V" } }, "children": [ { "name": "KY586603.1|2002", "node_attrs": { - "div": 0.28556340000000013, - "country": { - "value": "Thailand" - }, + "div": 0.286, "clade_membership": { "value": "2V_A" } @@ -19627,25 +16138,16 @@ "C6033T", "A7348G", "A7866G" - ], - "NS3": [ - "T435R" - ], - "NS4B": [ - "I175V" ] - }, - "labels": { - "aa": "NS3: T435R; NS4B: I175V" } } }, { - "name": "NODE_0000064", + "name": "NODE_0000065", "node_attrs": { - "div": 0.28752956000000013, + "div": 0.288, "clade_membership": { - "value": "2V_A.2" + "value": "2V_A.3" } }, "branch_attrs": { @@ -19681,19 +16183,19 @@ ] }, "labels": { - "lineage": "2V_A.2" + "lineage": "2V_A.3" } }, "children": [ { "name": "KY586595.1|2004", "node_attrs": { - "div": 0.28841649000000014, + "div": 0.288, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Thailand" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -19709,22 +16211,16 @@ "A7164G", "G7371A", "C8349T" - ], - "M": [ - "A137V" ] - }, - "labels": { - "aa": "M: A137V" } } }, { - "name": "NODE_0000065", + "name": "NODE_0000066", "node_attrs": { - "div": 0.2889161100000001, + "div": 0.289, "clade_membership": { - "value": "2V_A.2" + "value": "2V_A.3" } }, "branch_attrs": { @@ -19743,25 +16239,19 @@ "T7680C", "T9732C", "C10163T" - ], - "NS5": [ - "A865V" ] - }, - "labels": { - "aa": "NS5: A865V" } }, "children": [ { "name": "KY849765.1|2009-11-06", "node_attrs": { - "div": 0.29285481000000013, + "div": 0.293, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Laos" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -19805,23 +16295,16 @@ "G9861A", "A10161G", "T10188C" - ], - "NS1": [ - "S38A", - "S128P" ] - }, - "labels": { - "aa": "NS1: S38A, S128P" } } }, { - "name": "NODE_0000066", + "name": "NODE_0000067", "node_attrs": { - "div": 0.2890139700000001, + "div": 0.289, "clade_membership": { - "value": "2V_A.2" + "value": "2V_A.3" } }, "branch_attrs": { @@ -19836,12 +16319,12 @@ { "name": "KY849768.1|2010-08-13", "node_attrs": { - "div": 0.2927606500000001, + "div": 0.293, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Laos" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -19886,40 +16369,16 @@ "C9499A", "T9774A", "A9786G" - ], - "E": [ - "I170T" - ], - "M": [ - "E18D" - ], - "NS1": [ - "V236M", - "I264T" - ], - "NS2B": [ - "I116V" - ], - "NS3": [ - "H60Y" - ], - "NS5": [ - "M393I", - "K548R", - "Q644K" ] - }, - "labels": { - "aa": "E: I170T; M: E18D; NS1: V236M, I264T; NS2B: I116V; NS3: H60Y; NS5: M393I, K548R, Q644K" } } }, { - "name": "NODE_0000067", + "name": "NODE_0000068", "node_attrs": { - "div": 0.2898014600000001, + "div": 0.29, "clade_membership": { - "value": "2V_A.2" + "value": "2V_A.3" } }, "branch_attrs": { @@ -19937,12 +16396,12 @@ { "name": "MW946554.1|2011", "node_attrs": { - "div": 0.29305456000000013, + "div": 0.293, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Thailand" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -19983,31 +16442,16 @@ "C9843T", "A10029G", "T10063A" - ], - "NS1": [ - "D281V" - ], - "NS2A": [ - "A151T" - ], - "NS3": [ - "R337K" - ], - "NS5": [ - "S832T" ] - }, - "labels": { - "aa": "NS1: D281V; NS2A: A151T; NS3: R337K; NS5: S832T" } } }, { - "name": "NODE_0000068", + "name": "NODE_0000069", "node_attrs": { - "div": 0.28989929000000014, + "div": 0.29, "clade_membership": { - "value": "2V_A.2" + "value": "2V_A.3" } }, "branch_attrs": { @@ -20021,12 +16465,12 @@ { "name": "MN448920.1|2011", "node_attrs": { - "div": 0.29433549000000014, + "div": 0.294, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Thailand" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -20067,28 +16511,19 @@ "C9966T", "T10083C", "G10089A" - ], - "NS1": [ - "K11R" - ], - "NS2A": [ - "F18L" ] - }, - "labels": { - "aa": "NS1: K11R; NS2A: F18L" } } }, { "name": "MW946510.1|2011", "node_attrs": { - "div": 0.29384570000000015, + "div": 0.294, + "clade_membership": { + "value": "2V_A.3" + }, "country": { "value": "Thailand" - }, - "clade_membership": { - "value": "2V_A.2" } }, "branch_attrs": { @@ -20136,29 +16571,7 @@ "G9857A", "G10014A", "T10063A" - ], - "E": [ - "S478T" - ], - "NS3": [ - "R186K", - "R398K", - "V577M" - ], - "NS4A": [ - "R76K" - ], - "NS4B": [ - "I175V" - ], - "NS5": [ - "M393V", - "S763N", - "S832T" ] - }, - "labels": { - "aa": "E: S478T; NS3: R186K, R398K, V577M; NS4A: R76K; NS4B: I175V; NS5: M393V, S763N, S832T" } } } @@ -20175,9 +16588,9 @@ ] }, { - "name": "NODE_0000069", + "name": "NODE_0000070", "node_attrs": { - "div": 0.2856738000000001, + "div": 0.286, "clade_membership": { "value": "2V_A" } @@ -20204,23 +16617,14 @@ "C9120T", "C9252T", "T9491C" - ], - "NS5": [ - "V641A" ] - }, - "labels": { - "aa": "NS5: V641A" } }, "children": [ { "name": "MW946280.1|2004", "node_attrs": { - "div": 0.28734934000000006, - "country": { - "value": "Thailand" - }, + "div": 0.287, "clade_membership": { "value": "2V_A" } @@ -20245,23 +16649,14 @@ "A7209G", "T7662C", "G8583A" - ], - "NS2A": [ - "I152T" - ], - "NS4A": [ - "R22K" ] - }, - "labels": { - "aa": "NS2A: I152T; NS4A: R22K" } } }, { - "name": "NODE_0000070", + "name": "NODE_0000071", "node_attrs": { - "div": 0.2884983700000001, + "div": 0.288, "clade_membership": { "value": "2V_A.1" } @@ -20275,360 +16670,60 @@ "G1530A", "C2484T", "C3369T", - "G3528A", "C5475T", "A5649G", "G5682A", "T5688C", - "T6249C", "C6384T", - "C6444T", "G6678A", "T7158C", "C7161A", - "G7242A", "G7590A", "T8238C", "C8319T", - "C8389T", - "C8425G", "T8487C", "A9513T", - "A9612G", "C9759T", "G9861A", - "C9966T", - "C10263T" - ], - "E": [ - "K160M" - ], - "NS5": [ - "Q286E" + "C9966T" ] }, "labels": { - "aa": "E: K160M; NS5: Q286E", "lineage": "2V_A.1" } }, "children": [ { - "name": "NODE_0000071", + "name": "KY586586.1|2006", "node_attrs": { - "div": 0.2897207200000001, + "div": 0.289, "clade_membership": { "value": "2V_A.1" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { "mutations": { "nuc": [ - "T483C", - "C1576T", - "G3486A", - "C3618T", - "C6894T", - "C7018T", - "A7413G", - "A7692G", - "A8640G", - "C9453T", - "C9993T", - "A10029G" + "T2142C", + "A2447G", + "G3054A", + "G4275A", + "G4994C", + "T6094C", + "C6340T", + "A8466T", + "T9399C" ] } - }, - "children": [ - { - "name": "GU131924.1|2008", - "node_attrs": { - "div": 0.2904512300000001, - "country": { - "value": "Cambodia" - }, - "clade_membership": { - "value": "2V_A.1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A127C", - "A4515G", - "C4629T", - "T6192C", - "C7539A", - "T7544A", - "G9225A" - ], - "C": [ - "T11P" - ], - "NS4B": [ - "M240K" - ], - "NS5": [ - "M552I" - ] - }, - "labels": { - "aa": "C: T11P; NS4B: M240K; NS5: M552I" - } - } - }, - { - "name": "NODE_0000072", - "node_attrs": { - "div": 0.2919465100000001, - "clade_membership": { - "value": "2V_A.1.3" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C126T", - "G438A", - "T882C", - "G2166A", - "T2760C", - "T2778C", - "G2847A", - "T4179C", - "T4206C", - "T4248C", - "C4380T", - "G4386A", - "A4739G", - "T5067C", - "T5400C", - "C5973T", - "T6222C", - "G6522A", - "T7524C", - "A8022G", - "A9363G", - "T9479C", - "C9708T" - ], - "NS3": [ - 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"C7857T", + "G7862A", + "A7863G", + "G7869C", + "C7911T", + "T7914C", + "G7929T", + "A7938G", + "T7947G", + "G7950A", + "T7959C", + "C7962T", + "C7968T", + "C7971T", + "T7973C", + "C7974T", + "T7999C", + "A8019G", + "T8028C", + "A8034G", + "G8037T", + "A8040G", + "C8061T", + "T8064A", + "A8073G", + "T8079C", + "T8083C", + "C8088T", + "C8091T", + "C8094T", + "T8097C", + "C8103T", + "A8112G", + "C8118T", + "C8121T", + "C8133T", + "A8157G", + "G8160A", + "T8172C", + "C8181T", + "A8184G", + "A8190G", + "G8205A", + "C8208T", + "T8217C", + "C8238T", + "T8244C", + "G8280A", + "C8289T", + "T8292C", + "A8316G", + "T8319C", + "T8322A", + "G8328A", + "C8340T", + "C8349T", + "T8358C", + "T8364C", + "A8380G", + "C8388T", + "T8389C", + "G8424A", + "G8425C", + "C8451T", + "C8454T", + "C8487T", + "T8493C", + "T8496C", + "A8523G", + "C8572A", + "T8628C", + "T8634C", + "G8706A", + "G8712C", + "G9451A", + "C9499A", + "G9510A", + "T9513A", + "C9525T", + "A9528G", + "G9534A", + "T9576C", + "C9591T", + "G9603A", + "G9612A", + "A9628G", + "A9633G", + "G9645A", + "A9662G", + "C9693T", + "A9714G", + "C9715T", + "T9720C", + "T9729C", + "T9859C", + "T9867C", + "G9876A", + "C9885T", + "T9900C", + "C9903T", + "G9918C", + "C9927T" + ] + } + } + }, + { + "name": "OQ028222.1|2019-06-25", + "node_attrs": { + "div": 0.306, + "clade_membership": { + "value": "2V_A.1.1" + }, + "country": { + "value": "Viet Nam" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T528C", + "A1304G", + "T1365C", + "C2685T", + "T2730C", + "T2808C", + "A3567G", + "T3570C", + "G3886A", + "A4656G", + "C4659T", + "A4879G", + "C5421T", + "A5919G", + "T6094C", + "A6099G", + "A6270G", + "A6354G", + "A6519G", + "C6528T", + "A6531G", + "C6556T", + "T6561C", + "A6573C", + "G6576A", + "T6657C", + "T6658C", + "C7182T", + "A7329G", + "G7482A", + "T7509C", + "C7614T", + "T7680C", + "A7878G", + "T7996C", + "G8331A", + "G8886A", + "C9597T", + "A9654G", + "T9705C", + "A9969G" + ] + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } ] } ] @@ -22415,9 +18823,9 @@ ] }, { - "name": "NODE_0000087", + "name": "NODE_0000097", "node_attrs": { - "div": 0.25853153, + "div": 0.259, "clade_membership": { "value": "2III" } @@ -22709,64 +19117,17 @@ "A10230G", "A10242G", "A10260T" - ], - "C": [ - "N10S", - "M104V", - "V112A" - ], - "E": [ - "N203D", - "V308I", - "V491A" - ], - "M": [ - "S15G", - "M39I", - "A120V" - ], - "NS1": [ - "I212M" - ], - "NS2A": [ - "T104A", - "V109A", - "L153S", - "V174A" - ], - "NS3": [ - "K61R", - "I140V", - "K142R" - ], - "NS4A": [ - "R76K" - ], - "NS4B": [ - "Q22E", - "I48V", - "V175I" - ], - "NS5": [ - "V156I", - "A196T", - "S225T", - "R246K", - "V628I", - "R749K", - "I836V" ] }, "labels": { - "aa": "C: N10S, M104V, V112A; E: N203D, V308I, V491A; M: S15G, M39I, A120V; NS1: I212M; NS2A: T104A, V109A, L153S, V174A; NS3: K61R, I140V, K142R; NS4A: R76K; NS4B: Q22E, I48V, V175I; NS5: V156I, A196T, S225T, R246K, V628I, R749K, I836V", "lineage": "2III" } }, "children": [ { - "name": "NODE_0000088", + "name": "NODE_0000098", "node_attrs": { - "div": 0.26286764, + "div": 0.263, "clade_membership": { "value": "2III_A" } @@ -22815,30 +19176,17 @@ "C9957T", "A10062G", "G10089A" - ], - "E": [ - "V129I" - ], - "NS1": [ - "H261Y" - ], - "NS2B": [ - "A57T" - ], - "NS5": [ - "N166S" ] }, "labels": { - "aa": "E: V129I; NS1: H261Y; NS2B: A57T; NS5: N166S", "lineage": "2III_A" } }, "children": [ { - "name": "NODE_0000089", + "name": "NODE_0000099", "node_attrs": { - "div": 0.26753323, + "div": 0.268, "clade_membership": { "value": "2III_A" } @@ -22894,44 +19242,19 @@ "A9915G", "T10084C", "T10188C" - ], - "C": [ - "I106V" - ], - "E": [ - "N83K" - ], - "M": [ - "N7D", - "R151K" - ], - "NS1": [ - "I21V" - ], - "NS2A": [ - "V12I" - ], - "NS2B": [ - "I116L" - ], - "NS3": [ - "H348Y" ] - }, - "labels": { - "aa": "C: I106V; E: N83K; M: N7D, R151K; NS1: I21V; NS2A: V12I; NS2B: I116L; NS3: H348Y" } }, "children": [ { "name": "MW946461.1|1988", "node_attrs": { - "div": 0.27236457000000003, - "country": { - "value": "Thailand" - }, + "div": 0.272, "clade_membership": { "value": "2III_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -22984,41 +19307,19 @@ "T9708C", "A9750G", "C10077T" - ], - "E": [ - "T226K", - "S474P" - ], - "M": [ - "I135M" - ], - "NS1": [ - "A43T" - ], - "NS2A": [ - "A189T" - ], - "NS4B": [ - "V48I" - ], - "NS5": [ - "N555K" ] - }, - "labels": { - "aa": "E: T226K, S474P; M: I135M; NS1: A43T; NS2A: A189T; NS4B: V48I; NS5: N555K" } } }, { "name": "DQ181801.1|1990", "node_attrs": { - "div": 0.2751063, - "country": { - "value": "Thailand" - }, + "div": 0.275, "clade_membership": { "value": "2III_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -23102,39 +19403,16 @@ "T9657C", "T9811C", "G9816A" - ], - "E": [ - "M96I" - ], - "NS1": [ - "N24S", - "A99V" - ], - "NS2A": [ - "A37T" - ], - "NS3": [ - "N556S" - ], - "NS4B": [ - "L15F", - "N245S" - ], - "NS5": [ - "N645S" ] - }, - "labels": { - "aa": "E: M96I; NS1: N24S, A99V; NS2A: A37T; NS3: N556S; NS4B: L15F, N245S; NS5: N645S" } } } ] }, { - "name": "NODE_0000090", + "name": "NODE_0000100", "node_attrs": { - "div": 0.26906271000000004, + "div": 0.269, "clade_membership": { "value": "2III_A" } @@ -23202,35 +19480,14 @@ "C9453T", "A9780G", "C10083T" - ], - "E": [ - "V485I" - ], - "M": [ - "V120A" - ], - "NS1": [ - "N246S" - ], - "NS3": [ - "I567V" - ], - "NS4A": [ - "I78V" - ], - "NS5": [ - "N175D" ] - }, - "labels": { - "aa": "E: V485I; M: V120A; NS1: N246S; NS3: I567V; NS4A: I78V; NS5: N175D" } }, "children": [ { - "name": "NODE_0000091", + "name": "NODE_0000101", "node_attrs": { - "div": 0.27027655000000006, + "div": 0.27, "clade_membership": { "value": "2III_A" } @@ -23258,25 +19515,19 @@ "C8571T", "T9019C", "T9828C" - ], - "E": [ - "Q52E" ] - }, - "labels": { - "aa": "E: Q52E" } }, "children": [ { "name": "KF921931.1|2003", "node_attrs": { - "div": 0.2831029500000001, - "country": { - "value": "Cambodia" - }, + "div": 0.283, "clade_membership": { "value": "2III_A" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -23403,46 +19654,19 @@ "C10032T", "T10084C", "C10155T" - ], - "E": [ - "I170S", - "I432M" - ], - "M": [ - "A120V" - ], - "NS2A": [ - "F40L" - ], - "NS3": [ - "R322K" - ], - "NS4A": [ - "I68V" - ], - "NS4B": [ - "I105V" - ], - "NS5": [ - "R98K", - "S523G", - "V637A" ] - }, - "labels": { - "aa": "E: I170S, I432M; M: A120V; NS2A: F40L; NS3: R322K; NS4A: I68V; NS4B: I105V; NS5: R98K, S523G, V637A" } } }, { "name": "FJ639699.1|2002", "node_attrs": { - "div": 0.28226625000000005, - "country": { - "value": "Cambodia" - }, + "div": 0.282, "clade_membership": { "value": "2III_A" + }, + "country": { + "value": "Cambodia" } }, "branch_attrs": { @@ -23560,41 +19784,16 @@ "G10071A", "T10083C", "A10203G" - ], - "E": [ - "T120S", - "V358I" - ], - "NS1": [ - "R172K", - "S246G" - ], - "NS2A": [ - "V133I" - ], - "NS4A": [ - "A36V" - ], - "NS5": [ - "S23N", - "E379K", - "M393I", - "R401K", - "H634Y", - "I641V" ] - }, - "labels": { - "aa": "E: T120S, V358I; NS1: R172K, S246G; NS2A: V133I; NS4A: A36V; NS5: S23N, E379K, M393I, R401K, H634Y, I641V" } } } ] }, { - "name": "NODE_0000092", + "name": "NODE_0000102", "node_attrs": { - "div": 0.26956852000000003, + "div": 0.27, "clade_membership": { "value": "2III_A" } @@ -23612,9 +19811,9 @@ }, "children": [ { - "name": "NODE_0000093", + "name": "NODE_0000103", "node_attrs": { - "div": 0.27503322, + "div": 0.275, "clade_membership": { "value": "2III_A.1" } @@ -23671,20 +19870,9 @@ "A9969G", "A10035T", "A10089G" - ], - "E": [ - "S169P" - ], - "M": [ - "I144V", - "T159A" - ], - "NS2A": [ - "T63A" ] }, "labels": { - "aa": "E: S169P; M: I144V, T159A; NS2A: T63A", "lineage": "2III_A.1" } }, @@ -23692,12 +19880,12 @@ { "name": "FM210237.2|2003", "node_attrs": { - "div": 0.2819806, - "country": { - "value": "Vietnam" - }, + "div": 0.282, "clade_membership": { "value": "2III_A.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -23780,27 +19968,14 @@ "C9741T", "T9840C", "T9933C" - ], - "E": [ - "V461A" - ], - "NS2A": [ - "A37T", - "L181I" - ], - "NS5": [ - "K563R" ] - }, - "labels": { - "aa": "E: V461A; NS2A: A37T, L181I; NS5: K563R" } } }, { - "name": "NODE_0000094", + "name": "NODE_0000104", "node_attrs": { - "div": 0.27797579, + "div": 0.278, "clade_membership": { "value": "2III_A.1" } @@ -23837,20 +20012,14 @@ "C9034T", "A9273T", "A9354G" - ], - "NS2B": [ - "S79A" ] - }, - "labels": { - "aa": "NS2B: S79A" } }, "children": [ { - "name": "NODE_0000095", + "name": "NODE_0000105", "node_attrs": { - "div": 0.28160678, + "div": 0.282, "clade_membership": { "value": "2III_A.1" } @@ -23898,34 +20067,19 @@ "A9451G", "T9840C", "T9933C" - ], - "C": [ - "I72V" - ], - "NS2A": [ - "A37T" - ], - "NS4B": [ - "I150V" - ], - "NS5": [ - "I628V" ] - }, - "labels": { - "aa": "C: I72V; NS2A: A37T; NS4B: I150V; NS5: I628V" } }, "children": [ { "name": "FM210236.2|2004", "node_attrs": { - "div": 0.28416193, - "country": { - "value": "Vietnam" - }, + "div": 0.284, "clade_membership": { "value": "2III_A.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -23957,36 +20111,19 @@ "C9693T", "G9804A", "G10059A" - ], - "E": [ - "E202K" - ], - "NS1": [ - "F178L" - ], - "NS2A": [ - "L181I" - ], - "NS5": [ - "N96D", - "D521E", - "N701K" ] - }, - "labels": { - "aa": "E: E202K; NS1: F178L; NS2A: L181I; NS5: N96D, D521E, N701K" } } }, { "name": "FM210235.2|2005", "node_attrs": { - "div": 0.28495533, - "country": { - "value": "Vietnam" - }, + "div": 0.285, "clade_membership": { "value": "2III_A.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24026,33 +20163,16 @@ "A9156G", "A9470G", "C10110T" - ], - "E": [ - "K93R" - ], - "NS2A": [ - "A195E", - "L196W", - "T197S" - ], - "NS4B": [ - "Q21R" - ], - "NS5": [ - "H634R" ] - }, - "labels": { - "aa": "E: K93R; NS2A: A195E, L196W, T197S; NS4B: Q21R; NS5: H634R" } } } ] }, { - "name": "NODE_0000096", + "name": "NODE_0000106", "node_attrs": { - "div": 0.28051751, + "div": 0.281, "clade_membership": { "value": "2III_A.1" } @@ -24079,28 +20199,19 @@ "T9811C", "T9900C", "T9903C" - ], - "NS2A": [ - "A174T" - ], - "NS4A": [ - "Y97H" ] - }, - "labels": { - "aa": "NS2A: A174T; NS4A: Y97H" } }, "children": [ { "name": "FM210217.1|1999", "node_attrs": { - "div": 0.28552966, - "country": { - "value": "Vietnam" - }, + "div": 0.286, "clade_membership": { "value": "2III_A.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24153,34 +20264,19 @@ "T9708C", "C9729T", "T9774C" - ], - "M": [ - "E85D" - ], - "NS2A": [ - "M70I" - ], - "NS3": [ - "R322K" - ], - "NS5": [ - "V637A" ] - }, - "labels": { - "aa": "M: E85D; NS2A: M70I; NS3: R322K; NS5: V637A" } } }, { "name": "FM210222.1|2004", "node_attrs": { - "div": 0.28506329, - "country": { - "value": "Vietnam" - }, + "div": 0.285, "clade_membership": { "value": "2III_A.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24232,25 +20328,7 @@ "T9828C", "G9861A", "C10263T" - ], - "C": [ - "A8V", - "R9S", - "S10I", - "T11L", - "P12A", - "A112V" - ], - "E": [ - "T359I", - "T473S" - ], - "NS5": [ - "N96D" ] - }, - "labels": { - "aa": "C: A8V, R9S, S10I, T11L, P12A, A112V; E: T359I, T473S; NS5: N96D" } } } @@ -24261,9 +20339,9 @@ ] }, { - "name": "NODE_0000097", + "name": "NODE_0000107", "node_attrs": { - "div": 0.27576485000000006, + "div": 0.276, "clade_membership": { "value": "2III_A.2" } @@ -24333,17 +20411,9 @@ "T9732C", "A9744G", "G10200A" - ], - "E": [ - "V461A" - ], - "NS5": [ - "K563R", - "R698K" ] }, "labels": { - "aa": "E: V461A; NS5: K563R, R698K", "lineage": "2III_A.2" } }, @@ -24351,12 +20421,12 @@ { "name": "KY670633.1|1995-09", "node_attrs": { - "div": 0.27576585000000003, - "country": { - "value": "Taiwan" - }, + "div": 0.276, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Taiwan" } }, "branch_attrs": { @@ -24364,9 +20434,9 @@ } }, { - "name": "NODE_0000098", + "name": "NODE_0000108", "node_attrs": { - "div": 0.27596237000000007, + "div": 0.276, "clade_membership": { "value": "2III_A.2" } @@ -24380,9 +20450,9 @@ }, "children": [ { - "name": "NODE_0000099", + "name": "NODE_0000109", "node_attrs": { - "div": 0.28091423000000004, + "div": 0.281, "clade_membership": { "value": "2III_A.2" } @@ -24441,37 +20511,19 @@ "C9735T", "C9843T", "T9903C" - ], - "C": [ - "A52T" - ], - "E": [ - "I170V" - ], - "NS1": [ - "Y261H" - ], - "NS4B": [ - "I18V" - ], - "NS5": [ - "E715D" ] - }, - "labels": { - "aa": "C: A52T; E: I170V; NS1: Y261H; NS4B: I18V; NS5: E715D" } }, "children": [ { "name": "FM210204.1|2003", "node_attrs": { - "div": 0.28318608000000006, - "country": { - "value": "Vietnam" - }, + "div": 0.283, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24500,32 +20552,19 @@ "A9423G", "T9564C", "G9744A" - ], - "NS1": [ - "H50Y", - "P138L" - ], - "NS2A": [ - "R51K" - ], - "NS5": [ - "S189P" ] - }, - "labels": { - "aa": "NS1: H50Y, P138L; NS2A: R51K; NS5: S189P" } } }, { "name": "FM210227.1|2002", "node_attrs": { - "div": 0.28347517000000005, - "country": { - "value": "Vietnam" - }, + "div": 0.283, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24557,31 +20596,16 @@ "C9369T", "C9381T", "G9912A" - ], - "NS1": [ - "A205T" - ], - "NS2A": [ - "V133I" - ], - "NS3": [ - "S346F" - ], - "NS5": [ - "E558G" ] - }, - "labels": { - "aa": "NS1: A205T; NS2A: V133I; NS3: S346F; NS5: E558G" } } } ] }, { - "name": "NODE_0000100", + "name": "NODE_0000110", "node_attrs": { - "div": 0.27951828000000006, + "div": 0.28, "clade_membership": { "value": "2III_A.2" } @@ -24621,28 +20645,19 @@ "C9741T", "A9936T", "C10155T" - ], - "NS3": [ - "M333I" - ], - "NS4B": [ - "V115I" ] - }, - "labels": { - "aa": "NS3: M333I; NS4B: V115I" } }, "children": [ { "name": "FM210202.1|2004", "node_attrs": { - "div": 0.2839267200000001, - "country": { - "value": "Vietnam" - }, + "div": 0.284, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24685,27 +20700,14 @@ "T9657C", "C9672T", "T9972C" - ], - "E": [ - "S169P", - "A491V" - ], - "NS2A": [ - "L181I" - ], - "NS4B": [ - "I18V" ] - }, - "labels": { - "aa": "E: S169P, A491V; NS2A: L181I; NS4B: I18V" } } }, { - "name": "NODE_0000101", + "name": "NODE_0000111", "node_attrs": { - "div": 0.2810047500000001, + "div": 0.281, "clade_membership": { "value": "2III_A.2" } @@ -24740,12 +20742,12 @@ { "name": "EU482449.1|2006", "node_attrs": { - "div": 0.2855371500000001, - "country": { - "value": "Vietnam" - }, + "div": 0.286, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24797,34 +20799,19 @@ "G9816A", "G9822T", "T10155C" - ], - "E": [ - "I170N" - ], - "NS2A": [ - "V41M" - ], - "NS3": [ - "N345S" - ], - "NS4A": [ - "C86F" ] - }, - "labels": { - "aa": "E: I170N; NS2A: V41M; NS3: N345S; NS4A: C86F" } } }, { "name": "FM210241.2|2004", "node_attrs": { - "div": 0.2839671700000001, - "country": { - "value": "Vietnam" - }, + "div": 0.284, "clade_membership": { "value": "2III_A.2" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -24860,16 +20847,7 @@ "T9429C", "A9945G", "C10215T" - ], - "NS4B": [ - "L113S" - ], - "NS5": [ - "L619F" ] - }, - "labels": { - "aa": "NS4B: L113S; NS5: L619F" } } } @@ -24888,9 +20866,9 @@ ] }, { - "name": "NODE_0000102", + "name": "NODE_0000112", "node_attrs": { - "div": 0.26637155, + "div": 0.266, "clade_membership": { "value": "2III" } @@ -24981,44 +20959,19 @@ "A10035G", "G10071A", "T10212C" - ], - "E": [ - "V91I", - "Q131L" - ], - "NS2B": [ - "L109V" - ], - "NS3": [ - "K28R", - "T399A" - ], - "NS4B": [ - "A19T", - "P23S" - ], - "NS5": [ - "K437R", - "E501G", - "I717V", - "S763T", - "T811A" ] - }, - "labels": { - "aa": "E: V91I, Q131L; NS2B: L109V; NS3: K28R, T399A; NS4B: A19T, P23S; NS5: K437R, E501G, I717V, S763T, T811A" } }, "children": [ { "name": "OK469346.1|1981", "node_attrs": { - "div": 0.26860956, - "country": { - "value": "Jamaica" - }, + "div": 0.269, "clade_membership": { "value": "2III" + }, + "country": { + "value": "Jamaica" } }, "branch_attrs": { @@ -25048,33 +21001,14 @@ "C8329A", "C9420T", "C10011T" - ], - "E": [ - "I6M", - "I91L" - ], - "M": [ - "T81A" - ], - "NS2B": [ - "T94I" - ], - "NS3": [ - "R61K" - ], - "NS5": [ - "P254T" ] - }, - "labels": { - "aa": "E: I6M, I91L; M: T81A; NS2B: T94I; NS3: R61K; NS5: P254T" } } }, { - "name": "NODE_0000103", + "name": "NODE_0000113", "node_attrs": { - "div": 0.26784568000000003, + "div": 0.268, "clade_membership": { "value": "2III" } @@ -25097,24 +21031,14 @@ "A9110G", "G9241A", "T9903C" - ], - "NS4B": [ - "D156E" - ], - "NS5": [ - "K514R", - "E558K" ] - }, - "labels": { - "aa": "NS4B: D156E; NS5: K514R, E558K" } }, "children": [ { - "name": "NODE_0000104", + "name": "NODE_0000114", "node_attrs": { - "div": 0.26813743, + "div": 0.268, "clade_membership": { "value": "2III" } @@ -25132,10 +21056,7 @@ { "name": "GQ868603.1|1987", "node_attrs": { - "div": 0.27217558000000003, - "country": { - "value": "Virgin Islands" - }, + "div": 0.272, "clade_membership": { "value": "2III" } @@ -25185,40 +21106,14 @@ "T9399C", "C10011T", "G10059A" - ], - "C": [ - "P60S" - ], - "E": [ - "I91L" - ], - "NS1": [ - "F178L" - ], - "NS2A": [ - "V36A", - "A146V", - "Q186R" - ], - "NS4A": [ - "I78V" - ], - "NS4B": [ - "V48F" - ], - "NS5": [ - "T390I" ] - }, - "labels": { - "aa": "C: P60S; E: I91L; NS1: F178L; NS2A: V36A, A146V, Q186R; NS4A: I78V; NS4B: V48F; NS5: T390I" } } }, { - "name": "NODE_0000105", + "name": "NODE_0000115", "node_attrs": { - "div": 0.2706697, + "div": 0.271, "clade_membership": { "value": "2III_B" } @@ -25250,27 +21145,17 @@ "C8697T", "A8835T", "T9372C" - ], - "NS2B": [ - "I8V" - ], - "NS3": [ - "K418R" - ], - "NS5": [ - "K375R" ] }, "labels": { - "aa": "NS2B: I8V; NS3: K418R; NS5: K375R", "lineage": "2III_B" } }, "children": [ { - "name": "NODE_0000106", + "name": "NODE_0000116", "node_attrs": { - "div": 0.27520855, + "div": 0.275, "clade_membership": { "value": "2III_B" } @@ -25314,35 +21199,19 @@ "G8817A", "C9018T", "T9675C" - ], - "E": [ - "D203E" - ], - "M": [ - "T134A" - ], - "NS2A": [ - "Q162L", - "A189T" - ], - "NS3": [ - "G14E" ] - }, - "labels": { - "aa": "E: D203E; M: T134A; NS2A: Q162L, A189T; NS3: G14E" } }, "children": [ { "name": "KC294201.1|2009-02-13", "node_attrs": { - "div": 0.28933735, - "country": { - "value": "Peru" - }, + "div": 0.289, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "Peru" } }, "branch_attrs": { @@ -25489,61 +21358,19 @@ "C10208T", "A10209G", "C10263G" - ], - "C": [ - "L35F", - "R97K" - ], - "E": [ - "V428M" - ], - "M": [ - "R16K", - "T125N" - ], - "NS1": [ - "D208G", - "I242V" - ], - "NS2A": [ - "H2Y", - "T42A", - "M57I", - "A62V", - "A109T", - "L121F", - "A174V" - ], - "NS2B": [ - "D63E", - "I76V" - ], - "NS3": [ - "R418K", - "I461V" - ], - "NS5": [ - "I271T", - "R375K", - "Q864K", - "I874M", - "T880M" ] - }, - "labels": { - "aa": "C: L35F, R97K; E: V428M; M: R16K, T125N; NS1: D208G, I242V; NS2A: H2Y, T42A, M57I, A62V, A109T, L121F, A174V; NS2B: D63E, I76V; NS3: R418K, I461V; NS5: I271T, R375K, Q864K, I874M, T880M" } } }, { "name": "MN589880.1|1999-04-09", "node_attrs": { - "div": 0.28903105, - "country": { - "value": "Brazil" - }, + "div": 0.289, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -25658,59 +21485,16 @@ "C10155T", "A10161G", "T10173C" - ], - "C": [ - "I94T" - ], - "E": [ - "V129I", - "L131Q", - "M201I", - "M340T", - "G395V" - ], - "NS1": [ - "T164S" - ], - "NS2A": [ - "M57L", - "I116L", - "K135R" - ], - "NS2B": [ - "V8I" - ], - "NS3": [ - "T583I" - ], - "NS4A": [ - "N42K" - ], - "NS4B": [ - "E7Q" - ], - "NS5": [ - "V354L", - "F355L", - "T361X", - "K388E", - "I412V", - "R596K", - "H786Y", - "I797X" ] - }, - "labels": { - "aa": "C: I94T; E: V129I, L131Q, M201I, M340T, G395V; NS1: T164S; NS2A: M57L, I116L, K135R; NS2B: V8I; NS3: T583I; NS4A: N42K; NS4B: E7Q; NS5: V354L, F355L, T361X, K388E, I412V, R596K, H786Y, I797X" } } } ] }, { - "name": "NODE_0000107", + "name": "NODE_0000117", "node_attrs": { - "div": 0.27163127000000004, + "div": 0.272, "clade_membership": { "value": "2III_B" } @@ -25729,12 +21513,12 @@ { "name": "FJ898450.1|1990", "node_attrs": { - "div": 0.27403644000000005, - "country": { - "value": "Virgin Islands" - }, + "div": 0.274, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "Virgin Islands" } }, "branch_attrs": { @@ -25773,23 +21557,14 @@ "G9519A", "T9639C", "C10011T" - ], - "NS1": [ - "V177A" - ], - "NS5": [ - "K301R" ] - }, - "labels": { - "aa": "NS1: V177A; NS5: K301R" } } }, { - "name": "NODE_0000108", + "name": "NODE_0000118", "node_attrs": { - "div": 0.27337674000000006, + "div": 0.273, "clade_membership": { "value": "2III_B" } @@ -25813,28 +21588,19 @@ "G10086A", "T10140C", "A10167G" - ], - "E": [ - "A491V" - ], - "NS5": [ - "R596K" ] - }, - "labels": { - "aa": "E: A491V; NS5: R596K" } }, "children": [ { "name": "GQ398269.1|1994", "node_attrs": { - "div": 0.28807054000000004, - "country": { - "value": "Puerto Rico" - }, + "div": 0.288, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "Puerto Rico" } }, "branch_attrs": { @@ -25980,46 +21746,14 @@ "A10131G", "A10221T", "A10245G" - ], - "E": [ - "D203G" - ], - "M": [ - "T81A" - ], - "NS1": [ - "S80L", - "L124F", - "V346I" - ], - "NS2B": [ - "V109L" - ], - "NS3": [ - "R28K", - "R61K", - "T120A", - "V140I", - "R142K", - "K186R", - "R187K", - "N345S", - "A399T", - "R418K" - ], - "NS4B": [ - "T19A" ] - }, - "labels": { - "aa": "E: D203G; M: T81A; NS1: S80L, L124F, V346I; NS2B: V109L; NS3: R28K, R61K, T120A, V140I, R142K, K186R, R187K, N345S, A399T, R418K; NS4B: T19A" } } }, { - "name": "NODE_0000109", + "name": "NODE_0000119", "node_attrs": { - "div": 0.28494924000000005, + "div": 0.285, "clade_membership": { "value": "2III_B" } @@ -26113,44 +21847,19 @@ "C9859T", "G10230A", "G10241A" - ], - "E": [ - "L131Q" - ], - "NS1": [ - "S2T", - "T164S", - "V220I" - ], - "NS2A": [ - "V27I" - ], - "NS2B": [ - "Q93H" - ], - "NS3": [ - "L31F" - ], - "NS5": [ - "T196A", - "H634R", - "R891K" ] - }, - "labels": { - "aa": "E: L131Q; NS1: S2T, T164S, V220I; NS2A: V27I; NS2B: Q93H; NS3: L31F; NS5: T196A, H634R, R891K" } }, "children": [ { "name": "EU529706.1|2006", "node_attrs": { - "div": 0.29299053, - "country": { - "value": "USA" - }, + "div": 0.293, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -26224,40 +21933,19 @@ "T9402C", "C9532T", "T9561C" - ], - "NS1": [ - "F279L" - ], - "NS4A": [ - "A36V" - ], - "NS4B": [ - "K80R", - "A137T", - "I175V" - ], - "NS5": [ - "I156V", - "I180V", - "R326K", - "K387R", - "R514K" ] - }, - "labels": { - "aa": "NS1: F279L; NS4A: A36V; NS4B: K80R, A137T, I175V; NS5: I156V, I180V, R326K, K387R, R514K" } } }, { "name": "EU482721.1|2006", "node_attrs": { - "div": 0.29693504000000004, - "country": { - "value": "USA" - }, + "div": 0.297, "clade_membership": { "value": "2III_B" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -26329,24 +22017,7 @@ "C9405T", "G9736A", "A9897G" - ], - "E": [ - "V484I" - ], - "M": [ - "I135T" - ], - "NS2B": [ - "V8I" - ], - "NS5": [ - "R375K", - "S429G", - "V723M" ] - }, - "labels": { - "aa": "E: V484I; M: I135T; NS2B: V8I; NS5: R375K, S429G, V723M" } } } @@ -26361,9 +22032,9 @@ ] }, { - "name": "NODE_0000110", + "name": "NODE_0000120", "node_attrs": { - "div": 0.27347982000000004, + "div": 0.273, "clade_membership": { "value": "2III" } @@ -26427,34 +22098,14 @@ "T9043C", "C9411T", "T9577A" - ], - "C": [ - "I106V" - ], - "E": [ - "L131Q" - ], - "NS3": [ - "L115I", - "R549K" - ], - "NS4A": [ - "D23N" - ], - "NS5": [ - "S429G", - "L670I" ] - }, - "labels": { - "aa": "C: I106V; E: L131Q; NS3: L115I, R549K; NS4A: D23N; NS5: S429G, L670I" } }, "children": [ { - "name": "NODE_0000111", + "name": "NODE_0000121", "node_attrs": { - "div": 0.27741025, + "div": 0.277, "clade_membership": { "value": "2III_E" } @@ -26505,20 +22156,9 @@ "T9508C", "C10110T", "T10173C" - ], - "NS2A": [ - "V133A", - "R138K" - ], - "NS3": [ - "I77V" - ], - "NS4A": [ - "R39K" ] }, "labels": { - "aa": "NS2A: V133A, R138K; NS3: I77V; NS4A: R39K", "lineage": "2III_E" } }, @@ -26526,12 +22166,12 @@ { "name": "EU482545.1|1998", "node_attrs": { - "div": 0.28135188, - "country": { - "value": "USA" - }, + "div": 0.281, "clade_membership": { "value": "2III_E" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -26575,26 +22215,14 @@ "G9795A", "A9939G", "A9990G" - ], - "E": [ - "V129I", - "V140M", - "I432V" - ], - "NS2B": [ - "K87R", - "I116V" ] - }, - "labels": { - "aa": "E: V129I, V140M, I432V; NS2B: K87R, I116V" } } }, { - "name": "NODE_0000112", + "name": "NODE_0000122", "node_attrs": { - "div": 0.27997827000000003, + "div": 0.28, "clade_membership": { "value": "2III_E" } @@ -26627,28 +22255,19 @@ "C7473T", "T9411C", "G9596A" - ], - "NS2A": [ - "I108V" - ], - "NS5": [ - "S676N" ] - }, - "labels": { - "aa": "NS2A: I108V; NS5: S676N" } }, "children": [ { "name": "EU920835.1|2002-04", "node_attrs": { - "div": 0.28362754, - "country": { - "value": "French Guiana" - }, + "div": 0.284, "clade_membership": { "value": "2III_E" + }, + "country": { + "value": "French Guiana" } }, "branch_attrs": { @@ -26694,30 +22313,14 @@ "G9522A", "G9662A", "C9963T" - ], - "C": [ - "L50F" - ], - "E": [ - "E360G" - ], - "NS2A": [ - "K138R" - ], - "NS5": [ - "T390I", - "R698K" ] - }, - "labels": { - "aa": "C: L50F; E: E360G; NS2A: K138R; NS5: T390I, R698K" } } }, { - "name": "NODE_0000113", + "name": "NODE_0000123", "node_attrs": { - "div": 0.28244479, + "div": 0.282, "clade_membership": { "value": "2III_E" } @@ -26749,28 +22352,19 @@ "T9429C", "T9535A", "C10206T" - ], - "E": [ - "I61V" - ], - "NS5": [ - "S656T" ] - }, - "labels": { - "aa": "E: I61V; NS5: S656T" } }, "children": [ { "name": "FJ850085.1|2005", "node_attrs": { - "div": 0.2880733, - "country": { - "value": "Brazil" - }, + "div": 0.288, "clade_membership": { "value": "2III_E" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -26835,39 +22429,14 @@ "T10188C", "A10202G", "G10254A" - ], - "C": [ - "A102V" - ], - "E": [ - "T359A" - ], - "M": [ - "D29N" - ], - "NS1": [ - "I188V" - ], - "NS3": [ - "D20E", - "E169D" - ], - "NS5": [ - "I271V", - "T390I", - "V553I", - "E878G" ] - }, - "labels": { - "aa": "C: A102V; E: T359A; M: D29N; NS1: I188V; NS3: D20E, E169D; NS5: I271V, T390I, V553I, E878G" } } }, { - "name": "NODE_0000114", + "name": "NODE_0000124", "node_attrs": { - "div": 0.28559213, + "div": 0.286, "clade_membership": { "value": "2III_E" } @@ -26901,34 +22470,19 @@ "A8760G", "A9174G", "C10194T" - ], - "C": [ - "A112V" - ], - "M": [ - "I135M" - ], - "NS1": [ - "S125P" - ], - "NS3": [ - "A399S" ] - }, - "labels": { - "aa": "C: A112V; M: I135M; NS1: S125P; NS3: A399S" } }, "children": [ { "name": "EU920840.1|2005-10", "node_attrs": { - "div": 0.28895207, - "country": { - "value": "French Guiana" - }, + "div": 0.289, "clade_membership": { "value": "2III_E" + }, + "country": { + "value": "French Guiana" } }, "branch_attrs": { @@ -26969,28 +22523,19 @@ "C9783T", "A10098G", "G10254A" - ], - "NS2B": [ - "I26V" - ], - "NS3": [ - "P465S" ] - }, - "labels": { - "aa": "NS2B: I26V; NS3: P465S" } } }, { "name": "FJ850088.1|2006", "node_attrs": { - "div": 0.29132244, - "country": { - "value": "Brazil" - }, + "div": 0.291, "clade_membership": { "value": "2III_E" + }, + "country": { + "value": "Brazil" } }, "branch_attrs": { @@ -27054,39 +22599,7 @@ "T9942C", "C10134T", "T10188C" - ], - "E": [ - "I162V", - "I380V", - "S449N" - ], - "NS1": [ - "T146A" - ], - "NS2A": [ - "F40L", - "I136V" - ], - "NS2B": [ - "I8V" - ], - "NS3": [ - "G14E" - ], - "NS4A": [ - "T59A" - ], - "NS4B": [ - "I239V" - ], - 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"clade_membership": { + "value": "2III_C.1.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C5070T", + "A10095G" + ] + } + }, + "children": [ + { + "name": "ON634752.1|2022-03-17", + "node_attrs": { + "div": 0.304, + "clade_membership": { + "value": "2III_C.1.1" + }, + "country": { + "value": "Brazil" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G570A", + "T1287C", + "T1662C", + "T1926C", + "T1944G", + "T2221C", + "A2911T", + "C3666T", + "T3768C", + "G3787A", + "A3790T", + "C3801T", + "C3807G", + "C3808A", + "T3810G", + "T3811A", + "A3815C", + "C3819G", + "C3821A", + "C3822T", + "T3837C", + "T3839A", + "C3844T", + "C3854A", + "G3855C", + "T3856C", + "T4221A", + "G4336T", + "G4337T", + "A4339T", + "G4340T", + "C4341A", + "G4343T", + "C4345A", + "A4348G", + "T4349G", + "C4350A", + "C4351T", + "C4612T", + "T5145A", + "T6408C", + "G6465A", + "C6771T", + "A6936G", + "C7165T", + "C7704A", + "T7731C", + "T7776C", + "C8088T", + "A8107G", + "T8712C", + "G8880A", + "T9027C", + "G9861A", + "A9924G", + "C10084T", + "A10168G" + ] + } + } + }, + { + "name": "ON634701.1|2021-05-28", + "node_attrs": { + "div": 0.301, + "clade_membership": { + "value": "2III_C.1.1" + }, + "country": { + "value": "Brazil" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G1084A", + "G1152A", + "C1180T", + "A1248G", + "T1470C", + "T1737C", + "C2481T", + "A2714C", + "C3075T", + "T3514C", + "T3609C", + "G3756T", + "A3760G", + "A3761G", + "A3909G", + "T4098C", + "G4440A", + "A4557G", + "C4875T", + "T6081C", + "T6307C", + "A6402G", + "T6648C", + "T6918C", + "G7191A", + "G7401A", + "C7614T", + "A7878G", + "C8241T", + "C8571A", + "A9603G", + "T9811C" + ] + } + } + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + } + ] + }, + { + "name": "NODE_0000194", + "node_attrs": { + "div": 0.245, + "clade_membership": { + "value": "2II" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "A228G", + "G252A", + "G294A", + "T336C", + "G588T", + "G594T", + "T678C", + "A682G", + "A702G", + "T795C", + "C856T", + "C880T", + "C945T", + "A1148C", + "C1218T", + "T1251C", + "T1275C", + "C1353T", + "C1381A", + "C1576T", + "A1638G", + "C1713T", + "C1728T", + "A1740G", + "C1842T", + "C1926T", + "A2010T", + "C2073T", + "T2095C", + "A2105G", + "A2320G", + "C2395T", + "C2400T", + "C2442T", + "C2481T", + "G2496A", + "G2520A", + "A2544G", + "G2577A", + "T2644C", + "G2673A", + "T2730C", + "C2850T", + "G2880A", + "T2919C", + "A2928G", + "G2936A", + "A2942G", + "C3039T", + "C3072T", + "T3075C", "C3120T", "C3162T", "A3213G", @@ -34266,54 +29268,17 @@ "T10188A", "T10212C", "C10264T" - ], - "E": [ - "E71A", - "H149N", - "N390S", - "I462V" - ], - "M": [ - "K52N", - "T82A", - "H148Y" - ], - "NS1": [ - "R172K", - "K174R" - ], - "NS2B": [ - "K60R" - ], - "NS3": [ - "I140V", - "A160T", - "V395I" - ], - "NS4A": [ - "D23N", - "R76K" - ], - "NS4B": [ - "L13F", - "T244A" - ], - "NS5": [ - "I5T", - "S15N", - "V335I" ] }, "labels": { - "aa": "E: E71A, H149N, N390S, I462V; M: K52N, T82A, H148Y; NS1: R172K, K174R; NS2B: K60R; NS3: I140V, A160T, V395I; NS4A: D23N, R76K; NS4B: L13F, T244A; NS5: I5T, S15N, V335I", "lineage": "2II" } }, "children": [ { - "name": "NODE_0000170", + "name": "NODE_0000195", "node_attrs": { - "div": 0.24903195000000003, + "div": 0.249, "clade_membership": { "value": "2II_A" } @@ -34360,19 +29325,9 @@ "T9900C", "T10173C", "C10215T" - ], - "C": [ - "V112A" - ], - "E": [ - "I164V" - ], - "NS2A": [ - "I33V" ] }, "labels": { - "aa": "C: V112A; E: I164V; NS2A: I33V", "lineage": "2II_A" } }, @@ -34380,7 +29335,7 @@ { "name": "AP002|1969", "node_attrs": { - "div": 0.25502108, + "div": 0.255, "clade_membership": { "value": "2II_A" } @@ -34447,31 +29402,14 @@ "C9360T", "T9715C", "C10011T" - ], - "M": [ - "I49V" - ], - "NS2A": [ - "H2R", - "I171T" - ], - "NS3": [ - "V72I" - ], - "NS5": [ - "A250P", - "P254S" ] - }, - "labels": { - "aa": "M: I49V; NS2A: H2R, I171T; NS3: V72I; NS5: A250P, P254S" } } }, { - "name": "NODE_0000171", + "name": "NODE_0000196", "node_attrs": { - "div": 0.25192035, + "div": 0.252, "clade_membership": { "value": "2II_A" } @@ -34516,7 +29454,7 @@ { "name": "AP001|1969-02-11", "node_attrs": { - "div": 0.25408102, + "div": 0.254, "clade_membership": { "value": "2II_A" } @@ -34545,29 +29483,14 @@ "G6875A", "A7648G", "T9208C" - ], - "E": [ - "S390N" - ], - "NS3": [ - "S346T" - ], - "NS4B": [ - "S17N" - ], - "NS5": [ - "I27V" ] - }, - "labels": { - "aa": "E: S390N; NS3: S346T; NS4B: S17N; NS5: I27V" } } }, { - "name": "NODE_0000172", + "name": "NODE_0000197", "node_attrs": { - "div": 0.25335349, + "div": 0.253, "clade_membership": { "value": "2II_A" } @@ -34591,29 +29514,14 @@ "T7048C", "C8754T", "A9460G" - ], - "NS2A": [ - "V41M" - ], - "NS3": [ - "K73R" - ], - "NS5": [ - "S631G" ] - }, - "labels": { - "aa": "NS2A: V41M; NS3: K73R; NS5: S631G" } }, "children": [ { "name": "MW946478.1|1974", "node_attrs": { - "div": 0.25838699000000004, - "country": { - "value": "India" - }, + "div": 0.258, "clade_membership": { "value": "2II_A" } @@ -34668,29 +29576,14 @@ "T9777C", "A10116G", "A10131G" - ], - "NS1": [ - "K227R" - ], - "NS4B": [ - "I18T" - ], - "NS5": [ - "K29R", - "T390A", - "H513Y", - "R596K" ] - }, - "labels": { - "aa": "NS1: K227R; NS4B: I18T; NS5: K29R, T390A, H513Y, R596K" } } }, { - "name": "NODE_0000173", + "name": "NODE_0000198", "node_attrs": { - "div": 0.26434939, + "div": 0.264, "clade_membership": { "value": "2II_A" } @@ -34805,33 +29698,14 @@ "T10122A", "C10186T", "A10260G" - ], - "E": [ - "V129I" - ], - "NS2A": [ - "T63A", - "V133I", - "S215N" - ], - "NS4B": [ - "A244T" - ], - "NS5": [ - "E616G", - "V637A", - "N645D" ] - }, - "labels": { - "aa": "E: V129I; NS2A: T63A, V133I, S215N; NS4B: A244T; NS5: E616G, V637A, N645D" } }, "children": [ { - "name": "NODE_0000174", + "name": "NODE_0000199", "node_attrs": { - "div": 0.26435228, + "div": 0.264, "clade_membership": { "value": "2II_A" } @@ -34843,12 +29717,12 @@ { "name": "JQ922551.1|2005", "node_attrs": { - "div": 0.29204728, - "country": { - "value": "India" - }, + "div": 0.292, "clade_membership": { "value": "2II_A" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -35131,132 +30005,14 @@ "C10140T", "C10155T", "G10254A" - ], - "2K": [ - "V17A" - ], - "C": [ - "N3I", - "M15R", - "L16V", - "K17T", - "N21I", - "R22H", - "Q27H", - "K31Q", - "M37K", - "L38F", - "Q39H", - "V51L", - "G64V", - "W69C", - "A102V" - ], - "E": [ - "C92R", - "I139L", - "K157N", - "E174A", - "D192N", - "N194H", - "L198S", - "Q200P", - "L207M", - "K310W", - "E311G", - "E314R", - "I322H", - "F337L", - "E338N", - "D341G", - "L351P", - "E360G", - "F373L", - "L387V", - "S390T", - "W391C", - "F392S", - "K393Q" - ], - "M": [ - "R57K", - "W117C", - "G132S", - "L153V", - "I154F", - "F155L", - "I156M", - "L157V", - "P163L" - ], - "NS1": [ - "I21V", - "N145S", - "E154K", - "V155G", - "E156G", - "F178S", - "F247L", - "F279L" - ], - "NS2A": [ - "G1E", - "G3E", - "V159M" - ], - "NS2B": [ - "V43L", - "T45P", - "V59L", - "E89Q", - "E92K", - "R100K", - "G108E", - "S113Q" - ], - "NS3": [ - "R24G", - "K112R", - "R588K" - ], - "NS4B": [ - "Q22P", - "P50S" - ], - "NS5": [ - "I180V", - "A196T", - "V359S", - "A378P", - "E379K", - "V553G", - "T554A", - "M557L", - "H561P", - "A565Y", - "V577G", - "T588P", - "V589L", - "S594L", - "R599G", - "T636I", - "L655F", - "V687E", - "D690V", - "I691L", - "G699E", - "L764Q" ] - }, - "labels": { - "aa": "2K: V17A; C: N3I, M15R, L16V, K17T, N21I, R22H, Q27H, K31Q, M37K, L38F, Q39H, V51L, G64V, W69C, A102V; E: C92R, I139L, K157N, E174A, D192N, N194H, L198S, Q200P, L207M, K310W, E311G, E314R, I322H, F337L, E338N, D341G, L351P, E360G, F373L, L387V, S390T, W391C, F392S, K393Q; M: R57K, W117C, G132S, L153V, I154F, F155L, I156M, L157V, P163L; NS1: I21V, N145S, E154K, V155G, E156G, F178S, F247L, F279L; NS2A: G1E, G3E, V159M; NS2B: V43L, T45P, V59L, E89Q, E92K, R100K, G108E, S113Q; NS3: R24G, K112R, R588K; NS4B: Q22P, P50S; NS5: I180V, A196T, V359S, A378P, E379K, V553G, T554A, M557L, H561P, A565Y, V577G, T588P, V589L, S594L, R599G, T636I, L655F, V687E, D690V, I691L, G699E, L764Q" } } }, { - "name": "NODE_0000175", + "name": "NODE_0000200", "node_attrs": { - "div": 0.26626537, + "div": 0.266, "clade_membership": { "value": "2II_A" } @@ -35265,68 +30021,28 @@ "mutations": { "nuc": [ "C459T", - "T942C", - "T960C", - "A1068G", - "G1266A", - "T1287C", - "A1317G", - "T1476C", - "C1509T", - "T1597C", - "C1701T", "C2175T", "T2556C", - "G2979A", - "A3036G", - "C3261T", - "C3330T", - "A3504G", - "C3618T", "G3756A", - "C3801T", - "C3807T", - "T3958C", - "T4047C", "C4341T", "A4989T", "G4992A", - "A5910G", "C6048T", "A6087G", "A6220G", "G6279A", - "T6366C", - "T6391C", "T8298C", "G8667A", - "A9684G", - "G9834A", - "C9870T", - "G9968A", "G10089A", - "C10140T", - "T10179C" - ], - "NS3": [ - "I567V" - ], - "NS5": [ - "R800K" + "C10140T" ] - }, - "labels": { - "aa": "NS3: I567V; NS5: R800K" } }, "children": [ { - "name": "MG560143.1|2014", + "name": "NODE_0000201", "node_attrs": { - "div": 0.28669976, - "country": { - "value": "India" - }, + "div": 0.278, "clade_membership": { "value": "2II_A" } @@ -35334,7 +30050,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "A111G", "T126C", "G318A", "G324A", @@ -35356,56 +30071,19 @@ "A873G", "C885T", "T907C", - "T945C", - "G1035A", - "T1185C", "C1443T", - "C1555T", "G1671A", - "G1794A", - "A1848G", - "T1959C", - "A2019G", - "C2055T", - "A2250G", - "T2283C", - "T2349C", - "T2364C", - "A2370G", "T2409C", "C2484T", "T2568A", "T2571C", "G2784A", - "T2868C", "C2878T", "C2910T", "C2970T", - "T3042G", - "C3045T", - "T3069C", "T3072C", - "T3183C", - "C3215T", - "T3396C", "T3454C", - "T3483C", - "G3574T", - "T3675C", - "T3684C", - "C3709T", - "C3748T", - "G3864A", - "C3876T", - "A3900G", - "C3933T", - "T3989C", - "T4009A", - "A4034G", - "A4074G", - "T4119C", "C4185T", - "C4277T", "A4294C", "C4302T", "C4414T", @@ -35421,8 +30099,6 @@ "C4848T", "C4893T", "T5025G", - "A5078G", - "G5118A", "G5121A", "C5145T", "G5169A", @@ -35433,9 +30109,7 @@ "T5556C", "T5583C", "A5586G", - "A5649G", "C5717G", - "G5736A", "C5829T", "C6015T", "C6018T", @@ -35449,15 +30123,12 @@ "T6538C", "T6606C", "T6651C", - "T6727C", "C6732G", "G6750A", "C6783T", "G6807A", - "C6841T", "C6892A", "T7011C", - "C7107T", "T7162C", "A7173G", "T7179C", @@ -35470,7 +30141,6 @@ "T7530A", "G7602A", "T7680C", - "A7788G", "G7854A", "G7977A", "C8061T", @@ -35504,56 +30174,281 @@ "G9460A", "G9519A", "T9577C", - "A9606G", - "C9639T", - "C9729T", - "A9744T", - "T9777C", - "C9843T", - "G9888A", - "G9912A", - "A10203G" - ], - "NS1": [ - "N207K", - "A265V" - ], - "NS2A": [ - "V33L", - "I171T", - "S178T", - "Q186R" - ], - "NS2B": [ - "A49V" - ], - "NS3": [ - "G14E", - "K28R", - "L31F", - "K186R", - "T399S" - ], - "NS4B": [ - "P23T", - "I150V" - ], - "NS5": [ - "E379K", - "K418R", - "G627E", - "G631S" + "C9843T" ] + } + }, + "children": 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"clade_membership": { "value": "2II_A.1.1.1" } @@ -39740,42 +34438,32 @@ "G570A", "G750A", "C2595T", - "G2610A", - "A2640C", "G2671A", - "G3392A", "T3666C", "A3843G", "C4122T", + "G5073A", "T5640C", "C7107T", "T7782C", "T7926C", "T7959C", - "C8007T", "T8469C", "A9312G", "G10248A" - ], - "NS1": [ - "V84I", - "R324K" ] - }, - "labels": { - "aa": "NS1: V84I, R324K" } }, "children": [ { "name": "ON123651.1|2020", "node_attrs": { - "div": 0.30125903000000004, - "country": { - "value": "India" - }, + "div": 0.301, "clade_membership": { "value": "2II_A.1.1.1" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -39820,6 +34508,7 @@ "G4368A", "C4377T", "C4380T", + "T4479C", "C4497T", "A4518G", "G4533A", @@ -39840,6 +34529,8 @@ "T5745C", "G5997A", "T6078C", + "A6279G", + "A6284G", "C6292T", "C6324T", "A6375G", @@ -39850,6 +34541,7 @@ "A6435G", "C6465G", "T6471C", + "A6474G", "A6480G", "T6501C", "G6546A", @@ -39871,6 +34563,7 @@ "T6786C", "G6843A", "T6862C", + "T6881C", "C6942G", "A6951C", "C6969T", @@ -39898,47 +34591,15 @@ "G9912A", "C9951T", "A9984G", - "C9997T", - "G10137A" - ], - "C": [ - "R9K" - ], - "E": [ - "S363N" - ], - "NS1": [ - "I54V" - ], - "NS2A": [ - "D67G", - "I171T" - ], - "NS3": [ - "R184G", - "H348Y" - ], - "NS4A": [ - "M4L", - "K76R" - ], - "NS4B": [ - "F13L" - ], - "NS5": [ - "T637I", - "D672N" + "C9997T" ] - }, - "labels": { - "aa": "C: R9K; E: S363N; NS1: I54V; NS2A: D67G, I171T; NS3: R184G, H348Y; NS4A: M4L, K76R; NS4B: F13L; NS5: T637I, D672N" } } }, { - "name": "NODE_0000201", + "name": "NODE_0000240", "node_attrs": { - "div": 0.29097073, + "div": 0.291, "clade_membership": { "value": "2II_A.1.1.1" } @@ -39958,7 +34619,6 @@ "G3669A", "A3825G", "A4467G", - "C4479T", "G4521A", "C4746T", "A5175G", @@ -39969,12 +34629,8 @@ "T5307C", "C5847T", "G6108A", - "G6279A", - "G6284A", "C6448T", - "G6474A", "C6588T", - "C6881T", "T7158C", "T7161C", "C7743A", @@ -39987,44 +34643,23 @@ "A9426G", "T9456C", "A9642T", + "A10137G", "C10143T", "C10263T", 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}, "children": [ { - "name": "OR236112.1|2016-05", + "name": "OP684211.1|2019-10-19", "node_attrs": { - "div": 0.29397671000000003, - "country": { - "value": "Reunion" - }, + "div": 0.309, "clade_membership": { - "value": "2II_A.1.1.2" + "value": "2II_A.1.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { "mutations": { "nuc": [ - "T244C", - "C726T", - "A1155G", - "C3981T", - "T5070C", + "A111G", + "G225A", + "T348C", + "C399T", + "C414T", + "C431T", + "C1026T", + "A1032G", + "C1062T", + "G1083A", + "G1089A", + "A1122G", + "A1155C", + "T1197C", + "T1218C", + "A1305G", + "A1593C", + "G1878A", + "G2907A", + "C3081T", + "C3204T", + "G3213A", + "T3258C", + "C3327T", + "C3366T", + "A3381G", + "T3465C", + "G3510A", + "C3526T", + "G3555A", + "A3564G", + "G3574A", + "A3598G", + "G3660C", + "G3664A", + "T3706C", + "G3750A", + "A3874G", + "G3882A", + "G3891A", + "A3936G", + "T3942C", + "A4008T", + "T5067C", + "C5070T", + "C5364T", + "C5409T", + "T5421C", + "G5466A", + "A5502G", + "A5577G", + "C5598T", + "G5610A", + "C5703T", + "C5712T", + "T5730C", + "A6284G", + "C6292T", + "A6354G", + "G6357A", + "T6366G", + "A6385C", + "T6391C", "T6420C", - "C6651T", - "A8367G", + "T6423C", + "T6471C", + "A6474G", + "A6522G", + "C6543T", + "G6546A", + "C6555T", + "G6570A", + "T6588C", + "T6597C", + "A6603G", + "A6615G", + "T6633C", + "T7059A", + "T7146C", + "T7161C", + "C7176T", + "G7224T", + "A7242G", + "C7269T", + "A7314G", + "G7320A", + "C7327T", + "C7369T", + "A7506G", + "A7515G", + "A7602G", + "T7650C", + "T7782C", + "T7999C", + "G8070A", + "G8076A", + "C8090A", + "G8100A", + "A8118C", + "C8127T", + "C8139T", + "C8142A", + "G8148A", + "A8155G", + "G8160A", + "A8203C", + "T8226C", + "T8292C", + "T8310C", + "A8331G", + "C8381T", + "T8469C", + "T8535C", "A8541G", - "T8754C", - "T9208C", - "A10129G" - ], - "NS5": [ - "T854A" + "A8547G", + "A8745G", + "A8953C", + "A8958G", + "T8997C", + "C9043T", + "T9078C", + "C9084T", + "A9132C", + "C9168T", + "A9174C", + "T9237C", + "G9279A", + "C9318G", + "A10188T", + "G10196A", + "T10215C", + "G10260A" ] - }, - "labels": { - "aa": "NS5: T854A" } } }, { - "name": "OR236111.1|2016-05", + "name": "OP684207.1|2019-10-13", "node_attrs": { - "div": 0.29340296000000005, - "country": { - "value": "Reunion" - }, + "div": 0.302, "clade_membership": { - "value": "2II_A.1.1.2" + "value": "2II_A.1.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { "mutations": { "nuc": [ - "T201C", - "C579T", - "C1459T", + "A101T", + "G1107A", + "A1125G", + "A1257G", + "T2481C", + "C2484T", + "T2493C", "A2496G", - "T4875C", - "A5172G", - "A8471G", - "T8988C" - ], - "NS5": [ - "K301R" + "A2520G", + "C2538T", + "G2544A", + "G2547A", + "T2571A", + "C2580A", + "A2589G", + "A2598G", + "C2608T", + "A2610G", + "T2616C", + "C2640A", + "T2659G", + "A2673G", + "G2679A", + "C2730T", + "C2731T", + "G2754A", + "G2784A", + "C2803T", + "C2806T", + "G2814A", + "C2835T", + "A2838G", + "A2847G", + "T2850C", + "A2877G", + "C2878T", + "A2880G", + "A2883G", + "T2895C", + "C2919T", + "G2928A", + "G2942A", + "G2943A", + "T2951C", + "T2955C", + "T3012C", + "T3021C", + "C3033T", + "C3081A", + "G3086A", + "T3111C", + "T3160C", + "T3162C", + "A3177C", + "T3186C", + "C3189T", + "C3924T", + "C4118T", + "A4999G", + "C5043T", + "C5071A", + "G5073A", + "G5685A", + "T8181C", + "G8946A", + "A9876G", + "T9942C" ] - }, - "labels": { - "aa": "NS5: K301R" } } } @@ -41275,9 +35588,9 @@ ] }, { - "name": "NODE_0000207", + "name": "NODE_0000245", "node_attrs": { - "div": 0.24795663, + "div": 0.248, "clade_membership": { "value": "2II" } @@ -41309,20 +35622,14 @@ "C8289T", "C8389T", "C9693T" - ], - "NS1": [ - "P128L" ] - }, - "labels": { - "aa": "NS1: P128L" } }, "children": [ { - "name": "NODE_0000208", + "name": "NODE_0000246", "node_attrs": { - "div": 0.2516597, + "div": 0.252, "clade_membership": { "value": "2II_B" } @@ -41342,7 +35649,6 @@ "C2325T", "C2535T", "C2731T", - "T3138C", "A3297G", "C3660T", "T3663C", @@ -41367,21 +35673,17 @@ "T9675C", "T9705C", "T10084C" - ], - "E": [ - "S390N" ] }, "labels": { - "aa": "E: S390N", "lineage": "2II_B" } }, "children": [ { - "name": "NODE_0000209", + "name": "NODE_0000247", "node_attrs": { - "div": 0.25542147, + "div": 0.255, "clade_membership": { "value": "2II_B" } @@ -41399,6 +35701,7 @@ "T2401C", "G2619A", "C3108T", + "T3138C", "G3392A", "C3726T", "G3890A", @@ -41432,34 +35735,19 @@ "T9942C", "C9951T", "A10021G" - ], - "NS1": [ - "R324K" - ], - "NS2A": [ - "R138K" - ], - "NS4B": [ - "Q21H" - ], - "NS5": [ - "I818V" ] - }, - "labels": { - "aa": "NS1: R324K; NS2A: R138K; NS4B: Q21H; NS5: I818V" } }, "children": [ { "name": "GQ398259.1|1976", "node_attrs": { - "div": 0.25650603, - "country": { - "value": "Indonesia" - }, + "div": 0.257, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -41483,12 +35771,12 @@ { "name": "GQ398258.1|1975", "node_attrs": { - "div": 0.25581267999999996, - "country": { - "value": "Indonesia" - }, + "div": 0.256, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -41498,22 +35786,16 @@ "T2962C", "G4791A", "G10266A" - ], - "NS1": [ - "S181P" ] - }, - "labels": { - "aa": "NS1: S181P" } } } ] }, { - "name": "NODE_0000210", + "name": "NODE_0000248", "node_attrs": { - "div": 0.26114404999999996, + "div": 0.261, "clade_membership": { "value": "2II_B" } @@ -41605,32 +35887,14 @@ "A9744G", "C9792A", "A9975G" - ], - "C": [ - "M104I" - ], - "E": [ - "I322V" - ], - "NS1": [ - "I21V", - "D278N" - ], - "NS5": [ - "V156I", - "M337T", - "K570R" ] - }, - "labels": { - "aa": "C: M104I; E: I322V; NS1: I21V, D278N; NS5: V156I, M337T, K570R" } }, "children": [ { - "name": "NODE_0000211", + "name": "NODE_0000249", "node_attrs": { - "div": 0.28900285, + "div": 0.289, "clade_membership": { "value": "2II_B" } @@ -41715,6 +35979,7 @@ "G3079A", "T3081C", "C3108T", + "T3138C", "T3150C", "T3160C", "C3229T", @@ -41886,57 +36151,19 @@ "A10191T", "C10215T", "C10263T" - ], - "2K": [ - "V17M" - ], - "C": [ - "N10S", - "A114T" - ], - "E": [ - "V324I", - "M401V", - "M492V" - ], - "M": [ - "Y148H", - "I156T" - ], - "NS1": [ - "T146I", - "V220I", - "F247L", - "M275V" - ], - "NS2A": [ - "R94K", - "K99R", - "V147A" - ], - "NS5": [ - "A19T", - "I27A", - "K562R", - "E616G", - "A642T", - "R698K" ] - }, - "labels": { - "aa": "2K: V17M; C: N10S, A114T; E: V324I, M401V, M492V; M: Y148H, I156T; NS1: T146I, V220I, F247L, M275V; NS2A: R94K, K99R, V147A; NS5: A19T, I27A, K562R, E616G, A642T, R698K" } }, "children": [ { "name": "OL469512.1|2017-04-30", "node_attrs": { - "div": 0.29404103, - "country": { - "value": "Cote d'Ivoire" - }, + "div": 0.294, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Cote d'Ivoire" } }, "branch_attrs": { @@ -41995,51 +36222,19 @@ "C9597T", "T9620G", "A9756G" - ], - "E": [ - "W101S", - "G102A", - "N103D", - "V114L", - "A313V" - ], - "M": [ - "D65G", - "C68S", - "V96A" - ], - "NS1": [ - "G95D", - "A99S" - ], - "NS3": [ - "Y79F" - ], - "NS4B": [ - "I18V", - "P23S" - ], - "NS5": [ - "R263C", - "S269N", - "E464K", - "M684R" ] - }, - "labels": { - "aa": "E: W101S, G102A, N103D, V114L, A313V; M: D65G, C68S, V96A; NS1: G95D, A99S; NS3: Y79F; NS4B: I18V, P23S; NS5: R263C, S269N, E464K, M684R" } } }, { "name": "OM317565.1|2020-06-24", "node_attrs": { - "div": 0.29315159999999996, - "country": { - "value": "Cameroon" - }, + "div": 0.293, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Cameroon" } }, "branch_attrs": { @@ -42081,29 +36276,16 @@ "A9510G", "G9736A", "C10185A" - ], - "M": [ - "M39I" - ], - "NS1": [ - "N347S" - ], - "NS5": [ - "L274I", - "V723I" ] - }, - "labels": { - "aa": "M: M39I; NS1: N347S; NS5: L274I, V723I" } } } ] }, { - "name": "NODE_0000212", + "name": "NODE_0000250", "node_attrs": { - "div": 0.28733414999999995, + "div": 0.287, "clade_membership": { "value": "2II_B" } @@ -42181,7 +36363,6 @@ "C3066T", "A3099G", "T3120C", - "C3138T", "A3145G", "T3228C", "T3252C", @@ -42351,65 +36532,19 @@ "A10098G", "C10212T", "G10254A" - ], - "E": [ - "V365I", - "V382A", - "K394R" - ], - "M": [ - "V152I" - ], - "NS1": [ - "V60A", - "R174K", - "V177I", - "I188V", - "I242V", - "T288S" - ], - "NS2A": [ - "A189S", - "S215N" - ], - "NS2B": [ - "D63E" - ], - "NS3": [ - "K73R", - "Q243L", - "R248K", - "T399A" - ], - "NS4A": [ - "R39K" - ], - "NS4B": [ - "T20A" - ], - "NS5": [ - "S23N", - "I267V", - "T636A", - "T638S", - "V687I", - "I779V" ] - }, - "labels": { - "aa": "E: V365I, V382A, K394R; M: V152I; NS1: V60A, R174K, V177I, I188V, I242V, T288S; NS2A: A189S, S215N; NS2B: D63E; NS3: K73R, Q243L, R248K, T399A; NS4A: R39K; NS4B: T20A; NS5: S23N, I267V, T636A, T638S, V687I, I779V" } }, "children": [ { "name": "MN577562.1|2013-05", "node_attrs": { - "div": 0.28753668999999993, - "country": { - "value": "Kenya" - }, + "div": 0.288, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Kenya" } }, "branch_attrs": { @@ -42417,25 +36552,19 @@ "nuc": [ "G1120C", "T1440C" - ], - "E": [ - "E62Q" ] - }, - "labels": { - "aa": "E: E62Q" } } }, { "name": "MN577564.1|2014-06", "node_attrs": { - "div": 0.28733648999999994, - "country": { - "value": "Kenya" - }, + "div": 0.287, "clade_membership": { "value": "2II_B" + }, + "country": { + "value": "Kenya" } }, "branch_attrs": { @@ -42449,9 +36578,9 @@ ] }, { - "name": "NODE_0000213", + "name": "NODE_0000251", "node_attrs": { - "div": 0.25524566, + "div": 0.255, "clade_membership": { "value": "2II" } @@ -42533,38 +36662,14 @@ "G9987A", "G10059A", "C10083T" - ], - "C": [ - "L108M" - ], - "E": [ - "Q52H" - ], - "M": [ - "I127V" - ], - "NS1": [ - "Q131H" - ], - "NS5": [ - "R98K", - "G605V", - "Q644K", - "R800T" ] - }, - "labels": { - "aa": "C: L108M; E: Q52H; M: I127V; NS1: Q131H; NS5: R98K, G605V, Q644K, R800T" } }, "children": [ { "name": "GQ398263.1|1975", "node_attrs": { - "div": 0.26242700999999996, - "country": { - "value": "Indonesia" - }, + "div": 0.262, "clade_membership": { "value": "2II" } @@ -42647,33 +36752,14 @@ "T9906A", "C9957T", "C10215T" - ], - "E": [ - "I322V" - ], - "NS1": [ - "N145T", - "F178L", - "E340D" - ], - "NS3": [ - "K73R" - ], - "NS5": [ - "T271I", - "I276V", - "F413Y" ] - }, - "labels": { - "aa": "E: I322V; NS1: N145T, F178L, E340D; NS3: K73R; NS5: T271I, I276V, F413Y" } } }, { - "name": "NODE_0000214", + "name": "NODE_0000252", "node_attrs": { - "div": 0.26192825999999997, + "div": 0.262, "clade_membership": { "value": "2II" } @@ -42744,33 +36830,14 @@ "A9726G", "A9780G", "G9819A" - ], - "M": [ - "D29N" - ], - "NS2A": [ - "I171T" - ], - "NS3": [ - "I461V", - "I567V" - ], - "NS5": [ - "R430G" ] - }, - "labels": { - "aa": "M: D29N; NS2A: I171T; NS3: I461V, I567V; NS5: R430G" } }, "children": [ { "name": "OK469352.1|1993", "node_attrs": { - "div": 0.27637776, - "country": { - "value": "Singapore" - }, + "div": 0.276, "clade_membership": { "value": "2II" } @@ -42925,47 +36992,14 @@ "A10188G", "C10215T", "G10272A" - ], - "C": [ - "T101A", - "M104V" - ], - "E": [ - "V129I", - "I170S", - "V382I" - ], - "NS1": [ - "S80L", - "H129Q", - "K170R" - ], - "NS2A": [ - "K99R" - ], - "NS3": [ - "K73R" - ], - "NS4B": [ - "F47I" - ], - "NS5": [ - "N174S", - "K548R", - "H634Q", - "L670F", - "S676T" ] - }, - "labels": { - "aa": "C: T101A, M104V; E: V129I, I170S, V382I; NS1: S80L, H129Q, K170R; NS2A: K99R; NS3: K73R; NS4B: F47I; NS5: N174S, K548R, H634Q, L670F, S676T" } } }, { - "name": "NODE_0000215", + "name": "NODE_0000253", "node_attrs": { - "div": 0.26831435, + "div": 0.268, "clade_membership": { "value": "2II" } @@ -43031,32 +37065,14 @@ "T9601C", "T9903C", "A9975G" - ], - "C": [ - "M104I" - ], - "E": [ - "I164V" - ], - "NS1": [ - "T117A" - ], - "NS2B": [ - "D63E" - ], - "NS3": [ - "V273I" ] - }, - "labels": { - "aa": "C: M104I; E: I164V; NS1: T117A; NS2B: D63E; NS3: V273I" } }, "children": [ { - "name": "NODE_0000216", + "name": "NODE_0000254", "node_attrs": { - "div": 0.27367547999999997, + "div": 0.274, "clade_membership": { "value": "2II_C" } @@ -43117,30 +37133,17 @@ "T9735C", "C9963T", "A10233G" - ], - "C": [ - "I104V" - ], - "E": [ - "N203D" - ], - "NS4A": [ - "I93V" - ], - "NS5": [ - "T271I" ] }, "labels": { - "aa": "C: I104V; E: N203D; NS4A: I93V; NS5: T271I", "lineage": "2II_C" } }, "children": [ { - "name": "NODE_0000217", + "name": "NODE_0000255", "node_attrs": { - "div": 0.27932954, + "div": 0.279, "clade_membership": { "value": "2II_C" } @@ -43204,34 +37207,19 @@ "C10206T", "G10254A", "A10260G" - ], - "C": [ - "A63T" - ], - "E": [ - "N83S" - ], - "M": [ - "V127L" - ], - "NS2A": [ - "T171I" ] - }, - "labels": { - "aa": "C: A63T; E: N83S; M: V127L; NS2A: T171I" } }, "children": [ { "name": "MW512467.1|2016", "node_attrs": { - "div": 0.29316474, - "country": { - "value": "Singapore" - }, + "div": 0.293, "clade_membership": { "value": "2II_C" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -43369,46 +37357,19 @@ "G10071A", "A10080G", "C10215T" - ], - "E": [ - "K36R", - "T226I", - "E360G" - ], - "NS1": [ - "E52D", - "A141V", - "F178L", - "N293S" - ], - "NS2A": [ - "V147A", - "S215N" - ], - "NS4B": [ - "P23S", - "A244V" - ], - "NS5": [ - "T554K", - "S676N", - "E820D" ] - }, - "labels": { - "aa": "E: K36R, T226I, E360G; NS1: E52D, A141V, F178L, N293S; NS2A: V147A, S215N; NS4B: P23S, A244V; NS5: T554K, S676N, E820D" } } }, { "name": "MW512409.1|2013", "node_attrs": { - "div": 0.28836485, - "country": { - "value": "Singapore" - }, + "div": 0.288, "clade_membership": { "value": "2II_C" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -43503,26 +37464,16 @@ "C9330T", "C9690A", "G10089A" - ], - "E": [ - "V358A" - ], - "NS5": [ - "V156I", - "K389R" ] - }, - "labels": { - "aa": "E: V358A; NS5: V156I, K389R" } } } ] }, { - "name": "NODE_0000218", + "name": "NODE_0000256", "node_attrs": { - "div": 0.27428142, + "div": 0.274, "clade_membership": { "value": "2II_C" } @@ -43543,10 +37494,7 @@ { "name": "JN851131.1|2005", "node_attrs": { - "div": 0.28384488, - "country": { - "value": "Singapore" - }, + "div": 0.284, "clade_membership": { "value": "2II_C" } @@ -43650,40 +37598,14 @@ "C9903T", "A9948G", "G10071A" - ], - "E": [ - "N83K" - ], - "M": [ - "M39I" - ], - "NS1": [ - "A117T", - "D176E", - "L338S" - ], - "NS3": [ - "A249V", - "V351I" - ], - "NS4B": [ - "T20I" - ], - "NS5": [ - "I271K", - "D436N", - "A648V" ] - }, - "labels": { - "aa": "E: N83K; M: M39I; NS1: A117T, D176E, L338S; NS3: A249V, V351I; NS4B: T20I; NS5: I271K, D436N, A648V" } } }, { - "name": "NODE_0000219", + "name": "NODE_0000257", "node_attrs": { - "div": 0.27754374, + "div": 0.278, "clade_membership": { "value": "2II_C" } @@ -43723,26 +37645,14 @@ "C9585T", "T9753C", "C9951T" - ], - "C": [ - "M113V" - ], - "NS3": [ - "I395V" - ], - "NS5": [ - "V78M" ] - }, - "labels": { - "aa": "C: M113V; NS3: I395V; NS5: V78M" } }, "children": [ { - "name": "NODE_0000220", + "name": "NODE_0000258", "node_attrs": { - "div": 0.28143314999999997, + "div": 0.281, "clade_membership": { "value": "2II_C.2" } @@ -43790,21 +37700,9 @@ "C9735T", "T9811C", "G10041A" - ], - "NS2A": [ - "T171I" - ], - "NS4B": [ - "S17G" - ], - "NS5": [ - "H634Q", - "V637A", - "M824I" ] }, "labels": { - "aa": "NS2A: T171I; NS4B: S17G; NS5: H634Q, V637A, M824I", "lineage": "2II_C.2" } }, @@ -43812,12 +37710,12 @@ { "name": "KF744398.1|2005", "node_attrs": { - "div": 0.28666286999999996, - "country": { - "value": "Philippines" - }, + "div": 0.287, "clade_membership": { "value": "2II_C.2" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -43875,31 +37773,14 @@ "G9857A", "G9975A", "C10158T" - ], - "E": [ - "V129I", - "H346Y", - "V347A" - ], - "NS1": [ - "R174K" - ], - "NS4B": [ - "A116V" - ], - "NS5": [ - "S763N" ] - }, - "labels": { - "aa": "E: V129I, H346Y, V347A; NS1: R174K; NS4B: A116V; NS5: S763N" } } }, { - "name": "NODE_0000221", + "name": "NODE_0000259", "node_attrs": { - "div": 0.28143414999999994, + "div": 0.281, "clade_membership": { "value": "2II_C.2" } @@ -43911,12 +37792,12 @@ { "name": "MG599592.1|2001", "node_attrs": { - "div": 0.28202568999999994, - "country": { - "value": "Taiwan" - }, + "div": 0.282, "clade_membership": { "value": "2II_C.2" + }, + "country": { + "value": "Taiwan" } }, "branch_attrs": { @@ -43929,23 +37810,14 @@ "G8667T", "G8679T", "A8781G" - ], - "E": [ - "I46T" - ], - "NS5": [ - "E357V" ] - }, - "labels": { - "aa": "E: I46T; NS5: E357V" } } }, { - "name": "NODE_0000222", + "name": "NODE_0000260", "node_attrs": { - "div": 0.28231935999999996, + "div": 0.282, "clade_membership": { "value": "2II_C.2" } @@ -43961,25 +37833,19 @@ "C8349T", "T8381C", "C9186T" - ], - "NS5": [ - "I271T" ] - }, - "labels": { - "aa": "NS5: I271T" } }, "children": [ { "name": "MG599628.1|2002", "node_attrs": { - "div": 0.28310766, - "country": { - "value": "Taiwan" - }, + "div": 0.283, "clade_membership": { "value": "2II_C.2" + }, + "country": { + "value": "Taiwan" } }, "branch_attrs": { @@ -43993,26 +37859,14 @@ "C4896T", "T5010C", "T9735C" - ], - "E": [ - "K160R" - ], - "NS1": [ - "E240D" - ], - "NS2A": [ - "I116V" ] - }, - "labels": { - "aa": "E: K160R; NS1: E240D; NS2A: I116V" } } }, { - "name": "NODE_0000223", + "name": "NODE_0000261", "node_attrs": { - "div": 0.28232435999999994, + "div": 0.282, "clade_membership": { "value": "2II_C.2" } @@ -44024,12 +37878,12 @@ { "name": "MG599621.1|2002", "node_attrs": { - "div": 0.28311161999999995, - "country": { - "value": "Taiwan" - }, + "div": 0.283, "clade_membership": { "value": "2II_C.2" + }, + "country": { + "value": "Taiwan" } }, "branch_attrs": { @@ -44043,28 +37897,19 @@ "A8639T", "G8667T", "G8745A" - ], - "NS4B": [ - "F212L" - ], - "NS5": [ - "E357V" ] - }, - "labels": { - "aa": "NS4B: F212L; NS5: E357V" } } }, { "name": "MG599631.1|2002", "node_attrs": { - "div": 0.28311060999999993, - "country": { - "value": "Taiwan" - }, + "div": 0.283, "clade_membership": { "value": "2II_C.2" + }, + "country": { + "value": "Taiwan" } }, "branch_attrs": { @@ -44078,16 +37923,7 @@ "C6529T", "T7263C", "G7455A" - ], - "E": [ - "V181I" - ], - "M": [ - "I13V" ] - }, - "labels": { - "aa": "E: V181I; M: I13V" } } } @@ -44100,9 +37936,9 @@ ] }, { - "name": "NODE_0000224", + "name": "NODE_0000262", "node_attrs": { - "div": 0.27798917, + "div": 0.278, "clade_membership": { "value": "2II_C" } @@ -44117,25 +37953,19 @@ "T4980C", "T6861C", "C10143T" - ], - "E": [ - "I46T" ] - }, - "labels": { - "aa": "E: I46T" } }, "children": [ { "name": "KF744397.1|2001", "node_attrs": { - "div": 0.28025341, - "country": { - "value": "Philippines" - }, + "div": 0.28, "clade_membership": { "value": "2II_C" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -44163,37 +37993,14 @@ "T8799C", "C8925T", "A10209G" - ], - "C": [ - "N10K" - ], - "E": [ - "V129I", - "T359A" - ], - "M": [ - "M39L" - ], - "NS1": [ - "K9R", - "K189R" - ], - "NS2A": [ - "H2L" - ], - "NS4B": [ - "P157S" ] - }, - "labels": { - "aa": "C: N10K; E: V129I, T359A; M: M39L; NS1: K9R, K189R; NS2A: H2L; NS4B: P157S" } } }, { - "name": "NODE_0000225", + "name": "NODE_0000263", "node_attrs": { - "div": 0.27809329, + "div": 0.278, "clade_membership": { "value": "2II_C" } @@ -44202,23 +38009,14 @@ "mutations": { "nuc": [ "T880C" - ], - "M": [ - "Y148H" ] - }, - "labels": { - "aa": "M: Y148H" } }, "children": [ { "name": "KU509269.1|2009", "node_attrs": { - "div": 0.28861409, - "country": { - "value": "Philippines" - }, + "div": 0.289, "clade_membership": { "value": "2II_C" } @@ -44330,43 +38128,14 @@ "C9903T", "C9918T", "G9999A" - ], - "C": [ - "R9K", - "A102V" - ], - "E": [ - "V129I", - "E360D", - "V491A" - ], - "NS1": [ - "V177A" - ], - "NS4A": [ - "Y97H" - ], - "NS4B": [ - "T108M" - ], - "NS5": [ - "I284R", - "K285N", - "Q286E", - "H288T", - "E433K", - "K644Q" ] - }, - "labels": { - "aa": "C: R9K, A102V; E: V129I, E360D, V491A; NS1: V177A; NS4A: Y97H; NS4B: T108M; NS5: I284R, K285N, Q286E, H288T, E433K, K644Q" } } }, { - "name": "NODE_0000226", + "name": "NODE_0000264", "node_attrs": { - "div": 0.28155468, + "div": 0.282, "clade_membership": { "value": "2II_C.1" } @@ -44410,25 +38179,9 @@ "T7968C", "A8022G", "C9735T" - ], - "E": [ - "T226K" - ], - "M": [ - "M165L" - ], - "NS1": [ - "S103T" - ], - "NS2A": [ - "A189T" - ], - "NS3": [ - "K418R" ] }, "labels": { - "aa": "E: T226K; M: M165L; NS1: S103T; NS2A: A189T; NS3: K418R", "lineage": "2II_C.1" } }, @@ -44436,12 +38189,12 @@ { "name": "KU509277.1|2010", "node_attrs": { - "div": 0.28975232, - "country": { - "value": "Philippines" - }, + "div": 0.29, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -44529,64 +38282,14 @@ "T10081G", "T10143A", "C10215T" - ], - "2K": [ - "I14T" - ], - "E": [ - "I322V" - ], - "M": [ - "A120V" - ], - "NS1": [ - "S2R", - "C4Y", - "K9N" - ], - "NS2A": [ - "A151T", - "T171I" - ], - "NS3": [ - "V146I", - "E336D" - ], - "NS4A": [ - "A107D" - ], - "NS4B": [ - "E7Q", - "F47S", - "L65V", - "A127P", - "P157S" - ], - "NS5": [ - "S230A", - "I271T", - "H288R", - "Y305D", - "K375Q", - "E398Q", - "K460Q", - "K562T", - "S631N", - "H634Q", - "V637D", - "I691V", - "Y838D" ] - }, - "labels": { - "aa": "2K: I14T; E: I322V; M: A120V; NS1: S2R, C4Y, K9N; NS2A: A151T, T171I; NS3: V146I, E336D; NS4A: A107D; NS4B: E7Q, F47S, L65V, A127P, P157S; NS5: S230A, I271T, H288R, Y305D, K375Q, E398Q, K460Q, K562T, S631N, H634Q, V637D, I691V, Y838D" } } }, { - "name": "NODE_0000227", + "name": "NODE_0000265", "node_attrs": { - "div": 0.28276175, + "div": 0.283, "clade_membership": { "value": "2II_C.1" } @@ -44605,28 +38308,19 @@ "A8718G", "A9490G", "T9885A" - ], - "NS4B": [ - "L15I" - ], - "NS5": [ - "I641V" ] - }, - "labels": { - "aa": "NS4B: L15I; NS5: I641V" } }, "children": [ { "name": "KU509276.1|2008", "node_attrs": { - "div": 0.29705784999999996, - "country": { - "value": "Philippines" - }, + "div": 0.297, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -44777,60 +38471,14 @@ "A10216C", "G10218C", "A10257T" - ], - "C": [ - "N10S", - "K17N" - ], - "E": [ - "E136K", - "I322V", - "S390N", - "V491A" - ], - "NS1": [ - "V5D", - "R174K" - ], - "NS3": [ - "L115I", - "A211P", - "E233K", - "R248K", - "R268G", - "I300F", - "A558T" - ], - "NS4B": [ - "T108M", - "A197V", - "G227E" - ], - "NS5": [ - "N173S", - "A196T", - "S225T", - "R246K", - "K283R", - "I284R", - "N555D", - "G743E", - "T800K", - "P837S", - "T858A", - "Y882S", - "M883L" ] - }, - "labels": { - "aa": "C: N10S, K17N; E: E136K, I322V, S390N, V491A; NS1: V5D, R174K; NS3: L115I, A211P, E233K, R248K, R268G, I300F, A558T; NS4B: T108M, A197V, G227E; NS5: N173S, A196T, S225T, R246K, K283R, I284R, N555D, G743E, T800K, P837S, T858A, Y882S, M883L" } } }, { - "name": "NODE_0000228", + "name": "NODE_0000266", "node_attrs": { - "div": 0.28276410999999996, + "div": 0.283, "clade_membership": { "value": "2II_C.1" } @@ -44842,12 +38490,12 @@ { "name": "MW512432.1|2014", "node_attrs": { - "div": 0.29403851, - "country": { - "value": "Singapore" - }, + "div": 0.294, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -44963,37 +38611,14 @@ "T9972C", "A10029G", "A10209G" - ], - "C": [ - "V113M" - ], - "E": [ - "T46I", - "G177D", - "V484I" - ], - "NS1": [ - "I242V", - "F279L", - "N347S" - ], - "NS4B": [ - "I150V" - ], - "NS5": [ - "K375R", - "V637A" ] - }, - "labels": { - "aa": "C: V113M; E: T46I, G177D, V484I; NS1: I242V, F279L, N347S; NS4B: I150V; NS5: K375R, V637A" } } }, { - "name": "NODE_0000229", + "name": "NODE_0000267", "node_attrs": { - "div": 0.28479145999999994, + "div": 0.285, "clade_membership": { "value": "2II_C.1" } @@ -45024,33 +38649,19 @@ "A8973T", "G9297A", "G10089A" - ], - "E": [ - "T46I" - ], - "NS1": [ - "V177A", - "I188V", - "K214R" - ], - "NS4B": [ - "S17N" ] - }, - "labels": { - "aa": "E: T46I; NS1: V177A, I188V, K214R; NS4B: S17N" } }, "children": [ { "name": "MT832057.1|2015", "node_attrs": { - "div": 0.2956359599999999, - "country": { - "value": "Philippines" - }, + "div": 0.296, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -45166,30 +38777,14 @@ "C9909T", "A9939G", "A10188G" - ], - "E": [ - "K51R", - "V129I", - "I170T", - "H346Q" - ], - "NS2A": [ - "T115A", - "T171I" - ], - "NS4B": [ - "D156E" ] - }, - "labels": { - "aa": "E: K51R, V129I, I170T, H346Q; NS2A: T115A, T171I; NS4B: D156E" } } }, { - "name": "NODE_0000230", + "name": "NODE_0000268", "node_attrs": { - "div": 0.28863179999999994, + "div": 0.289, "clade_membership": { "value": "2II_C.1" } @@ -45233,36 +38828,19 @@ "C9801T", "T9993C", "C10047T" - ], - "E": [ - "K160T", - "I379V" - ], - "NS1": [ - "S80T" - ], - "NS2A": [ - "S184T" - ], - "NS5": [ - "N273D", - "V641I" ] - }, - "labels": { - "aa": "E: K160T, I379V; NS1: S80T; NS2A: S184T; NS5: N273D, V641I" } }, "children": [ { "name": "MW881533.1|2021-02-02", "node_attrs": { - "div": 0.29903859999999993, - "country": { - "value": "China" - }, + "div": 0.299, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -45371,42 +38949,19 @@ "C9769T", "C9843T", "A10209G" - ], - "C": [ - "A52V" - ], - "E": [ - "E360D" - ], - "M": [ - "H148Y" - ], - "NS1": [ - "K272R" - ], - "NS3": [ - "A249T" - ], - "NS5": [ - "R401K", - "V426G", - "V643A" ] - }, - "labels": { - "aa": "C: A52V; E: E360D; M: H148Y; NS1: K272R; NS3: A249T; NS5: R401K, V426G, V643A" } } }, { "name": "MK783205.1|2018", "node_attrs": { - "div": 0.29929579999999995, - "country": { - "value": "China" - }, + "div": 0.299, "clade_membership": { "value": "2II_C.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -45515,23 +39070,7 @@ "T9906C", "A10176G", "C10194T" - ], - "C": [ - "I105V" - ], - "NS1": [ - "H50R" - ], - "NS4B": [ - "I121L", - "V175L" - ], - "NS5": [ - "N555K" ] - }, - "labels": { - "aa": "C: I105V; NS1: H50R; NS4B: I121L, V175L; NS5: N555K" } } } @@ -45556,9 +39095,9 @@ ] }, { - "name": "NODE_0000231", + "name": "NODE_0000269", "node_attrs": { - "div": 0.27136497, + "div": 0.271, "clade_membership": { "value": "2II" } @@ -45602,26 +39141,14 @@ "C9138T", "C9512T", "T9810C" - ], - "NS1": [ - "K272R" - ], - "NS5": [ - "A648V" ] - }, - "labels": { - "aa": "NS1: K272R; NS5: A648V" } }, "children": [ { "name": "MT921572.1|2000", "node_attrs": { - "div": 0.27789406, - "country": { - "value": "Australia" - }, + "div": 0.278, "clade_membership": { "value": "2II" } @@ -45696,29 +39223,14 @@ "C9456T", "A9499G", "T9840C" - ], - "NS1": [ - "K48R", - "R174K", - "R272S" - ], - "NS5": [ - "E379K", - "T400R", - "M530I", - "H556Y", - "K644E" ] - }, - "labels": { - "aa": "NS1: K48R, R174K, R272S; NS5: E379K, T400R, M530I, H556Y, K644E" } } }, { - "name": "NODE_0000232", + "name": "NODE_0000270", "node_attrs": { - "div": 0.27136769, + "div": 0.271, "clade_membership": { "value": "2II" } @@ -45730,10 +39242,7 @@ { "name": "FJ196853.1|2003", "node_attrs": { - "div": 0.27490682, - "country": { - "value": "China" - }, + "div": 0.275, "clade_membership": { "value": "2II" } @@ -45776,49 +39285,14 @@ "T9630C", "A9638G", "T9753C" - ], - "E": [ - "F193L", - "N194H", - "I414T" - ], - "M": [ - "A82T" - ], - "NS1": [ - "F20L", - "I21V", - "E154K" - ], - "NS2A": [ - "K135R", - "L208I" - ], - "NS2B": [ - "T94I" - ], - "NS3": [ - "G103R" - ], - "NS4A": [ - "S1Y" - ], - "NS4B": [ - "H54L" - ], - "NS5": [ - "D690G" ] - }, - "labels": { - "aa": "E: F193L, N194H, I414T; M: A82T; NS1: F20L, I21V, E154K; NS2A: K135R, L208I; NS2B: T94I; NS3: G103R; NS4A: S1Y; NS4B: H54L; NS5: D690G" } } }, { - "name": "NODE_0000233", + "name": "NODE_0000271", "node_attrs": { - "div": 0.27271275, + "div": 0.273, "clade_membership": { "value": "2II" } @@ -45837,23 +39311,16 @@ "C6528T", "G6880A", "G7149A", - "T8310C", "C8349T", "T8853C" - ], - "NS4B": [ - "A19T" ] - }, - "labels": { - "aa": "NS4B: A19T" } }, "children": [ { - "name": "NODE_0000234", + "name": "NODE_0000272", "node_attrs": { - "div": 0.27367112, + "div": 0.274, "clade_membership": { "value": "2II" } @@ -45868,22 +39335,17 @@ "A5625G", "C5688T", "G7416A", + "T8310C", "C9471A", "T9753C" - ], - "NS5": [ - "H634Q" ] - }, - "labels": { - "aa": "NS5: H634Q" } }, "children": [ { - "name": "NODE_0000235", + "name": "NODE_0000273", "node_attrs": { - "div": 0.27837199, + "div": 0.278, "clade_membership": { "value": "2II_E" } @@ -45937,21 +39399,879 @@ "C9597T", "T9840C", "A10080G" - ], - "M": [ - "A162T" ] }, "labels": { - "aa": "M: A162T", "lineage": "2II_E" } }, "children": [ { - "name": "NODE_0000236", + "name": "NODE_0000274", + "node_attrs": { + "div": 0.279, + "clade_membership": { + "value": "2II_E" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T927C", + "G5454T", + "G6534A", + "A6880G", + "T8889C", + "C10140T" + ] + } + }, + "children": [ + { + "name": "MT921573.1|2004", + "node_attrs": { + "div": 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+ "T9411C", + "T9597C", + "C9846T", + "G10071A", + "T10224C" ] - }, - "labels": { - "aa": "C: K73R; E: I129V, T176A; NS1: L128P, A205T; NS2B: E54D; NS3: T160A; NS4B: V175I, A244T; NS5: T5I, N15S, G85E, V628I, T800K, Q819R, T865A" } } }, { - "name": "KU517845.1|2013-04-23", + "name": "KX380821.1|2012", "node_attrs": { - "div": 0.29178985999999996, - "country": { - "value": "Papua New Guinea" - }, + "div": 0.298, "clade_membership": { - "value": "2II_E.2" + "value": "2II_E.1" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { "mutations": { "nuc": [ - "G435A", - "C1230T", - "C1299T", + "A177G", + "A228G", + "A246G", + "T252A", + "C423T", + "C459T", + "T480C", + "G492A", + "C507T", + "C684T", + "A729G", + "T732C", + "C798G", + "A817G", + "C840T", + "A841G", + "A876G", + "C894T", + "T906C", + "A922G", + "G934A", + "T1002C", + "G1032A", + "G1056A", + "G1117A", + "C1206T", + "C1272T", + "G1321A", "C1338T", - "T1353C", + "G1344A", + "C1353T", + "C1398T", + "T1410C", "A1428G", - "G1638A", - "T1719C", - "A1743G", - "C1795T", - "G1938A", - "C1947T", - "C1959T", - "A2004G", - "C2034T", - "C2061T", - "T2112C", - "G2148A", - "A2155C", - "G2163A", - "T2187C", - "T2262A", - "A6393C", - "C8686A", - "C8712T" - ], - "C": [ - "M113I" - ], - "NS5": [ - "L373I" + "T1440C", + "A1464C", + "T1478C", + "G1557A", + "C1645T", + "T1692G", + "T1698A", + "C1713T", + "G1722A", + "G1788A", + "G6558A", + "A8718G", + "A10260G" ] - }, - "labels": { - "aa": "C: M113I; NS5: L373I" } } } @@ -47805,9 +40969,9 @@ ] }, { - "name": "NODE_0000247", + "name": "NODE_0000287", "node_attrs": { - "div": 0.27792329, + "div": 0.278, "clade_membership": { "value": "2II_D" } @@ -47860,21 +41024,17 @@ "C9690T", "C9759T", "C10236T" - ], - "E": [ - "V129I" ] }, "labels": { - "aa": "E: V129I", "lineage": "2II_D" } }, "children": [ { - "name": "NODE_0000248", + "name": "NODE_0000288", "node_attrs": { - "div": 0.28064486, + "div": 0.281, "clade_membership": { "value": "2II_D.3" } @@ -47910,21 +41070,17 @@ "C9199T", "T9372C", "G9894A" - ], - "NS1": [ - "A117T" ] }, "labels": { - "aa": "NS1: A117T", "lineage": "2II_D.3" } }, "children": [ { - "name": "NODE_0000249", + "name": "NODE_0000289", "node_attrs": { - "div": 0.29025987999999997, + "div": 0.29, "clade_membership": { "value": "2II_D.3" } @@ -48025,40 +41181,19 @@ "T9512C", "T9696C", "T10179C" - ], - "C": [ - "K73R" - ], - "NS1": [ - "P73Q", - "R174K", - "H224N", - "D278E" - ], - "NS2A": [ - "S39T", - "T104A", - "K166R" - ], - "NS5": [ - "K387R", - "V648A" ] - }, - "labels": { - "aa": "C: K73R; NS1: P73Q, R174K, H224N, D278E; NS2A: S39T, T104A, K166R; NS5: K387R, V648A" } }, "children": [ { "name": "MK564482.1|2017-08-07", "node_attrs": { - "div": 0.29479962, - "country": { - "value": "China" - }, + "div": 0.295, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -48110,40 +41245,14 @@ "C9741T", "A10168G", "A10251G" - ], - "M": [ - "Y148H" - ], - "NS1": [ - "K189R", - "S233N", - "K245R", - "V251E", - "L321I" - ], - "NS2A": [ - "A88V" - ], - "NS4A": [ - "T8A" - ], - "NS4B": [ - "K86E" - ], - "NS5": [ - "Y201H", - "I867V" ] - }, - "labels": { - "aa": "M: Y148H; NS1: K189R, S233N, K245R, V251E, L321I; NS2A: A88V; NS4A: T8A; NS4B: K86E; NS5: Y201H, I867V" } } }, { - "name": "NODE_0000250", + "name": "NODE_0000290", "node_attrs": { - "div": 0.29183571999999997, + "div": 0.292, "clade_membership": { "value": "2II_D.3" } @@ -48163,31 +41272,19 @@ "C3544A", "T3545A", "C3546A" - ], - "E": [ - "R288T", - "K291N" - ], - "NS2A": [ - "E21F", - "M22T", - "L23K" ] - }, - "labels": { - "aa": "E: R288T, K291N; NS2A: E21F, M22T, L23K" } }, "children": [ { "name": "MN018349.1|2015-05-09", "node_attrs": { - "div": 0.29566760999999997, - "country": { - "value": "China" - }, + "div": 0.296, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -48226,54 +41323,19 @@ "T8448G", "T8449G", "A8879G" - ], - "C": [ - "Q27K" - ], - "E": [ - "V97E", - "R99G", - "D290G", - "N291T", - "Q293W", - "G445W" - ], - "M": [ - "T5P" - ], - "NS1": [ - "L124P", - "S125P", - "G199D" - ], - "NS2A": [ - "K23R" - ], - "NS3": [ - "E88G", - "K589E" - ], - "NS5": [ - "R246G", - "H293Q", - "Y294D", - "K437R" ] - }, - "labels": { - "aa": "C: Q27K; E: V97E, R99G, D290G, N291T, Q293W, G445W; M: T5P; NS1: L124P, S125P, G199D; NS2A: K23R; NS3: E88G, K589E; NS5: R246G, H293Q, Y294D, K437R" } } }, { "name": "MN018352.1|2015-09-07", "node_attrs": { - "div": 0.29551052999999994, - "country": { - "value": "China" - }, + "div": 0.296, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -48325,45 +41387,7 @@ "T9264C", "A10090-", "A10160-" - ], - "E": [ - "M289E", - "N291C", - "L292G", - "I378N", - "I379T", - "I380T", - "G381W", - "V382I" - ], - "NS1": [ - "E173K", - "E203G" - ], - "NS2A": [ - "R24K", - "G46V" - ], - "NS2B": [ - "L53M", - "R55X" - ], - "NS3": [ - "W69X", - "I165N", - "E483A" - ], - "NS5": [ - "P152X", - "R362G", - "L564R", - "A565T", - "K841X", - "Q864X" ] - }, - "labels": { - "aa": "E: M289E, N291C, L292G, I378N, I379T, I380T, G381W, V382I; NS1: E173K, E203G; NS2A: R24K, G46V; NS2B: L53M, R55X; NS3: W69X, I165N, E483A; NS5: P152X, R362G, L564R, A565T, K841X, Q864X" } } } @@ -48372,9 +41396,9 @@ ] }, { - "name": "NODE_0000251", + "name": "NODE_0000291", "node_attrs": { - "div": 0.28419528, + "div": 0.284, "clade_membership": { "value": "2II_D.3" } @@ -48417,31 +41441,19 @@ "C9165T", "A9321G", "C9472T" - ], - "NS1": [ - "H224Y" - ], - "NS2A": [ - "V133A" - ], - "NS5": [ - "T271I" ] - }, - "labels": { - "aa": "NS1: H224Y; NS2A: V133A; NS5: T271I" } }, "children": [ { "name": "JN851130.1|2005", "node_attrs": { - "div": 0.28471561, - "country": { - "value": "Singapore" - }, + "div": 0.285, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -48457,9 +41469,9 @@ } }, { - "name": "NODE_0000252", + "name": "NODE_0000292", "node_attrs": { - "div": 0.28559996, + "div": 0.286, "clade_membership": { "value": "2II_D.3" } @@ -48480,34 +41492,19 @@ "T7929C", "A8052T", "A8471G" - ], - "M": [ - "Y148H" - ], - "NS1": [ - "F178Y" - ], - "NS3": [ - "S392F" - ], - "NS5": [ - "K301R" ] - }, - "labels": { - "aa": "M: Y148H; NS1: F178Y; NS3: S392F; NS5: K301R" } }, "children": [ { "name": "KC762675.1|2008-03-08", "node_attrs": { - "div": 0.28723769, - "country": { - "value": "Indonesia" - }, + "div": 0.287, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -48528,26 +41525,19 @@ "T9216A", "C10077T", "A10242G" - ], - "NS5": [ - "K285Q", - "N549K" ] - }, - "labels": { - "aa": "NS5: K285Q, N549K" } } }, { "name": "KC762673.1|2008-03-11", "node_attrs": { - "div": 0.28742097, - "country": { - "value": "Indonesia" - }, + "div": 0.287, "clade_membership": { "value": "2II_D.3" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -48572,16 +41562,7 @@ "A9153G", "T9216C", "G9891A" - ], - "E": [ - "S474P" - ], - "NS3": [ - "R248K" ] - }, - "labels": { - "aa": "E: S474P; NS3: R248K" } } } @@ -48592,9 +41573,9 @@ ] }, { - "name": "NODE_0000253", + "name": "NODE_0000293", "node_attrs": { - "div": 0.27821502, + "div": 0.278, "clade_membership": { "value": "2II_D" } @@ -48612,12 +41593,12 @@ { "name": "MN923111.1|2019-08-24", "node_attrs": { - "div": 0.29575471999999997, - "country": { - "value": "China" - }, + "div": 0.296, "clade_membership": { "value": "2II_D" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -48801,43 +41782,14 @@ "G9912A", "C10077T", "T10236C" - ], - "M": [ - "E28V" - ], - "NS1": [ - "V220I" - ], - "NS2A": [ - "T25S", - "F87Y", - "T171V" - ], - "NS2B": [ - "L21F" - ], - "NS3": [ - "N119T" - ], - "NS4B": [ - "I150M" - ], - "NS5": [ - "E558V", - "V637A", - "I641N", - "N645D" ] - }, - "labels": { - "aa": "M: E28V; NS1: V220I; NS2A: T25S, F87Y, T171V; NS2B: L21F; NS3: N119T; NS4B: I150M; NS5: E558V, V637A, I641N, N645D" } } }, { - "name": "NODE_0000254", + "name": "NODE_0000294", "node_attrs": { - "div": 0.27837009999999995, + "div": 0.278, "clade_membership": { "value": "2II_D" } @@ -48853,10 +41805,7 @@ { "name": "MW512364.1|2011", "node_attrs": { - "div": 0.28951319999999997, - "country": { - "value": "Singapore" - }, + "div": 0.29, "clade_membership": { "value": "2II_D" } @@ -48976,42 +41925,14 @@ "G9662A", "C9801A", "A10245G" - ], - "E": [ - "I322V", - "V484F" - ], - "NS1": [ - "A141T", - "T146A" - ], - "NS2A": [ - "H2R", - "V38F" - ], - "NS3": [ - "R248K", - "H251Y" - ], - "NS4B": [ - "A244T" - ], - "NS5": [ - "S59L", - "K437R", - "K644E", - "R698K" ] - }, - "labels": { - "aa": "E: I322V, V484F; NS1: A141T, T146A; NS2A: H2R, V38F; NS3: R248K, H251Y; NS4B: A244T; NS5: S59L, K437R, K644E, R698K" } } }, { - "name": "NODE_0000255", + "name": "NODE_0000295", "node_attrs": { - "div": 0.2788728, + "div": 0.279, "clade_membership": { "value": "2II_D" } @@ -49030,9 +41951,9 @@ }, "children": [ { - "name": "NODE_0000256", + "name": "NODE_0000296", "node_attrs": { - "div": 0.27976829999999997, + "div": 0.28, "clade_membership": { "value": "2II_D" } @@ -49048,25 +41969,19 @@ "T6120C", "T7162C", "C7815T" - ], - "NS1": [ - "N191S" ] - }, - "labels": { - "aa": "NS1: N191S" } }, "children": [ { "name": "EU179859.1|2006", "node_attrs": { - "div": 0.30261629999999995, - "country": { - "value": "Brunei" - }, + "div": 0.303, "clade_membership": { "value": "2II_D" + }, + "country": { + "value": "Brunei" } }, "branch_attrs": { @@ -49300,80 +42215,14 @@ "T9512C", "T9811A", "G10266T" - ], - "E": [ - "E235K", - "A419V" - ], - "M": [ - "A160T" - ], - "NS1": [ - "K69R", - "A205T", - "K227R", - "F247I" - ], - "NS2A": [ - "V12I", - "V27I", - "T29A", - "A32T", - "V36T", - "V38I", - "S39T", - "M48L", - "F50Y", - "R51K", - "M57I", - "V58I", - "T63A", - "D67E", - "I68M", - "A89V", - "L92V", - "T104A", - "T115A", - "I116L", - "E118N", - "T119D", - "I120V", - "E122A", - "M131I", - "V133I", - "I136L", - "N139K", - "V147A", - "I149V", - "I152L", - "A158I", - "V159M", - "L161I", - "Q186R" - ], - "NS4A": [ - "Q19H", - "R22I" - ], - "NS4B": [ - "I89M" - ], - "NS5": [ - "N273D", - "V648A", - "L748M", - "L899F" ] - }, - "labels": { - "aa": "E: E235K, A419V; M: A160T; NS1: K69R, A205T, K227R, F247I; NS2A: V12I, V27I, T29A, A32T, V36T, V38I, S39T, M48L, F50Y, R51K, M57I, V58I, T63A, D67E, I68M, A89V, L92V, T104A, T115A, I116L, E118N, T119D, I120V, E122A, M131I, V133I, I136L, N139K, V147A, I149V, I152L, A158I, V159M, L161I, Q186R; NS4A: Q19H, R22I; NS4B: I89M; NS5: N273D, V648A, L748M, L899F" } } }, { - "name": "NODE_0000257", + "name": "NODE_0000297", "node_attrs": { - "div": 0.27995285, + "div": 0.28, "clade_membership": { "value": "2II_D" } @@ -49390,10 +42239,7 @@ { "name": "MH048673.1|2014-12", "node_attrs": { - "div": 0.28914224, - "country": { - "value": "Malaysia" - }, + "div": 0.289, "clade_membership": { "value": "2II_D" } @@ -49493,41 +42339,14 @@ "C9576T", "T9732A", "G9771T" - ], - "C": [ - "T101N" - ], - "E": [ - "H346Q" - ], - "NS1": [ - "S222N", - "H224Y" - ], - "NS2A": [ - "I33V", - "V36I" - ], - "NS4A": [ - "T3A" - ], - "NS4B": [ - "I18S" - ], - "NS5": [ - "S23G", - "T290I" ] - }, - "labels": { - "aa": "C: T101N; E: H346Q; NS1: S222N, H224Y; NS2A: I33V, V36I; NS4A: T3A; NS4B: I18S; NS5: S23G, T290I" } } }, { - "name": "NODE_0000258", + "name": "NODE_0000298", "node_attrs": { - "div": 0.28279668999999996, + "div": 0.283, "clade_membership": { "value": "2II_D.2" } @@ -49564,21 +42383,17 @@ "C9549T", "T9675C", "A10059G" - ], - "NS2A": [ - "S114A" ] }, "labels": { - "aa": "NS2A: S114A", "lineage": "2II_D.2" } }, "children": [ { - "name": "NODE_0000259", + "name": "NODE_0000299", "node_attrs": { - "div": 0.28730188999999995, + "div": 0.287, "clade_membership": { "value": "2II_D.2" } @@ -49632,34 +42447,19 @@ "A9969G", "T10023C", "A10062G" - ], - "NS1": [ - "L171M" - ], - "NS2A": [ - "S215N" - ], - "NS2B": [ - "I106V" - ], - "NS4B": [ - "S25N" ] - }, - "labels": { - "aa": "NS1: L171M; NS2A: S215N; NS2B: I106V; NS4B: S25N" } }, "children": [ { "name": "JX470186.1|2010", "node_attrs": { - "div": 0.28749938999999997, - "country": { - "value": "China" - }, + "div": 0.287, "clade_membership": { "value": "2II_D.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -49667,28 +42467,19 @@ "nuc": [ "T1559C", "T4472C" - ], - "E": [ - "V208A" - ], - "NS2B": [ - "I114T" ] - }, - "labels": { - "aa": "E: V208A; NS2B: I114T" } } }, { "name": "MF043956.1|2016", "node_attrs": { - "div": 0.28818691999999996, - "country": { - "value": "China" - }, + "div": 0.288, "clade_membership": { "value": "2II_D.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -49703,32 +42494,16 @@ "A4854G", "G7189A", "A8739G" - ], - "E": [ - "T120K" - ], - "NS2B": [ - "T94I" - ], - "NS3": [ - "A108T", - "V109F" - ], - "NS4B": [ - "G122R" ] - }, - "labels": { - "aa": "E: T120K; NS2B: T94I; NS3: A108T, V109F; NS4B: G122R" } } } ] }, { - "name": "NODE_0000260", + "name": "NODE_0000300", "node_attrs": { - "div": 0.28537967, + "div": 0.285, "clade_membership": { "value": "2II_D.2" } @@ -49765,25 +42540,19 @@ "T9789A", "G9999A", "C10005T" - ], - "NS5": [ - "K524M" ] - }, - "labels": { - "aa": "NS5: K524M" } }, "children": [ { "name": "KC762680.1|2010-04-05", "node_attrs": { - "div": 0.28901337, - "country": { - "value": "Indonesia" - }, + "div": 0.289, "clade_membership": { "value": "2II_D.2" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -49823,28 +42592,14 @@ "C10155T", "T10190A", "A10250G" - ], - "E": [ - "H346Y", - "S390N" - ], - "NS3": [ - "S392F" - ], - "NS5": [ - "I874K", - "E894G" ] - }, - "labels": { - "aa": "E: H346Y, S390N; NS3: S392F; NS5: I874K, E894G" } } }, { - "name": "NODE_0000261", + "name": "NODE_0000301", "node_attrs": { - "div": 0.29528361999999997, + "div": 0.295, "clade_membership": { "value": "2II_D.2" } @@ -49949,42 +42704,19 @@ "C10186T", "G10241A", "A10257G" - ], - "E": [ - "I379V" - ], - "M": [ - "I139V" - ], - "NS1": [ - "R174K" - ], - "NS3": [ - "S392T" - ], - "NS4A": [ - "T59A" - ], - "NS5": [ - "R520K", - "E560R", - "R891K" ] - }, - "labels": { - "aa": "E: I379V; M: I139V; NS1: R174K; NS3: S392T; NS4A: T59A; NS5: R520K, E560R, R891K" } }, "children": [ { "name": "MK783204.1|2018", "node_attrs": { - "div": 0.29567771, - "country": { - "value": "China" - }, + "div": 0.296, "clade_membership": { "value": "2II_D.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -49995,25 +42727,19 @@ "G9228C", "A9789C", "G10125A" - ], - "NS5": [ - "F243L" ] - }, - "labels": { - "aa": "NS5: F243L" } } }, { "name": "ON890351.1|2017-08-07", "node_attrs": { - "div": 0.29616813999999997, - "country": { - "value": "China" - }, + "div": 0.296, "clade_membership": { "value": "2II_D.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50027,13 +42753,7 @@ "T6189C", "T6528C", "T8742C" - ], - "NS2A": [ - "K166E" ] - }, - "labels": { - "aa": "NS2A: K166E" } } } @@ -50048,9 +42768,9 @@ ] }, { - "name": "NODE_0000262", + "name": "NODE_0000302", "node_attrs": { - "div": 0.28566505, + "div": 0.286, "clade_membership": { "value": "2II_D.1" } @@ -50127,28 +42847,17 @@ "A9327G", "C9384T", "C9792T" - ], - "NS1": [ - "A117T" - ], - "NS2A": [ - "T63A", - "I116M" - ], - "NS4B": [ - "I18T" ] }, "labels": { - "aa": "NS1: A117T; NS2A: T63A, I116M; NS4B: I18T", "lineage": "2II_D.1" } }, "children": [ { - "name": "NODE_0000263", + "name": "NODE_0000303", "node_attrs": { - "div": 0.28894596, + "div": 0.289, "clade_membership": { "value": "2II_D.1.2" } @@ -50190,19 +42899,9 @@ "C9825T", "A10050G", "C10155T" - ], - "NS2B": [ - "P27S" - ], - "NS4A": [ - "T63A" - ], - "NS5": [ - "V648A" ] }, "labels": { - "aa": "NS2B: P27S; NS4A: T63A; NS5: V648A", "lineage": "2II_D.1.2" } }, @@ -50210,12 +42909,12 @@ { "name": "KX655788.1|2015", "node_attrs": { - "div": 0.2893391, - "country": { - "value": "China" - }, + "div": 0.289, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50230,9 +42929,9 @@ } }, { - "name": "NODE_0000264", + "name": "NODE_0000304", "node_attrs": { - "div": 0.28894696, + "div": 0.289, "clade_membership": { "value": "2II_D.1.2" } @@ -50242,9 +42941,9 @@ }, "children": [ { - "name": "NODE_0000265", + "name": "NODE_0000305", "node_attrs": { - "div": 0.29023287, + "div": 0.29, "clade_membership": { "value": "2II_D.1.2" } @@ -50273,12 +42972,12 @@ { "name": "OR236115.1|2014-12", "node_attrs": { - "div": 0.29103421999999995, - "country": { - "value": "Reunion" - }, + "div": 0.291, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -50290,23 +42989,14 @@ "A8664G", "T9138C", "T9735C" - ], - "NS3": [ - "A367T" - ], - "NS4B": [ - "L112F" ] - }, - "labels": { - "aa": "NS3: A367T; NS4B: L112F" } } }, { - "name": "NODE_0000266", + "name": "NODE_0000306", "node_attrs": { - "div": 0.29034411, + "div": 0.29, "clade_membership": { "value": "2II_D.1.2" } @@ -50325,12 +43015,12 @@ { "name": "OR236087.1|2014-05", "node_attrs": { - "div": 0.29176147999999996, - "country": { - "value": "Reunion" - }, + "div": 0.292, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -50353,12 +43043,12 @@ { "name": "OR236114.1|2014-03", "node_attrs": { - "div": 0.29238048, - "country": { - "value": "Reunion" - }, + "div": 0.292, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -50380,13 +43070,7 @@ "C9411T", "T10155C", "T10236C" - ], - "NS2A": [ - "A37V" ] - }, - "labels": { - "aa": "NS2A: A37V" } } } @@ -50395,9 +43079,9 @@ ] }, { - "name": "NODE_0000267", + "name": "NODE_0000307", "node_attrs": { - "div": 0.28912753999999996, + "div": 0.289, "clade_membership": { "value": "2II_D.1.2" } @@ -50410,26 +43094,19 @@ "G4035-", "C4036G", "G6678A" - ], - "NS2A": [ - "Q186-", - "Q187E" ] - }, - "labels": { - "aa": "NS2A: Q186-, Q187E" } }, "children": [ { "name": "MZ857214.1|2014", "node_attrs": { - "div": 0.29013503999999996, - "country": { - "value": "Tanzania" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Tanzania" } }, "branch_attrs": { @@ -50445,20 +43122,14 @@ "T8742C", "C9199T", "T9829C" - ], - "NS2A": [ - "I33M" ] - }, - "labels": { - "aa": "NS2A: I33M" } } }, { - "name": "NODE_0000268", + "name": "NODE_0000308", "node_attrs": { - "div": 0.28984491999999995, + "div": 0.29, "clade_membership": { "value": "2II_D.1.2" } @@ -50480,12 +43151,12 @@ { "name": "MZ857208.1|2013", "node_attrs": { - "div": 0.29006526999999993, - "country": { - "value": "Kenya" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Kenya" } }, "branch_attrs": { @@ -50500,12 +43171,12 @@ { "name": "OR236116.1|2014-05", "node_attrs": { - "div": 0.29157305999999994, - "country": { - "value": "Reunion" - }, + "div": 0.292, "clade_membership": { "value": "2II_D.1.2" + }, + "country": { + "value": "Reunion" } }, "branch_attrs": { @@ -50531,23 +43202,7 @@ "A8946G", "T9208C", "C9672T" - ], - "NS1": [ - "S222N" - ], - "NS2A": [ - "-186Q", - "E187Q" - ], - "NS4B": [ - "L112F" - ], - "NS5": [ - "L434M" ] - }, - "labels": { - "aa": "NS1: S222N; NS2A: -186Q, E187Q; NS4B: L112F; NS5: L434M" } } } @@ -50560,9 +43215,9 @@ ] }, { - "name": "NODE_0000269", + "name": "NODE_0000309", "node_attrs": { - "div": 0.28588355, + "div": 0.286, "clade_membership": { "value": "2II_D.1" } @@ -50579,12 +43234,12 @@ { "name": "MW512415.1|2014", "node_attrs": { - "div": 0.28855629, - "country": { - "value": "Singapore" - }, + "div": 0.289, "clade_membership": { "value": "2II_D.1" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -50618,26 +43273,14 @@ "A8301T", "A9499G", "C9504T" - ], - "NS1": [ - "K214R" - ], - "NS2A": [ - "T171I" - ], - "NS5": [ - "K644E" ] - }, - "labels": { - "aa": "NS1: K214R; NS2A: T171I; NS5: K644E" } } }, { - "name": "NODE_0000270", + "name": "NODE_0000310", "node_attrs": { - "div": 0.2866151, + "div": 0.287, "clade_membership": { "value": "2II_D.1" } @@ -50659,12 +43302,12 @@ { "name": "MK564478.1|2016-04-22", "node_attrs": { - "div": 0.2921806, - "country": { - "value": "China" - }, + "div": 0.292, "clade_membership": { "value": "2II_D.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50726,33 +43369,14 @@ "C9741T", "C9957T", "C10032T" - ], - "E": [ - "S363N", - "V365I" - ], - "NS1": [ - "L171M", - "F247L" - ], - "NS2A": [ - "K95R", - "T171I" - ], - "NS3": [ - "L216F", - "I395T" ] - }, - "labels": { - "aa": "E: S363N, V365I; NS1: L171M, F247L; NS2A: K95R, T171I; NS3: L216F, I395T" } } }, { - "name": "NODE_0000271", + "name": "NODE_0000311", "node_attrs": { - "div": 0.28895814000000003, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" } @@ -50784,19 +43408,9 @@ "G9857A", "T9927C", "A10029G" - ], - "NS3": [ - "N499S" - ], - "NS4A": [ - "T63A" - ], - "NS5": [ - "S763N" ] }, "labels": { - "aa": "NS3: N499S; NS4A: T63A; NS5: S763N", "lineage": "2II_D.1.1" } }, @@ -50804,12 +43418,12 @@ { "name": "KT187553.1|2014", "node_attrs": { - "div": 0.28925290000000003, - "country": { - "value": "China" - }, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50823,9 +43437,9 @@ } }, { - "name": "NODE_0000272", + "name": "NODE_0000312", "node_attrs": { - "div": 0.28895914, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" } @@ -50835,9 +43449,9 @@ }, "children": [ { - "name": "NODE_0000273", + "name": "NODE_0000313", "node_attrs": { - "div": 0.28896014, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" } @@ -50849,12 +43463,12 @@ { "name": "KT187557.1|2014", "node_attrs": { - "div": 0.28964799999999996, - "country": { - "value": "China" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50867,25 +43481,19 @@ "T3861C", "C3981T", "A7884G" - ], - "NS1": [ - "V251M" ] - }, - "labels": { - "aa": "NS1: V251M" } } }, { "name": "KP012546.1|2014", "node_attrs": { - "div": 0.29013961, - "country": { - "value": "China" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50910,9 +43518,9 @@ ] }, { - "name": "NODE_0000274", + "name": "NODE_0000314", "node_attrs": { - "div": 0.28896014, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" } @@ -50928,12 +43536,12 @@ { "name": "MW721466.1|2014-10", "node_attrs": { - "div": 0.29004146, - "country": { - "value": "China" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50949,30 +43557,14 @@ "C7524T", "C7973T", "A9143G" - ], - "E": [ - "H52Y" - ], - "NS1": [ - "Y256H" - ], - "NS4B": [ - "T19I" - ], - "NS5": [ - "T135I", - "K525R" ] - }, - "labels": { - "aa": "E: H52Y; NS1: Y256H; NS4B: T19I; NS5: T135I, K525R" } } }, { - "name": "NODE_0000275", + "name": "NODE_0000315", "node_attrs": { - "div": 0.28905938, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" } @@ -50984,12 +43576,12 @@ { "name": "KX225485.1|2015", "node_attrs": { - "div": 0.28945446999999996, - "country": { - "value": "China" - }, + "div": 0.289, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -50999,25 +43591,19 @@ "G5568A", "T5688A", "G8569A" - ], - "NS5": [ - "V334I" ] - }, - "labels": { - "aa": "NS5: V334I" } } }, { "name": "MW721468.1|2014-10", "node_attrs": { - "div": 0.28964903999999997, - "country": { - "value": "China" - }, + "div": 0.29, "clade_membership": { "value": "2II_D.1.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -51029,13 +43615,7 @@ "A6174G", "A6372G", "C6864T" - ], - "NS2A": [ - "K135R" ] - }, - "labels": { - "aa": "NS2A: K135R" } } } @@ -51064,9 +43644,9 @@ ] }, { - "name": "NODE_0000276", + "name": "NODE_0000316", "node_attrs": { - "div": 0.27564512, + "div": 0.276, "clade_membership": { "value": "2II_F" } @@ -51092,6 +43672,7 @@ "C4938T", "G5280A", "T5508C", + "T6072C", "T6117A", "G6309A", "G6375A", @@ -51105,24 +43686,17 @@ "C8340T", "A9278G", "A9318G" - ], - "E": [ - "V129I" - ], - "NS5": [ - "K570R" ] }, "labels": { - "aa": "E: V129I; NS5: K570R", "lineage": "2II_F" } }, "children": [ { - "name": "NODE_0000277", + "name": "NODE_0000317", "node_attrs": { - "div": 0.27718304000000005, + "div": 0.277, "clade_membership": { "value": "2II_F" } @@ -51143,7 +43717,6 @@ "T5766C", "A7038G", "A7905G", - "C8310T", "C9042T", "C9741T", "C10032T" @@ -51154,12 +43727,12 @@ { "name": "MK578532.1|2016-04-01", "node_attrs": { - "div": 0.29092784000000005, - "country": { - "value": "China" - }, + "div": 0.291, "clade_membership": { "value": "2II_F" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -51249,7 +43822,6 @@ "G5902A", "T5967C", "T6009C", - "T6072C", "C6075T", "C6321T", "G6354A", @@ -51304,41 +43876,14 @@ "T10173C", "G10200A", "C10215T" - ], - "C": [ - "A102V" - ], - "E": [ - "V181I" - ], - "NS1": [ - "V84I", - "T109I" - ], - "NS2A": [ - "V83I" - ], - "NS3": [ - "V461I" - ], - "NS5": [ - "G148W", - "K181M", - "Q198H", - "N223D", - "V605I", - "S757F" ] - }, - "labels": { - "aa": "C: A102V; E: V181I; NS1: V84I, T109I; NS2A: V83I; NS3: V461I; NS5: G148W, K181M, Q198H, N223D, V605I, S757F" } } }, { - "name": "NODE_0000278", + "name": "NODE_0000318", "node_attrs": { - "div": 0.27821968, + "div": 0.278, "clade_membership": { "value": "2II_F" } @@ -51353,6 +43898,7 @@ "A4713G", "T5316C", "T5340C", + "C6072T", "T6238C", "T6987C", "C8676T" @@ -51363,10 +43909,7 @@ { "name": "MW730833.1|2017-07", "node_attrs": { - "div": 0.28415055, - "country": { - "value": "Nepal" - }, + "div": 0.284, "clade_membership": { "value": "2II_F" } @@ -51434,27 +43977,14 @@ "C9480T", "T9558C", "A9660T" - ], - "NS1": [ - "I21V", - "A117T" - ], - "NS2A": [ - "S212A" - ], - "NS5": [ - "G430E" ] - }, - "labels": { - "aa": "NS1: I21V, A117T; NS2A: S212A; NS5: G430E" } } }, { - "name": "NODE_0000279", + "name": "NODE_0000319", "node_attrs": { - "div": 0.2808157, + "div": 0.281, "clade_membership": { "value": "2II_F.2" } @@ -51490,16 +44020,9 @@ "T9512A", "T10084C", "G10272A" - ], - "E": [ - "V484I" - ], - "NS5": [ - "V648E" ] }, "labels": { - "aa": "E: V484I; NS5: V648E", "lineage": "2II_F.2" } }, @@ -51507,12 +44030,12 @@ { "name": "MW512377.1|2012", "node_attrs": { - "div": 0.2856996, - "country": { - "value": "Singapore" - }, + "div": 0.286, "clade_membership": { "value": "2II_F.2" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -51567,37 +44090,16 @@ "T9906C", "A10000G", "A10029G" - ], - "C": [ - "A102V" - ], - "E": [ - "R210K", - "I432T" - ], - "NS2A": [ - "S39A", - "V41M" - ], - "NS4A": [ - "I116T" - ], - "NS5": [ - "N440S", - "T811A" ] - }, - "labels": { - "aa": "C: A102V; E: R210K, I432T; NS2A: S39A, V41M; NS4A: I116T; NS5: N440S, T811A" } } }, { - "name": "NODE_0000280", + "name": "NODE_0000320", "node_attrs": { - "div": 0.28189792, + "div": 0.282, "clade_membership": { - "value": "2II_F.2" + "value": "2II_F.2.1" } }, "branch_attrs": { @@ -51615,22 +44117,19 @@ "G8640A", "C9387T", "G9726A" - ], - "NS2A": [ - "T171I" ] }, "labels": { - "aa": "NS2A: T171I" + "lineage": "2II_F.2.1" } }, "children": [ { - "name": "NODE_0000281", + "name": "NODE_0000321", "node_attrs": { - "div": 0.28237875, + "div": 0.282, "clade_membership": { - "value": "2II_F.2" + "value": "2II_F.2.1" } }, "branch_attrs": { @@ -51648,12 +44147,12 @@ { "name": "ON890422.1|2019-09-16", "node_attrs": { - "div": 0.29293125000000003, + "div": 0.293, + "clade_membership": { + "value": "2II_F.2.1" + }, "country": { "value": "China" - }, - "clade_membership": { - "value": "2II_F.2" } }, "branch_attrs": { @@ -51764,41 +44263,14 @@ "T9811C", "C10001T", "C10140T" - ], - "E": [ - "N203D", - "T303I", - "V461I" - ], - "M": [ - "F149L" - ], - "NS1": [ - "R174K", - "N191K", - "F279L" - ], - "NS3": [ - "I273V", - "I395V" - ], - "NS4B": [ - "I96V" - ], - "NS5": [ - "E653D", - "T811I" ] - }, - "labels": { - "aa": "E: N203D, T303I, V461I; M: F149L; NS1: R174K, N191K, F279L; NS3: I273V, I395V; NS4B: I96V; NS5: E653D, T811I" } } }, { - "name": "NODE_0000282", + "name": "NODE_0000322", "node_attrs": { - "div": 0.28489983, + "div": 0.285, "clade_membership": { "value": "2II_F.2.1" } @@ -51832,26 +44304,19 @@ "A9489G", "C9825T", "C10158T" - ], - "NS2B": [ - "Q93L" ] - }, - "labels": { - "aa": "NS2B: Q93L", - "lineage": "2II_F.2.1" } }, "children": [ { "name": "KU517846.1|2014-05-07", "node_attrs": { - "div": 0.28973378, - "country": { - "value": "Indonesia" - }, + "div": 0.29, "clade_membership": { "value": "2II_F.2.1" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -51906,24 +44371,14 @@ "G9627A", "G9628A", "C9918T" - ], - "NS2A": [ - "V41M" - ], - "NS5": [ - "N184S", - "V687I" ] - }, - "labels": { - "aa": "NS2A: V41M; NS5: N184S, V687I" } } }, { - "name": "NODE_0000283", + "name": "NODE_0000323", "node_attrs": { - "div": 0.28509596000000004, + "div": 0.285, "clade_membership": { "value": "2II_F.2.1" } @@ -51933,25 +44388,19 @@ "nuc": [ "T2289G", "A2930G" - ], - "NS1": [ - "K170R" ] - }, - "labels": { - "aa": "NS1: K170R" } }, "children": [ { "name": "MN018353.1|2016-06-15", "node_attrs": { - "div": 0.29191294, - "country": { - "value": "China" - }, + "div": 0.292, "clade_membership": { "value": "2II_F.2.1" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -52026,33 +44475,14 @@ "C9618T", "A10035G", "C10212T" - ], - "E": [ - "I23V", - "I322V", - "V461A" - ], - "NS1": [ - "Y256H" - ], - "NS3": [ - "G32N", - "Y33S" - ], - "NS5": [ - "T400S", - "S631T" ] - }, - "labels": { - "aa": "E: I23V, I322V, V461A; NS1: Y256H; NS3: G32N, Y33S; NS5: T400S, S631T" } } }, { - "name": "NODE_0000284", + "name": "NODE_0000324", "node_attrs": { - "div": 0.28537694, + "div": 0.285, "clade_membership": { "value": "2II_F.2.1" } @@ -52072,12 +44502,12 @@ { "name": "MW512465.1|2016", "node_attrs": { - "div": 0.29051727000000005, - "country": { - "value": "Singapore" - }, + "div": 0.291, "clade_membership": { "value": "2II_F.2.1" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -52133,32 +44563,14 @@ "C9605T", "C9708T", "T10083C" - ], - "E": [ - "S81A" - ], - "NS2A": [ - "I171T" - ], - "NS4B": [ - "F13L" - ], - "NS5": [ - "P336S", - "R649K", - "V650A", - "T679I" ] - }, - "labels": { - "aa": "E: S81A; NS2A: I171T; NS4B: F13L; NS5: P336S, R649K, V650A, T679I" } } }, { - "name": "NODE_0000285", + "name": "NODE_0000325", "node_attrs": { - "div": 0.29033403, + "div": 0.29, "clade_membership": { "value": "2II_F.2.1" } @@ -52215,33 +44627,19 @@ "G9489A", "T9558C", "T10173C" - ], - "NS2A": [ - "V137I" - ], - "NS4B": [ - "L15F" - ], - "NS5": [ - "K193R", - "G430E", - "N440S" ] - }, - "labels": { - "aa": "NS2A: V137I; NS4B: L15F; NS5: K193R, G430E, N440S" } }, "children": [ { "name": "MW730819.1|2017-07", "node_attrs": { - "div": 0.29122286000000003, - "country": { - "value": "Nepal" - }, + "div": 0.291, "clade_membership": { "value": "2II_F.2.1" + }, + "country": { + "value": "Nepal" } }, "branch_attrs": { @@ -52255,26 +44653,19 @@ "A9503C", "T9518C", "G10254A" - ], - "NS5": [ - "N645T", - "V650A" ] - }, - "labels": { - "aa": "NS5: N645T, V650A" } } }, { "name": "MW730830.1|2017-07", "node_attrs": { - "div": 0.29141507, - "country": { - "value": "Nepal" - }, + "div": 0.291, "clade_membership": { "value": "2II_F.2.1" + }, + "country": { + "value": "Nepal" } }, "branch_attrs": { @@ -52291,19 +44682,7 @@ "A8160G", "A8315G", "A9213G" - ], - "E": [ - "P364S" - ], - "NS3": [ - "A558V" - ], - "NS5": [ - "K249R" ] - }, - "labels": { - "aa": "E: P364S; NS3: A558V; NS5: K249R" } } } @@ -52318,11 +44697,11 @@ ] }, { - "name": "NODE_0000286", + "name": "NODE_0000326", "node_attrs": { - "div": 0.28190061000000005, + "div": 0.282, "clade_membership": { - "value": "2II_F.2" + "value": "2II_F.2.1" } }, "branch_attrs": { @@ -52332,12 +44711,12 @@ { "name": "OQ028230.1|2020-09-07", "node_attrs": { - "div": 0.29388681000000005, - "country": { - "value": "Vietnam" - }, + "div": 0.294, "clade_membership": { - "value": "2II_F.2" + "value": "2II_F.2.1" + }, + "country": { + "value": "Viet Nam" } }, "branch_attrs": { @@ -52459,35 +44838,16 @@ "C10005T", "G10119A", "C10186T" - ], - "E": [ - "K307R" - ], - "NS1": [ - "K85R", - "V177A", - "F178L" - ], - "NS2A": [ - "L121F", - "V137I" - ], - "NS3": [ - "L31F", - "I519V" ] - }, - "labels": { - "aa": "E: K307R; NS1: K85R, V177A, F178L; NS2A: L121F, V137I; NS3: L31F, I519V" } } }, { - "name": "NODE_0000287", + "name": "NODE_0000327", "node_attrs": { - "div": 0.28217742000000007, + "div": 0.282, "clade_membership": { - "value": "2II_F.2" + "value": "2II_F.2.1" } }, "branch_attrs": { @@ -52503,12 +44863,12 @@ { "name": "MW512430.1|2014", "node_attrs": { - "div": 0.29001396000000007, + "div": 0.29, + "clade_membership": { + "value": "2II_F.2.1" + }, "country": { "value": "Singapore" - }, - "clade_membership": { - "value": "2II_F.2" } }, "branch_attrs": { @@ -52593,41 +44953,14 @@ "C9859T", "C9882T", "C9889T" - ], - "E": [ - "H52Y", - "N203S", - "D362E" - ], - "NS1": [ - "S114T", - "F178L", - "N344T" - ], - "NS2A": [ - "V41M" - ], - "NS2B": [ - "I99V" - ], - "NS3": [ - "N277S", - "K592R" - ], - "NS5": [ - "M337T", - "R749K" ] - }, - "labels": { - "aa": "E: H52Y, N203S, D362E; NS1: S114T, F178L, N344T; NS2A: V41M; NS2B: I99V; NS3: N277S, K592R; NS5: M337T, R749K" } } }, { - "name": "NODE_0000288", + "name": "NODE_0000328", "node_attrs": { - "div": 0.28605246000000006, + "div": 0.286, "clade_membership": { "value": "2II_F.2.2" } @@ -52674,21 +45007,9 @@ "T9753C", "A9876G", "C9938T" - ], - "E": [ - "V181A" - ], - "M": [ - "I135V" - ], - "NS5": [ - "R246K", - "K562R", - "T790I" ] }, "labels": { - "aa": "E: V181A; M: I135V; NS5: R246K, K562R, T790I", "lineage": "2II_F.2.2" } }, @@ -52696,12 +45017,12 @@ { "name": "KX380836.1|2013", "node_attrs": { - "div": 0.29050369000000004, - "country": { - "value": "Singapore" - }, + "div": 0.291, "clade_membership": { "value": "2II_F.2.2" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -52752,23 +45073,14 @@ "T7182C", "A7275G", "T9273C" - ], - "NS4A": [ - "R22K" - ], - "NS4B": [ - "I150M" ] - }, - "labels": { - "aa": "NS4A: R22K; NS4B: I150M" } } }, { - "name": "NODE_0000289", + "name": "NODE_0000329", "node_attrs": { - "div": 0.28693380000000007, + "div": 0.287, "clade_membership": { "value": "2II_F.2.2" } @@ -52785,135 +45097,37 @@ "T7176C", "C7245T", "A7320G" - ], - "NS4B": [ - "E24D" ] - }, - "labels": { - "aa": "NS4B: E24D" } }, "children": [ { - "name": "NODE_0000290", + "name": "MW512379.1|2012", "node_attrs": { - "div": 0.28733954000000006, + "div": 0.287, "clade_membership": { "value": "2II_F.2.2" + }, + "country": { + "value": 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-1,3 +1,7 @@ +## Unreleased + +- Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages. + ## 2024-08-31T20:44:06Z Initial release of a DENV-3 dataset for Lineage classification! diff --git a/data/community/v-gen-lab/dengue/denv3/tree.json b/data/community/v-gen-lab/dengue/denv3/tree.json index 8b277449..2effc252 100644 --- a/data/community/v-gen-lab/dengue/denv3/tree.json +++ b/data/community/v-gen-lab/dengue/denv3/tree.json @@ -2,7 +2,7 @@ "version": "v2", "meta": { "title": "Dengue Lineages of DENV-3", - "updated": "2024-08-16", + "updated": "2024-09-10", "build_url": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade", "data_provenance": [ { @@ -24,86 +24,8 @@ "color_by": "country" }, "genome_annotations": { - "2K": { - "end": 6820, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 6752, - "strand": "+", - "type": "CDS" - }, - "C": { - "end": 436, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 95, - "strand": "+", - "type": "CDS" - }, - "E": { - "end": 2413, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 935, - "strand": "+", - "type": "CDS" - }, - "M": { - "end": 934, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 437, - "strand": "+", - "type": "CDS" - }, - "NS1": { - "end": 3469, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 2414, - "strand": "+", - "type": "CDS" - }, - "NS2A": { - "end": 4123, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 3470, - "strand": "+", - "type": "CDS" - }, - "NS2B": { - "end": 4513, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 4124, - "strand": "+", - "type": "CDS" - }, - "NS3": { - "end": 6370, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 4514, - "strand": "+", - "type": "CDS" - }, - "NS4A": { - "end": 6751, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 6371, - "strand": "+", - "type": "CDS" - }, - "NS4B": { - "end": 7564, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 6821, - "strand": "+", - "type": "CDS" - }, - "NS5": { - "end": 10264, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv3.gb", - "start": 7565, - "strand": "+", - "type": "CDS" - }, 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"div": 0.0385954, - "country": { - "value": "Puerto Rico" - }, + "div": 0.0386, "clade_membership": { "value": "Outgroup" } @@ -1575,125 +1382,9 @@ "G10233A", "A10249G", "C10258T" - ], - "2K": [ - "I20V", - "V21I" - ], - "C": [ - "N39D", - "A63T", - "K86R", - "K100R" - ], - "E": [ - "A50V", - "E62G", - "G63A", - "I68T", - "I81T", - "Q120H", - "S124L", - "V139I", - "E154K", - "A171V", - "I172T", - "T224A", - "T226V", - "T270I", - "L301S", - "N302G", - "I380T", - "K386R", - "K391R", - "L430F", - "V459I", - "A479V" - ], - "M": [ - "G15R", - "I31T", - "K90R", - "L128F", - "I135L", - "I156T" - ], - "NS1": [ - "S17N", - "N52S", - "K69R", - "V96I", - "T103I", - "Y113H", - "T128I", - "S145N", - "V174M", - "R192K", - "H256Y" - ], - "NS2A": [ - "L37F", - "S45L", - "V72I", - "I83V", - "T147A", - "I171V", - "I208V", - "S210N", - "L215F" - ], - "NS2B": [ - "V59I", - "N93S", - "T123A" - ], - "NS3": [ - "K33R", - "V155I", - "I283V", - "I352V", - "K585R" - ], - "NS4A": [ - "L4F", - "N23S", - "A90T" - ], - "NS4B": [ - "T16I", - "P24S", - "M87V", - "T108I", - "I201M" - ], - "NS5": [ - "K23R", - "E24D", - "L27F", - "I50T", - "M127T", - "T155A", - "T188A", - "H200Y", - "R248K", - "I251M", - "K281E", - "I375T", - "T399I", - "V402I", - "M408I", - "Y482F", - "Q554R", - "K650E", - "K698R", - "Q705L", - "T763A", - "V836I", - "R890K" ] }, "labels": { - "aa": "2K: I20V, V21I; C: N39D, A63T, K86R, K100R; E: A50V, E62G, G63A, I68T, I81T, Q120H, S124L, V139I, E154K, A171V, I172T, T224A, T226V, T270I, L301S, N302G, I380T, K386R, K391R, L430F, V459I, A479V; M: G15R, I31T, K90R, L128F, I135L, I156T; NS1: S17N, N52S, K69R, V96I, T103I, Y113H, T128I, S145N, V174M, R192K, H256Y; NS2A: L37F, S45L, V72I, I83V, T147A, I171V, I208V, S210N, L215F; NS2B: V59I, N93S, T123A; NS3: K33R, V155I, I283V, I352V, K585R; NS4A: L4F, N23S, A90T; NS4B: T16I, P24S, M87V, T108I, I201M; NS5: K23R, E24D, L27F, I50T, M127T, T155A, T188A, H200Y, R248K, I251M, K281E, I375T, T399I, V402I, M408I, Y482F, Q554R, K650E, K698R, Q705L, T763A, V836I, R890K", "lineage": "Outgroup" } } @@ -1701,7 +1392,7 @@ { "name": "NODE_0000001", "node_attrs": { - "div": 0.0377074, + "div": 0.0377, "clade_membership": { "value": "unassigned" } @@ -1750,46 +1441,14 @@ "A9754C", "A9884C", "A10200T" - ], - "E": [ - "E22D" - ], - "M": [ - "M148L" - ], - "NS1": [ - "I178L" - ], - "NS2A": [ - "N55H", - "I159F" - ], - "NS2B": [ - "V4L" - ], - "NS3": [ - "K482N" - ], - "NS4B": [ - "T16S" - ], - "NS5": [ - "T629S", - "I639L", - "K645Q", - "I774L", - "Y879F" ] - }, - "labels": { - "aa": "E: E22D; M: M148L; NS1: I178L; NS2A: N55H, I159F; NS2B: V4L; NS3: K482N; NS4B: T16S; NS5: T629S, I639L, K645Q, I774L, Y879F" } }, "children": [ { "name": "NODE_0000002", "node_attrs": { - "div": 0.0487446, + "div": 0.0487, "clade_membership": { "value": "3V" } @@ -1901,26 +1560,9 @@ "T10060G", "C10117A", "T10183C" - ], - "NS1": [ - "N139S", - "T288S", - "V350A" - ], - "NS2A": [ - "T112A", - "Q115R" - ], - "NS4B": [ - "T108A", - "A193V" - ], - "NS5": [ - "L638P" ] }, "labels": { - "aa": "NS1: N139S, T288S, V350A; NS2A: T112A, Q115R; NS4B: T108A, A193V; NS5: L638P", "lineage": "3V" } }, @@ -1928,12 +1570,12 @@ { "name": "KM190937.1|1964", "node_attrs": { - "div": 0.05546407, - "country": { - "value": "Philippines" - }, + "div": 0.0555, "clade_membership": { "value": "3V" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -2006,44 +1648,14 @@ "T9787C", "A9851G", "T9922C" - ], - "E": [ - "T155M", - "A171V", - "L196S", - "T224A", - "N302S", - "T303S", - "S447G", - "I452M" - ], - "M": [ - "L95I" - ], - "NS1": [ - "L217F" - ], - "NS2A": [ - "K30I", - "V201A", - "P202Q" - ], - "NS2B": [ - "I76V" - ], - "NS5": [ - "T763A" ] - }, - "labels": { - "aa": "E: T155M, A171V, L196S, T224A, N302S, T303S, S447G, I452M; M: L95I; NS1: L217F; NS2A: K30I, V201A, P202Q; NS2B: I76V; NS5: T763A" } } }, { "name": "NODE_0000003", "node_attrs": { - "div": 0.04979586, + "div": 0.0498, "clade_membership": { "value": "3V" } @@ -2062,30 +1674,19 @@ "G5822A", "T6907C", "T8056C" - ], - "E": [ - "P164S", - "K391R", - "A489V" - ], - "NS3": [ - "D437N" ] - }, - "labels": { - "aa": "E: P164S, K391R, A489V; NS3: D437N" } }, "children": [ { "name": "KU050695.1|1956", "node_attrs": { - "div": 0.050000619999999996, - "country": { - "value": "Philippines" - }, + "div": 0.05, "clade_membership": { "value": "3V" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -2093,25 +1694,19 @@ "nuc": [ "T988C", "C6890T" - ], - "NS4B": [ - "P24S" ] - }, - "labels": { - "aa": "NS4B: P24S" } } }, { "name": "JQ922554.1|1963", "node_attrs": { - "div": 0.05563182, - "country": { - "value": "USA" - }, + "div": 0.0556, "clade_membership": { "value": "3V" + }, + "country": { + "value": "USA" } }, "branch_attrs": { @@ -2176,61 +1771,7 @@ "A9772G", "G9774A", "A9775G" - ], - "E": [ - "E225K", - "S474A", - "L487V" - ], - "M": [ - "V59L" - ], - "NS1": [ - "K101E" - ], - "NS2A": [ - "G28R" - ], - "NS3": [ - "Q90A", - "E93G", - "V95T", - "P172L", - "V276G", - "P277S", - "R298I", - "A323V", - "N330I", - "A331P", - "D425Y", - "P426L", - "K591N", - "L592W" - ], - "NS4A": [ - "R20T", - "T21V" - ], - "NS4B": [ - "T46P", - "A189P", - "T195A" - ], - "NS5": [ - "I72F", - "L172V", - "T188S", - "R195N", - "M203I", - "G469D", - "D557A", - "P558R", - "I735L", - "R737K" ] - }, - "labels": { - "aa": "E: E225K, S474A, L487V; M: V59L; NS1: K101E; NS2A: G28R; NS3: Q90A, E93G, V95T, P172L, V276G, P277S, R298I, A323V, N330I, A331P, D425Y, P426L, K591N, L592W; NS4A: R20T, T21V; NS4B: T46P, A189P, T195A; NS5: I72F, L172V, T188S, R195N, M203I, G469D, D557A, P558R, I735L, R737K" } } } @@ -2241,7 +1782,7 @@ { "name": "NODE_0000004", "node_attrs": { - "div": 0.04094806, + "div": 0.0409, "clade_membership": { "value": "unassigned" } @@ -2280,23 +1821,14 @@ "C9472T", "T9511C", "G9934A" - ], - "NS1": [ - "T94I" - ], - "NS3": [ - "M476T" ] - }, - "labels": { - "aa": "NS1: T94I; NS3: M476T" } }, "children": [ { "name": "NODE_0000005", "node_attrs": { - "div": 0.05182366, + "div": 0.0518, "clade_membership": { "value": "3I" } @@ -2413,31 +1945,9 @@ "C9760T", "A9772G", "G9810A" - ], - "C": [ - "K82R", - "K97R" - ], - "E": [ - "I68V", - "A169V", - "R231K", - "A479V" - ], - "M": [ - "H55L", - "L128F" - ], - "NS1": [ - "V174M" - ], - "NS5": [ - "K281R", - "R749K" ] }, "labels": { - "aa": "C: K82R, K97R; E: I68V, A169V, R231K, A479V; M: H55L, L128F; NS1: V174M; NS5: K281R, R749K", "lineage": "3I" } }, @@ -2445,12 +1955,12 @@ { "name": "AY496879.2|1997", "node_attrs": { - "div": 0.07252955999999999, - "country": { - "value": "Philippines" - }, + "div": 0.0725, "clade_membership": { "value": "3I" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -2670,56 +2180,14 @@ "T10078C", "C10096T", "T10183C" - ], - "C": [ - "K45R", - "L103F" - ], - "E": [ - "A489T" - ], - "M": [ - "T166A" - ], - "NS1": [ - "I94T" - ], - "NS2A": [ - "L57F", - "V150I", - "I175V", - "M194V", - "T195A", - "P203S" - ], - "NS3": [ - "K26N", - "A207T", - "K589R" - ], - "NS4A": [ - "T81A", - "A90V" - ], - "NS4B": [ - "A110V" - ], - "NS5": [ - "L639P", - "T763S", - "V785A", - "W803R" ] - }, - "labels": { - "aa": "C: K45R, L103F; E: A489T; M: T166A; NS1: I94T; NS2A: L57F, V150I, I175V, M194V, T195A, P203S; NS3: K26N, A207T, K589R; NS4A: T81A, A90V; NS4B: A110V; NS5: L639P, T763S, V785A, W803R" } } }, { "name": "NODE_0000006", "node_attrs": { - "div": 0.0603412, + "div": 0.0603, "clade_membership": { "value": "3I" } @@ -2811,32 +2279,14 @@ "C10117T", "C10156T", "A10159G" - ], - "E": [ - "T303A" - ], - "NS1": [ - "H256Y" - ], - "NS2A": [ - "T153M" - ], - "NS4A": [ - "I89V" - ], - "NS4B": [ - "L190F" ] - }, - "labels": { - "aa": "E: T303A; NS1: H256Y; NS2A: T153M; NS4A: I89V; NS4B: L190F" } }, "children": [ { "name": "NODE_0000007", "node_attrs": { - "div": 0.0708265, + "div": 0.0708, "clade_membership": { "value": "3I" } @@ -2958,44 +2408,14 @@ "C9559T", "T9734C", "C10042T" - ], - "NS1": [ - "S17N" - ], - "NS2A": [ - "I127V" - ], - "NS2B": [ - "V11I" - ], - "NS3": [ - "V40I", - "A207T", - "R255K" - ], - "NS4A": [ - "H19Y", - "N23S" - ], - "NS5": [ - "I50T", - "M336T", - "I524T", - "L639P" ] - }, - "labels": { - "aa": "NS1: S17N; NS2A: I127V; NS2B: V11I; NS3: V40I, A207T, R255K; NS4A: H19Y, N23S; NS5: I50T, M336T, I524T, L639P" } }, "children": [ { "name": "DQ675519.1|1995", "node_attrs": { - "div": 0.07645859, - "country": { - "value": "Taiwan" - }, + "div": 0.0765, "clade_membership": { "value": "3I" } @@ -3062,32 +2482,14 @@ "C9852G", "C9892T", "A10039G" - ], - "C": [ - "K79R", - "L103I" - ], - "E": [ - "K332R" - ], - "NS1": [ - "M174V", - "Y256H" - ], - "NS5": [ - "E40K", - "T763S" ] - }, - "labels": { - "aa": "C: K79R, L103I; E: K332R; NS1: M174V, Y256H; NS5: E40K, T763S" } } }, { "name": "NODE_0000008", "node_attrs": { - "div": 0.07763102, + "div": 0.0776, "clade_membership": { "value": "3I_C" } @@ -3160,20 +2562,9 @@ "C9463T", "A9513G", "T9862C" - ], - "NS1": [ - "I94T" - ], - "NS2A": [ - "I175V" - ], - "NS5": [ - "S128T", - "K650R" ] }, "labels": { - "aa": "NS1: I94T; NS2A: I175V; NS5: S128T, K650R", "lineage": "3I_C" } }, @@ -3181,12 +2572,12 @@ { "name": "KU509279.1|2008", "node_attrs": { - "div": 0.09180951999999999, - "country": { - "value": "Philippines" - }, + "div": 0.0918, "clade_membership": { "value": "3I_C" + }, + "country": { + "value": "Philippines" } }, "branch_attrs": { @@ -3339,57 +2730,14 @@ "A10045G", "C10202T", "G10252A" - ], - "C": [ - "M106I", - "T112A" - ], - "E": [ - "T76S", - "T95S", - "K325R", - "G347S", - "T357I", - "I482V" - ], - "NS1": [ - "S297A" - ], - "NS2B": [ - "N93H", - "L99F", - "I109V" - ], - "NS3": [ - "Q90K", - "T207A", - "V356A", - "V452A", - "A453T", - "R459K", - "E469G" - ], - "NS4B": [ - "T108A" - ], - "NS5": [ - "I78M", - "V114I", - "S288N", - "T290I", - "A303P", - "E458G" ] - }, - "labels": { - "aa": "C: M106I, T112A; E: T76S, T95S, K325R, G347S, T357I, I482V; NS1: S297A; NS2B: N93H, L99F, I109V; NS3: Q90K, T207A, V356A, V452A, A453T, R459K, E469G; NS4B: T108A; NS5: I78M, V114I, S288N, T290I, A303P, E458G" } } }, { "name": "NODE_0000009", "node_attrs": { - "div": 0.08152389, + "div": 0.0815, "clade_membership": { "value": "3I_C" } @@ -3437,32 +2785,19 @@ "T9343C", "G9658A", "G9946A" - ], - "E": [ - "I81T" - ], - "NS2A": [ - "M123T", - "M153T" - ], - "NS3": [ - "I115V" ] - }, - "labels": { - "aa": "E: I81T; NS2A: M123T, M153T; NS3: I115V" } }, "children": [ { "name": "MN018380.1|2015-09-16", "node_attrs": { - "div": 0.09574689, - "country": { - "value": "China" - }, + "div": 0.0957, "clade_membership": { "value": "3I_C" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -3607,63 +2942,14 @@ "C9988T", "A9995G", "C10105T" - ], - "C": [ - "M108L" - ], - "E": [ - "I140V" - ], - "NS1": [ - "I338V", - "V350A" - ], - "NS2A": [ - "S45Q", - "I58M", - "F159L" - ], - "NS3": [ - "R84K", - "L179W", - "E180K", - "T476A" - ], - "NS4B": [ - "I159V" - ], - "NS5": [ - "V71I", - "M167V", - "V168D", - "P170Q", - "W171K", - "L172P", - "N174E", - "N175G", - "Q176L", - "F177K", - "C178S", - "L384Q", - "G385E", - "K466I", - "K468R", - "T524I", - "M556K", - "P636L", - "H701Q", - "T811A" ] - }, - "labels": { - "aa": "C: M108L; E: I140V; NS1: I338V, V350A; NS2A: S45Q, I58M, F159L; NS3: R84K, L179W, E180K, T476A; NS4B: I159V; NS5: V71I, M167V, V168D, P170Q, W171K, L172P, N174E, N175G, Q176L, F177K, C178S, L384Q, G385E, K466I, K468R, T524I, M556K, P636L, H701Q, T811A" } } }, { "name": "NODE_0000010", "node_attrs": { - "div": 0.08616456, + "div": 0.0862, "clade_membership": { "value": "3I_C" } @@ -3712,33 +2998,19 @@ "G10198A", "G10246A", "T10247C" - ], - "M": [ - "T107A", - "I135V" - ], - "NS4B": [ - "T245N" - ], - "NS5": [ - "L679F", - "S895P" ] - }, - "labels": { - "aa": "M: T107A, I135V; NS4B: T245N; NS5: L679F, S895P" } }, "children": [ { "name": "MN018379.1|2015-10-03", "node_attrs": { - "div": 0.09871966, - "country": { - "value": "China" - }, + "div": 0.0987, "clade_membership": { "value": "3I_C" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -3869,52 +3141,14 @@ "G10219A", "G10234A", "G10237A" - ], - "C": [ - "R35K" - ], - "E": [ - "S124P", - "N230T", - "K231R" - ], - "M": [ - "I31N" - ], - "NS2A": [ - "S45Y", - "G46R", - "M132D" - ], - "NS3": [ - "N470S" - ], - "NS4B": [ - "L105K", - "T106P" - ], - "NS5": [ - "S151P", - "R198K", - "T250R", - "I251L", - "S288T", - "H547T", - "E550G", - "K585T", - "I619V", - "S629L" ] - }, - "labels": { - "aa": "C: R35K; E: S124P, N230T, K231R; M: I31N; NS2A: S45Y, G46R, M132D; NS3: N470S; NS4B: L105K, T106P; NS5: S151P, R198K, T250R, I251L, S288T, H547T, E550G, K585T, I619V, S629L" } } }, { "name": "NODE_0000011", "node_attrs": { - "div": 0.08624666, + "div": 0.0862, "clade_membership": { "value": "3I_C" } @@ -3932,12 +3166,12 @@ { "name": "MN018389.1|2017-02-15", "node_attrs": { - "div": 0.09425877, - "country": { - "value": "China" - }, + "div": 0.0943, "clade_membership": { "value": "3I_C" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -4025,51 +3259,19 @@ "A10135C", "G10147A", "G10219A" - ], - "E": [ - "M295L", - "L430I" - ], - "M": [ - "F128I" - ], - "NS1": [ - "A47V" - ], - "NS2A": [ - "P203A" - ], - "NS2B": [ - "I76V" - ], - "NS3": [ - "I40V", - "E43D", - "V258I" - ], - "NS4B": [ - "P24S" - ], - "NS5": [ - "T270A", - "Y482F", - "T524I" ] - }, - "labels": { - "aa": "E: M295L, L430I; M: F128I; NS1: A47V; NS2A: P203A; NS2B: I76V; NS3: I40V, E43D, V258I; NS4B: P24S; NS5: T270A, Y482F, T524I" } } }, { "name": "MN922037.1|2019-08-02", "node_attrs": { - "div": 0.09844576000000001, - "country": { - "value": "China" - }, + "div": 0.0984, "clade_membership": { "value": "3I_C" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -4197,32 +3399,7 @@ "C9544T", "G9757A", "T9808C" - ], - "E": [ - "S124L", - "K469R" - ], - "NS1": [ - "N17S", - "R41K", - "I93V" - ], - "NS2A": [ - "V150I" - ], - "NS2B": [ - "M75L" - ], - "NS4A": [ - "A68T" - ], - "NS5": [ - "I123V", - "E640D" ] - }, - "labels": { - "aa": "E: S124L, K469R; NS1: N17S, R41K, I93V; NS2A: V150I; NS2B: M75L; NS4A: A68T; NS5: I123V, E640D" } } } @@ -4239,7 +3416,7 @@ { "name": "NODE_0000012", "node_attrs": { - "div": 0.06298226999999999, + "div": 0.063, "clade_membership": { "value": "3I" } @@ -4267,20 +3444,14 @@ "A8497G", "T8980C", "C9754T" - ], - "NS3": [ - "V356A" ] - }, - "labels": { - "aa": "NS3: V356A" } }, "children": [ { "name": "NODE_0000013", "node_attrs": { - "div": 0.06797036999999999, + "div": 0.068, "clade_membership": { "value": "3I_B" } @@ -4336,17 +3507,9 @@ "A9810G", "T9862C", "T10060C" - ], - "NS3": [ - "R84K" - ], - "NS5": [ - "I643V", - "K749R" ] }, "labels": { - "aa": "NS3: R84K; NS5: I643V, K749R", "lineage": "3I_B" } }, @@ -4354,12 +3517,12 @@ { "name": "MW946955.1|1978", "node_attrs": { - "div": 0.07106006, - "country": { - "value": "Indonesia" - }, + "div": 0.0711, "clade_membership": { "value": "3I_B" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -4394,34 +3557,14 @@ "G8281T", "T9100C", "C10056A" - ], - "E": [ - "Y90H" - ], - "NS2A": [ - "T195A" - ], - "NS3": [ - "V147L", - "T476M" - ], - "NS4A": [ - "V89A" - ], - "NS5": [ - "S21P", - "T831K" ] - }, - "labels": { - "aa": "E: Y90H; NS2A: T195A; NS3: V147L, T476M; NS4A: V89A; NS5: S21P, T831K" } } }, { "name": "NODE_0000014", "node_attrs": { - "div": 0.07801356999999999, + "div": 0.078, "clade_membership": { "value": "3I_B" } @@ -4526,41 +3669,14 @@ "T10024C", "A10039G", "G10219A" - ], - "E": [ - "V129A", - "V355I" - ], - "NS1": [ - "V88I", - "I93V" - ], - "NS2A": [ - "V5A", - "V36A", - "G174V" - ], - "NS2B": [ - "L21F" - ], - "NS3": [ - "S71N", - "I283V" - ], - "NS5": [ - "T399I", - "T763A" ] - }, - "labels": { - "aa": "E: V129A, V355I; NS1: V88I, I93V; NS2A: V5A, V36A, G174V; NS2B: L21F; NS3: S71N, I283V; NS5: T399I, T763A" } }, "children": [ { "name": "NODE_0000015", "node_attrs": { - "div": 0.08258260999999999, + "div": 0.0826, "clade_membership": { "value": "3I_B" } @@ -4615,35 +3731,19 @@ "T9574C", "C9841T", "T9979C" - ], - "NS1": [ - "M174K" - ], - "NS2A": [ - "A5T", - "V150I" - ], - "NS3": [ - "P466S" - ], - "NS5": [ - "Y503H" ] - }, - "labels": { - "aa": "NS1: M174K; NS2A: A5T, V150I; NS3: P466S; NS5: Y503H" } }, "children": [ { "name": "JQ920485.1|1996-10-21", "node_attrs": { - "div": 0.08538350999999998, - "country": { - "value": "New Caledonia" - }, + "div": 0.0854, "clade_membership": { "value": "3I_B" + }, + "country": { + "value": "New Caledonia" } }, "branch_attrs": { @@ -4677,37 +3777,19 @@ "A9424G", "G9970A", "T10247C" - ], - "E": [ - "V68I" - ], - "NS1": [ - "Y175H", - "T293I" - ], - "NS3": [ - "T176I" - ], - "NS5": [ - "T39I", - "D274N", - "S895P" ] - }, - "labels": { - "aa": "E: V68I; NS1: Y175H, T293I; NS3: T176I; NS5: T39I, D274N, S895P" } } }, { "name": "JQ920480.1|1996-09-04", "node_attrs": { - "div": 0.08522813999999998, - "country": { - "value": "French Polynesia" - }, + "div": 0.0852, "clade_membership": { "value": "3I_B" + }, + "country": { + "value": "French Polynesia" } }, "branch_attrs": { @@ -4740,22 +3822,7 @@ "T7237A", "G7468A", "C8980T" - ], - "E": [ - "E175D", - "F212L" - ], - "NS1": [ - "S147L", - "G208E" - ], - "NS2A": [ - "T39M", - "A54V" ] - }, - "labels": { - "aa": "E: E175D, F212L; NS1: S147L, G208E; NS2A: T39M, A54V" } } } @@ -4764,7 +3831,7 @@ { "name": "NODE_0000016", "node_attrs": { - "div": 0.08145569, + "div": 0.0815, "clade_membership": { "value": "3I_B" } @@ -4804,29 +3871,19 @@ "C9754A", "T9853C", "T9958C" - ], - "NS3": [ - "D392N" - ], - "NS5": [ - "D37E", - "Q562R" ] - }, - "labels": { - "aa": "NS3: D392N; NS5: D37E, Q562R" } }, "children": [ { "name": "MW946691.1|1992", "node_attrs": { - "div": 0.08243671, - "country": { - "value": "Fiji" - }, + "div": 0.0824, "clade_membership": { "value": "3I_B" + }, + "country": { + "value": "Fiji" } }, "branch_attrs": { @@ -4841,26 +3898,19 @@ "C8657T", "G9370A", "C9784T" - ], - "NS5": [ - "K95R", - "P365S" ] - }, - "labels": { - "aa": "NS5: K95R, P365S" } } }, { "name": "FJ898456.1|1995", "node_attrs": { - "div": 0.08481576, - "country": { - "value": "Samoa" - }, + "div": 0.0848, "clade_membership": { "value": "3I_B" + }, + "country": { + "value": "Samoa" } }, "branch_attrs": { @@ -4901,23 +3951,7 @@ "A9913G", "A10124G", "C10165T" - ], - "NS1": [ - "V96I" - ], - "NS2A": [ - "L18F", - "P203S" - ], - "NS3": [ - "N108S" - ], - "NS5": [ - "T854A" ] - }, - "labels": { - "aa": "NS1: V96I; NS2A: L18F, P203S; NS3: N108S; NS5: T854A" } } } @@ -4930,7 +3964,7 @@ { "name": "NODE_0000017", "node_attrs": { - "div": 0.07007240999999999, + "div": 0.0701, "clade_membership": { "value": "3I_A" } @@ -5010,26 +4044,9 @@ "T9952C", "G10159C", "G10174A" - ], - "C": [ - "V65I" - ], - "E": [ - "L301S" - ], - "NS2A": [ - "H55R" - ], - "NS3": [ - "R255K" - ], - "NS5": [ - "M336T", - "T763A" ] }, "labels": { - "aa": "C: V65I; E: L301S; NS2A: H55R; NS3: R255K; NS5: M336T, T763A", "lineage": "3I_A" } }, @@ -5037,7 +4054,7 @@ { "name": "NODE_0000018", "node_attrs": { - "div": 0.07036011999999998, + "div": 0.0704, "clade_membership": { "value": "3I_A" } @@ -5062,12 +4079,12 @@ { "name": "MF004386.1|2012-10-04", "node_attrs": { - "div": 0.09627431999999998, - "country": { - "value": "Malaysia" - }, + "div": 0.0963, "clade_membership": { "value": "3I_A" + }, + "country": { + "value": "Malaysia" } }, "branch_attrs": { @@ -5319,69 +4336,19 @@ "G10147A", "C10159T", "A10168G" - ], - "C": [ - "I95V" - ], - "E": [ - "S124F", - "S301L", - "G340E", - "I437V" - ], - "M": [ - "T107A" - ], - "NS1": [ - "I251V" - ], - "NS2A": [ - "I60T", - "N63I", - "M194V" - ], - "NS2B": [ - "T60I" - ], - "NS3": [ - "I115T", - "E251V", - "I283V" - ], - "NS4A": [ - "S15T", - "N23S", - "A68V" - ], - "NS4B": [ - "I159V" - ], - "NS5": [ - "V132A", - "D295E", - "V372A", - "K445R", - "Y503F", - "A616V", - "K642E", - "N676D", - "T854A" ] - }, - "labels": { - "aa": "C: I95V; E: S124F, S301L, G340E, I437V; M: T107A; NS1: I251V; NS2A: I60T, N63I, M194V; NS2B: T60I; NS3: I115T, E251V, I283V; NS4A: S15T, N23S, A68V; NS4B: I159V; NS5: V132A, D295E, V372A, K445R, Y503F, A616V, K642E, N676D, T854A" } } }, { "name": "OK605763.1|1985", "node_attrs": { - "div": 0.07508151999999998, - "country": { - "value": "Indonesia" - }, + "div": 0.0751, "clade_membership": { "value": "3I_A" + }, + "country": { + "value": "Indonesia" } }, "branch_attrs": { @@ -5433,27 +4400,7 @@ "C9823G", "T10000C", "G10084A" - ], - "E": [ - "I61V", - "R348K" - ], - "NS1": [ - "T128I", - "V286A" - ], - "NS4A": [ - "D99E" - ], - "NS4B": [ - "I159L" - ], - "NS5": [ - "C753W" ] - }, - "labels": { - "aa": "E: I61V, R348K; NS1: T128I, V286A; NS4A: D99E; NS4B: I159L; NS5: C753W" } } } @@ -5462,7 +4409,7 @@ { "name": "NODE_0000019", "node_attrs": { - "div": 0.08002853999999998, + "div": 0.08, "clade_membership": { "value": "3I_A" } @@ -5569,45 +4516,19 @@ "A9790G", "T9955C", "T10024C" - ], - "E": [ - "S124L", - "V377I" - ], - "M": [ - "T107A" - ], - "NS1": [ - "S145N" - ], - "NS3": [ - "H60Y", - "E350D" - ], - "NS4A": [ - "I78V", - "V100I" - ], - "NS5": [ - "H246Y", - "R364K", - "A631T" ] - }, - "labels": { - "aa": "E: S124L, V377I; M: T107A; NS1: S145N; NS3: H60Y, E350D; NS4A: I78V, V100I; NS5: H246Y, R364K, A631T" } }, "children": [ { "name": "MT921575.1|2016", "node_attrs": { - "div": 0.09873803999999999, - "country": { - "value": "Australia" - }, + "div": 0.0987, "clade_membership": { "value": "3I_A" + }, + "country": { + "value": "Australia" } }, "branch_attrs": { @@ -5789,51 +4710,14 @@ "T9864A", "C9952T", "C10054T" - ], - "E": [ - "E62G", - "L124S", - "K358N" - ], - "M": [ - "F128L", - "I156T" - ], - "NS2A": [ - "T39M", - "V41A", - "D52N", - "A133V", - "M153T", - "V180M" - ], - "NS2B": [ - "T96A" - ], - "NS3": [ - "Y60H", - "T119I", - "T393S", - "A548S" - ], - "NS4B": [ - "P157S" - ], - "NS5": [ - "T155I", - "L638P", - "F767Y" ] - }, - "labels": { - "aa": "E: E62G, L124S, K358N; M: F128L, I156T; NS2A: T39M, V41A, D52N, A133V, M153T, V180M; NS2B: T96A; NS3: Y60H, T119I, T393S, A548S; NS4B: P157S; NS5: T155I, L638P, F767Y" } } }, { "name": "NODE_0000020", "node_attrs": { - "div": 0.08011902999999998, + "div": 0.0801, "clade_membership": { "value": "3I_A" } @@ -5849,7 +4733,7 @@ { "name": "NODE_0000021", "node_attrs": { - "div": 0.08147281999999997, + "div": 0.0815, "clade_membership": { "value": "3I_A" } @@ -5884,39 +4768,19 @@ "A8599G", "A8797G", "C9895T" - ], - "M": [ - "G42R", - "M44R" - ], - "NS1": [ - "V96I" - ], - "NS2A": [ - "V180L" - ], - "NS4A": [ - "A68V" - ], - "NS5": [ - "T51P", - "T188A" ] - }, - "labels": { - "aa": "M: G42R, M44R; NS1: V96I; NS2A: V180L; NS4A: A68V; NS5: T51P, T188A" } }, "children": [ { "name": "MN018370.1|2015-07-24", "node_attrs": { - "div": 0.10082101999999997, - "country": { - "value": "China" - }, + "div": 0.101, "clade_membership": { "value": "3I_A" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -6103,69 +4967,19 @@ "C10159T", "A10163G", "A10255G" - ], - "E": [ - "A367T", - "I483N" - ], - "M": [ - "R42I", - "E43A", - "C45R", - "V49I" - ], - "NS1": [ - "T29M", - "T176S" - ], - "NS2A": [ - "S2D", - "T162S", - "A164T", - "T169I", - "V196I" - ], - "NS2B": [ - "L37M", - "M84I", - "N93S", - "Q127R" - ], - "NS3": [ - "I282V", - "K590E", - "L592I", - "R593E", - "P594T" - ], - "NS4B": [ - "V22A" - ], - "NS5": [ - "T250D", - "I251V", - "R422K", - "L461H", - "H547Q", - "I643V", - "T811I", - "I867V" ] - }, - "labels": { - "aa": "E: A367T, I483N; M: R42I, E43A, C45R, V49I; NS1: T29M, T176S; NS2A: S2D, T162S, A164T, T169I, V196I; NS2B: L37M, M84I, N93S, Q127R; NS3: I282V, K590E, L592I, R593E, P594T; NS4B: V22A; NS5: T250D, I251V, R422K, L461H, H547Q, I643V, T811I, I867V" } } }, { "name": "MN018374.1|2015-09-28", "node_attrs": { - "div": 0.10114841999999998, - "country": { - "value": "China" - }, + "div": 0.101, "clade_membership": { "value": "3I_A" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -6344,61 +5158,7 @@ "C10114T", "C10202T", "C10257T" - ], - "C": [ - "K86R" - ], - "E": [ - "I140S", - "V459A" - ], - "M": [ - "M39L", - "L41R", - "R42K", - "R44G", - "C45S" - ], - "NS1": [ - "Y256H", - "K341R" - ], - "NS2A": [ - "V5M", - "L42H", - "L43W", - "L44M", - "S45Q", - "L129S", - "G130P", - "L131T", - "M132V", - "I137V", - "S185G" - ], - "NS2B": [ - "N93I", - "L98T" - ], - "NS3": [ - "S86N", - "Q467R", - "W596G", - "L597R" - ], - "NS4B": [ - "V111L" - ], - "NS5": [ - "A406E", - "R620T", - "D663G", - "L679F", - "A898V" ] - }, - "labels": { - "aa": "C: K86R; E: I140S, V459A; M: M39L, L41R, R42K, R44G, C45S; NS1: Y256H, K341R; NS2A: V5M, L42H, L43W, L44M, S45Q, L129S, G130P, L131T, M132V, I137V, S185G; NS2B: N93I, L98T; NS3: S86N, Q467R, W596G, L597R; NS4B: V111L; NS5: A406E, R620T, D663G, L679F, A898V" } } } @@ -6407,7 +5167,7 @@ { "name": "NODE_0000022", "node_attrs": { - "div": 0.08907732999999998, + "div": 0.0891, "clade_membership": { "value": "3I_A" } @@ -6507,29 +5267,14 @@ "G10012A", "A10093G", "G10219T" - ], - "E": [ - "P362L" - ], - "M": [ - "V120I" - ], - "NS2A": [ - "L178F" - ], - "NS5": [ - "L639P" ] - }, - "labels": { - "aa": "E: P362L; M: V120I; NS2A: L178F; NS5: L639P" } }, "children": [ { "name": "NODE_0000023", "node_attrs": { - "div": 0.09556703999999998, + "div": 0.0956, "clade_membership": { "value": "3I_A.2" } @@ -6606,37 +5351,9 @@ "T10183C", "G10204A", "A10249C" - ], - "C": [ - "K86R" - ], - "E": [ - "T223I" - ], - "NS1": [ - "V188I" - ], - "NS2A": [ - "S184T" - ], - "NS3": [ - "I126V", - "T476M" - ], - "NS4A": [ - "A68V" - ], - "NS5": [ - "H52R", - "V114I", - "K139R", - "T404A", - "Y503H", - "T644I" ] }, "labels": { - "aa": "C: K86R; E: T223I; NS1: V188I; NS2A: S184T; NS3: I126V, T476M; NS4A: A68V; NS5: H52R, V114I, K139R, T404A, Y503H, T644I", "lineage": "3I_A.2" } }, @@ -6644,12 +5361,12 @@ { "name": "MN018377.1|2015-12-22", "node_attrs": { - "div": 0.10194582999999997, - "country": { - "value": "China" - }, + "div": 0.102, "clade_membership": { "value": "3I_A.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -6720,67 +5437,14 @@ "T9139C", "T9313C", "T9472C" - ], - "C": [ - "I65V" - ], - "E": [ - "I65N", - "S184L", - "P185T", - "F191S", - "N192M", - "E193K", - "N201K", - "Y390I", - "K391D", - "G393A", - "S394E", - "S395P", - "I478L" - ], - "M": [ - "M39I", - "D40G", - "L41S", - "E43A" - ], - "NS1": [ - "S304P" - ], - "NS2A": [ - "L44R", - "S45Y", - "G46R", - "M110I" - ], - "NS2B": [ - "L74V" - ], - "NS3": [ - "G438V", - "W596M", - "D598V", - "A599P", - "R600H", - "T601H" - ], - "NS4B": [ - "W38L" - ], - "NS5": [ - "M476T" ] - }, - "labels": { - "aa": "C: I65V; E: I65N, S184L, P185T, F191S, N192M, E193K, N201K, Y390I, K391D, G393A, S394E, S395P, I478L; M: M39I, D40G, L41S, E43A; NS1: S304P; NS2A: L44R, S45Y, G46R, M110I; NS2B: L74V; NS3: G438V, W596M, D598V, A599P, R600H, T601H; NS4B: W38L; NS5: M476T" } } }, { "name": "NODE_0000024", "node_attrs": { - "div": 0.09720393999999997, + "div": 0.0972, "clade_membership": { "value": "3I_A.2" } @@ -6811,12 +5475,12 @@ { "name": "MW396463.1|2019-07-02", "node_attrs": { - "div": 0.10045595999999997, - "country": { - "value": "Bangladesh" - }, + "div": 0.1, "clade_membership": { "value": "3I_A.2" + }, + "country": { + "value": "Bangladesh" } }, "branch_attrs": { @@ -6855,33 +5519,14 @@ "A8350G", "C9148T", "A9316G" - ], - "2K": [ - "I20T", - "V21I" - ], - "E": [ - "L45R", - "V130I" - ], - "NS1": [ - "P106T", - "E110D" - ], - "NS2B": [ - "V120L", - "W121L" ] - }, - "labels": { - "aa": "2K: I20T, V21I; E: L45R, V130I; NS1: P106T, E110D; NS2B: V120L, W121L" } } }, { "name": "NODE_0000025", "node_attrs": { - "div": 0.09720493999999998, + "div": 0.0972, "clade_membership": { "value": "3I_A.2" } @@ -6893,12 +5538,12 @@ { "name": "MN922035.1|2019-06-23", "node_attrs": { - "div": 0.09937057999999997, - "country": { - "value": "China" - }, + "div": 0.0994, "clade_membership": { "value": "3I_A.2" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -6926,33 +5571,14 @@ "T8596C", "T8902C", "G9487A" - ], - "C": [ - "R35K" - ], - "E": [ - "V459I" - ], - "NS1": [ - "N151K", - "V236G" - ], - "NS2A": [ - "V201I" - ], - "NS3": [ - "L236M" ] - }, - "labels": { - "aa": "C: R35K; E: V459I; NS1: N151K, V236G; NS2A: V201I; NS3: L236M" } } }, { "name": "NODE_0000026", "node_attrs": { - "div": 0.09778242999999998, + "div": 0.0978, "clade_membership": { "value": "3I_A.2" } @@ -6973,12 +5599,12 @@ { "name": "ON127534.1|2021-08", "node_attrs": { - "div": 0.10198590999999997, - "country": { - "value": "Bangladesh" - }, + "div": 0.102, "clade_membership": { "value": "3I_A.2" + }, + "country": { + "value": "Bangladesh" } }, "branch_attrs": { @@ -7023,29 +5649,19 @@ "C9937T", "T10048C", "T10156C" - ], - "NS3": [ - "S86N", - "A170V", - "S250P", - "D392N", - "K557R" ] - }, - "labels": { - "aa": "NS3: S86N, A170V, S250P, D392N, K557R" } } }, { "name": "ON116130.1|2021-08", "node_attrs": { - "div": 0.10014661999999998, - "country": { - "value": "Bangladesh" - }, + "div": 0.1, "clade_membership": { "value": "3I_A.2" + }, + "country": { + "value": "Bangladesh" } }, "branch_attrs": { @@ -7075,28 +5691,7 @@ "T9636C", "A9643G", "G10237A" - ], - "E": [ - "I223T" - ], - "M": [ - "S22T" - ], - "NS1": [ - "M174T" - ], - "NS2A": [ - "V36A" - ], - "NS3": [ - "T436M" - ], - "NS5": [ - "I691T" ] - }, - "labels": { - "aa": "E: I223T; M: S22T; NS1: M174T; NS2A: V36A; NS3: T436M; NS5: I691T" } } } @@ -7111,7 +5706,7 @@ { "name": "NODE_0000027", "node_attrs": { - "div": 0.09232689999999998, + "div": 0.0923, "clade_membership": { "value": "3I_A.1" } @@ -7151,16 +5746,9 @@ "T9343A", "C9510A", "T10126C" - ], - "E": [ - "K386R" - ], - "NS5": [ - "T649N" ] }, "labels": { - "aa": "E: K386R; NS5: T649N", "lineage": "3I_A.1" } }, @@ -7168,12 +5756,12 @@ { "name": "KY921906.1|2015-06", "node_attrs": { - "div": 0.09496817999999997, - "country": { - "value": "Singapore" - }, + "div": 0.095, "clade_membership": { "value": "3I_A.1" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -7207,23 +5795,14 @@ 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"clade_membership": { "value": "unassigned" } @@ -8908,31 +7541,14 @@ "A9419G", "A9739G", "C9852G" - ], - "E": [ - "T270N" - ], - "NS2A": [ - "I175V" - ], - "NS3": [ - "V452A" - ], - "NS5": [ - "S288N", - "I619V", - "T763S" ] - }, - "labels": { - "aa": "E: T270N; NS2A: I175V; NS3: V452A; NS5: S288N, I619V, T763S" } }, "children": [ { - "name": "NODE_0000042", + "name": "NODE_0000045", "node_attrs": { - "div": 0.05508978, + "div": 0.0551, "clade_membership": { "value": "3II" } @@ -9042,28 +7658,17 @@ "A9661T", "G9810A", "C9931T" - ], - "M": [ - "T57A", - "T166A" - ], - "NS2A": [ - "T195A" - ], - "NS5": [ - "R749K" ] }, "labels": { - "aa": "M: T57A, T166A; NS2A: T195A; NS5: R749K", "lineage": "3II" } }, "children": [ { - "name": "NODE_0000043", + "name": "NODE_0000046", "node_attrs": { - "div": 0.06543357999999999, + "div": 0.0654, "clade_membership": { "value": "3II" } @@ -9172,46 +7777,19 @@ "G10179C", "A10195G", "T10216C" - ], - "E": [ - "V459A", - "A479V" - ], - "M": [ - "V153I" - ], - "NS1": [ - "V54I", - "I94T" - ], - "NS2A": [ - "V36I" - ], - "NS3": [ - "R338K" - ], - "NS5": [ - "I50T", - "A60S", - "E640D", - "T644I", - "S872T" ] - }, - "labels": { - "aa": "E: V459A, A479V; M: V153I; NS1: V54I, I94T; NS2A: V36I; NS3: R338K; NS5: I50T, A60S, E640D, T644I, S872T" } }, "children": [ { "name": "OK469355.1|1973", "node_attrs": { - "div": 0.06592852999999999, - "country": { - "value": "Myanmar" - }, + "div": 0.0659, "clade_membership": { "value": "3II" + }, + "country": { + "value": "Myanmar" } }, "branch_attrs": { @@ -9222,23 +7800,14 @@ "C6010T", "A6421G", "G6586T" - ], - "NS4A": [ - "L72F" ] - }, - "labels": { - "aa": "NS4A: L72F" } } }, { "name": "OK469356.1|1976", "node_attrs": { - "div": 0.06552889999999999, - "country": { - "value": "Myanmar" - }, + "div": 0.0655, "clade_membership": { "value": "3II" } @@ -9254,9 +7823,9 @@ ] }, { - "name": "NODE_0000044", + "name": "NODE_0000047", "node_attrs": { - "div": 0.05979038, + "div": 0.0598, "clade_membership": { "value": "3II" } @@ -9312,25 +7881,19 @@ "A9451G", "T9710C", "T10078C" - ], - "E": [ - "A169V" ] - }, - "labels": { - "aa": "E: A169V" } }, "children": [ { "name": "KF955476.1|1983", "node_attrs": { - "div": 0.06464159, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0646, "clade_membership": { "value": "3II" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -9382,34 +7945,14 @@ "T9577C", "G10171A", "G10233A" - ], - "M": [ - "M159I" - ], - "NS1": [ - "V350A" - ], - "NS2A": [ - "F38L" - ], - "NS4B": [ - "V115A" - ], - "NS5": [ - "H52R", - "T338I", - "R890K" ] - }, - "labels": { - "aa": "M: M159I; NS1: V350A; NS2A: F38L; NS4B: V115A; NS5: H52R, T338I, R890K" } } }, { - "name": "NODE_0000045", + "name": "NODE_0000048", "node_attrs": { - "div": 0.06726396, + "div": 0.0673, "clade_membership": { "value": "3II" } @@ -9495,40 +8038,14 @@ "T9958C", "C10096T", "A10190G" - ], - "E": [ - "E154D" - ], - "M": [ - "H55L" - ], - "NS1": [ - "L178S", - "V188I" - ], - "NS3": [ - "D324E", - "K589R" - ], - "NS5": [ - "I50T", - "H200Y", - "N288S", - "N876D" ] - }, - "labels": { - "aa": "E: E154D; M: H55L; NS1: L178S, V188I; NS3: D324E, K589R; NS5: I50T, H200Y, N288S, N876D" } }, "children": [ { "name": "OK469354.1|1989", "node_attrs": { - "div": 0.07258408, - "country": { - "value": "Thailand" - }, + "div": 0.0726, "clade_membership": { "value": "3II" } @@ -9590,34 +8107,14 @@ "T9979C", "A10055G", "C10207T" - ], - "2K": [ - "V21I" - ], - "NS1": [ - "P106L" - ], - "NS2A": [ - "I33V", - "M123I" - ], - "NS4A": [ - "L63V" - ], - "NS5": [ - "R561K", - "T831A" ] - }, - "labels": { - "aa": "2K: V21I; NS1: P106L; NS2A: I33V, M123I; NS4A: L63V; NS5: R561K, T831A" } } }, { - "name": "NODE_0000046", + "name": "NODE_0000049", "node_attrs": { - "div": 0.06825818, + "div": 0.0683, "clade_membership": { "value": "3II" } @@ -9638,26 +8135,14 @@ "C6664T", "G8158A", "C9268T" - ], - "E": [ - "A160V" - ], - "NS1": [ - "L217F" - ], - "NS4A": [ - "A90V" ] - }, - "labels": { - "aa": "E: A160V; NS1: L217F; NS4A: A90V" } }, "children": [ { - "name": "NODE_0000047", + "name": "NODE_0000050", "node_attrs": { - "div": 0.06841789, + "div": 0.0684, "clade_membership": { "value": "3II" } @@ -9674,10 +8159,7 @@ { "name": "KJ737430.1|1983", "node_attrs": { - "div": 0.06899516, - "country": { - "value": "Thailand" - }, + "div": 0.069, "clade_membership": { "value": "3II" } @@ -9689,20 +8171,14 @@ "G2932A", "C6766T", "C8577T" - ], - "NS5": [ - "T338I" ] - }, - "labels": { - "aa": "NS5: T338I" } } }, { - "name": "NODE_0000048", + "name": "NODE_0000051", "node_attrs": { - "div": 0.07108787, + "div": 0.0711, "clade_membership": { "value": "3II_B" } @@ -9727,13 +8203,9 @@ "T9115C", "T9661C", "C9700T" - ], - "E": [ - "A479V" ] }, "labels": { - "aa": "E: A479V", "lineage": "3II_B" } }, @@ -9741,12 +8213,12 @@ { "name": "KY586818.1|2007", "node_attrs": { - "div": 0.08331846999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0833, "clade_membership": { "value": "3II_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -9873,37 +8345,14 @@ "T9139C", "T9613C", "G10147A" - ], - "E": [ - "I68V" - ], - "M": [ - "A166T" - ], - "NS3": [ - "E324D", - "E350D", - "V356A", - "A452V" - ], - "NS4B": [ - "L190F" - ], - "NS5": [ - "H246Y", - "A266V", - "K281R" ] - }, - "labels": { - "aa": "E: I68V; M: A166T; NS3: E324D, E350D, V356A, A452V; NS4B: L190F; NS5: H246Y, A266V, K281R" } } }, { - "name": "NODE_0000049", + "name": "NODE_0000052", "node_attrs": { - "div": 0.07482031, + "div": 0.0748, "clade_membership": { "value": "3II_B" } @@ -9954,33 +8403,19 @@ "T9904C", "T9931C", "T9979C" - ], - "E": [ - "I140T", - "S447G", - "A489T" - ], - "NS1": [ - "S178T" - ], - "NS2A": [ - "M194V" ] - }, - "labels": { - "aa": "E: I140T, S447G, A489T; NS1: S178T; NS2A: M194V" } }, "children": [ { "name": "AY496871.2|2002", "node_attrs": { - "div": 0.08870421, - "country": { - "value": "Bangladesh" - }, + "div": 0.0887, "clade_membership": { "value": "3II_B" + }, + "country": { + "value": "Bangladesh" } }, "branch_attrs": { @@ -10119,60 +8554,14 @@ "T9918C", "T9997C", "G10190A" - ], - "C": [ - "L103F" - ], - "E": [ - "I81T", - "S124P", - "I172V" - ], - "M": [ - "L55F", - "I156V" - ], - "NS1": [ - "T125I", - "N290D" - ], - "NS2A": [ - "H55N", - "L57F", - "V150I", - "P203S" - ], - "NS3": [ - "T265P", - "A310T" - ], - "NS4A": [ - "K76R", - "T81A" - ], - "NS5": [ - "R248K", - "E286G", - "H287V", - "S289K", - "A424V", - "T542Q", - "L639P", - "K650E", - "L679F", - "V785A", - "D876N" ] - }, - "labels": { - "aa": "C: L103F; E: I81T, S124P, I172V; M: L55F, I156V; NS1: T125I, N290D; NS2A: H55N, L57F, V150I, P203S; NS3: T265P, A310T; NS4A: K76R, T81A; NS5: R248K, E286G, H287V, S289K, A424V, T542Q, L639P, K650E, L679F, V785A, D876N" } } }, { - "name": "NODE_0000050", + "name": "NODE_0000053", "node_attrs": { - "div": 0.07954653, + "div": 0.0795, "clade_membership": { "value": "3II_B" } @@ -10225,31 +8614,19 @@ "T9670C", "T9967C", "G10147A" - ], - "E": [ - "V160A" - ], - "NS3": [ - "T168A" - ], - "NS5": [ - "D419E" ] - }, - "labels": { - "aa": "E: V160A; NS3: T168A; NS5: D419E" } }, "children": [ { "name": "MW946664.1|2011", "node_attrs": { - "div": 0.08795171, - "country": { - "value": "Thailand" - }, + "div": 0.088, "clade_membership": { "value": "3II_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -10337,23 +8714,14 @@ "C10123T", "C10138T", "T10216C" - ], - "NS5": [ - "A266T", - "Q554R", - "V785A", - "T832A" ] - }, - "labels": { - "aa": "NS5: A266T, Q554R, V785A, T832A" } } }, { - "name": "NODE_0000051", + "name": "NODE_0000054", "node_attrs": { - "div": 0.08400989, + "div": 0.084, "clade_membership": { "value": "3II_B" } @@ -10404,26 +8772,19 @@ "A9799G", "A10066G", "C10114T" - ], - "NS5": [ - "D26E", - "Y200H" ] - }, - "labels": { - "aa": "NS5: D26E, Y200H" } }, "children": [ { "name": "MF682971.1|2013-07-22", "node_attrs": { - "div": 0.09277025, - "country": { - "value": "China" - }, + "div": 0.0928, "clade_membership": { "value": "3II_B" + }, + "country": { + "value": "China" } }, "branch_attrs": { @@ -10514,52 +8875,19 @@ "C9868T", "T9961A", "T10216C" - ], - "E": [ - "E267G", - "C300G", - "V305G", - "S311F" - ], - "M": [ - "A113T" - ], - "NS1": [ - "T103A", - "T128I" - ], - "NS2A": [ - "V41M" - ], - "NS3": [ - "K104R", - "D173E", - "G438R" - ], - "NS5": [ - "K23R", - "T118P", - "I123T", - "D131E", - "D435G", - "V619I", - "A752P" ] - }, - "labels": { - "aa": "E: E267G, C300G, V305G, S311F; M: A113T; NS1: T103A, T128I; NS2A: V41M; NS3: K104R, D173E, G438R; NS5: K23R, T118P, I123T, D131E, D435G, V619I, A752P" } } }, { "name": "KT424097.1|2014-08-28", "node_attrs": { - "div": 0.09372133, - "country": { - "value": "Thailand" - }, + "div": 0.0937, "clade_membership": { "value": "3II_B" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -10657,55 +8985,7 @@ "C9460T", "C9463T", "A9509G" - ], - "E": [ - "I81T" - ], - "M": [ - "D89N" - ], - "NS2A": [ - "I60V" - ], - "NS3": [ - "G32W", - "T34N", - "Q35P", - "V36S", - "V38G", - "R64S", - "L65W", - "S71R", - "V72T", - "K74L", - "D75G", - "L76P", - "I77A", - "Y79W", - "C564R", - "K591N" - ], - "NS4A": [ - "S1P" - ], - "NS4B": [ - "V22I", - "V91L", - "P92S", - "L93P", - "L94V", - "A95C", - "G97A", - "C98S", - "Y99H", - "S100D" - ], - "NS5": [ - "T649A" ] - }, - "labels": { - "aa": "E: I81T; M: D89N; NS2A: I60V; NS3: G32W, T34N, Q35P, V36S, V38G, R64S, L65W, S71R, V72T, K74L, D75G, L76P, I77A, Y79W, C564R, K591N; NS4A: S1P; NS4B: V22I, V91L, P92S, L93P, L94V, A95C, G97A, C98S, Y99H, S100D; NS5: T649A" } } } @@ -10720,9 +9000,9 @@ ] }, { - "name": "NODE_0000052", + "name": "NODE_0000055", "node_attrs": { - "div": 0.0740212, + "div": 0.074, "clade_membership": { "value": "3II_A" } @@ -10786,34 +9066,17 @@ "T9661G", "C9784T", "G10198A" - ], - "E": [ - "S124P", - "A479V" - ], - "M": [ - "A166T" - ], - "NS2A": [ - "A133T", - "V180L", - "A195T", - "L215P" - ], - "NS3": [ - "K399R" ] }, "labels": { - "aa": "E: S124P, A479V; M: A166T; NS2A: A133T, V180L, A195T, L215P; NS3: K399R", "lineage": "3II_A" } }, "children": [ { - "name": "NODE_0000053", + "name": "NODE_0000056", "node_attrs": { - "div": 0.07520405, + "div": 0.0752, "clade_membership": { "value": "3II_A" } @@ -10832,25 +9095,19 @@ "T7940C", "C9235T", "C9412T" - ], - "M": [ - "G15A" ] - }, - "labels": { - "aa": "M: G15A" } }, "children": [ { "name": "MW946876.1|2003", "node_attrs": { - "div": 0.08547805, - "country": { - "value": "Thailand" - }, + "div": 0.0855, "clade_membership": { "value": "3II_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -10960,52 +9217,19 @@ "C9978G", "T9979C", "C10125A" - ], - "2K": [ - "A22T" - ], - "M": [ - "I156V" - ], - "NS1": [ - "M2T", - "L86I" - ], - "NS2A": [ - "V12I" - ], - "NS3": [ - "T248I", - "K562R" - ], - "NS4A": [ - "G66S" - ], - "NS4B": [ - "P19S", - "V175I" - ], - "NS5": [ - "V181I", - "D520E", - "T805S", - "T854N" ] - }, - "labels": { - "aa": "2K: A22T; M: I156V; NS1: M2T, L86I; NS2A: V12I; NS3: T248I, K562R; NS4A: G66S; NS4B: P19S, V175I; NS5: V181I, D520E, T805S, T854N" } } }, { "name": "MZ857226.1|1991-09-17", "node_attrs": { - "div": 0.07558814999999999, - "country": { - "value": "Thailand" - }, + "div": 0.0756, "clade_membership": { "value": "3II_A" + }, + "country": { + "value": "Thailand" } }, "branch_attrs": { @@ -11022,9 +9246,9 @@ ] }, { - "name": "NODE_0000054", + "name": "NODE_0000057", "node_attrs": { - "div": 0.07640881999999999, + "div": 0.0751, "clade_membership": { "value": "3II_A" } @@ -11032,313 +9256,302 @@ "branch_attrs": { "mutations": { "nuc": [ - "C550T", - "C589T", - "C754T", "G982A", "C1328T", - "A1448G", - "T1498C", "T3332C", "G4144A", - "T4771C", - "G5308A", - "C5482T", - "T5494C", - "G5836A", - "A6169C", - "G6748A", - "C6820T", - "G7228A", - "A7560G", - "T7936C", - "G8566T", - "C8689T", "G8730A", "T9148C", - "A9775G", - "C10117T" - ], - "E": [ - "H132Y", - "I172V" - ], - "NS4B": [ - "K247R" - ], - "NS5": [ - "R389K" + 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"NS3": [ - "T476A" - ], - "NS4B": [ - "A178S" - ], - "NS5": [ - "Q19L", - "D876G" - ] + "mutations": {} + }, + "children": [ + { + "name": "KY586704.1|2008", + "node_attrs": { + "div": 0.0895, + "clade_membership": { + "value": "3II_A.3" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G405A", + "C919T", + "G950A", + "C1132T", + "T1840C", + "T2044C", + "G2332A", + "C2941T", + "C3175T", + "T4978C", + "C5032G", + "G5905A", + "A6751G", + "C7133T", + "G7468A", + "T8273C", + "T9124C", + "C9203T", + "C9748T", + "T9961C", + "G10237A" + ] + } + } }, - "labels": { - "aa": "NS3: T476A; NS4B: A178S; NS5: Q19L, D876G" - } - } - } - ] - } - ] - } + { + "name": "MW946622.1|2006", + "node_attrs": { + "div": 0.0888, + "clade_membership": { + "value": "3II_A.3" + }, + "country": { + "value": "Thailand" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C1060T", + "G1720C", + "T3427C", + "C4895T", + "A5939G", + "C6443T", + "T6694C", + "C6757T", + "G7352T", + "C7582T", + "A7620T", + "A7669G", + "G7846A", + "G9256A", + "C9442T", + "A10191G" + ] + } + } + } + ] + } + ] + } + ] + } ] } ] @@ -14088,9 +11991,9 @@ ] }, { - "name": "NODE_0000084", + "name": "NODE_0000091", "node_attrs": { - "div": 0.058466649999999995, + "div": 0.0585, "clade_membership": { "value": "3III" } @@ -14223,40 +12126,9 @@ "G10067A", "C10117T", "T10155C" - ], - "2K": [ - "V21I" - ], - "C": [ - "R35K", - "M108I", - "T112A" - ], - "E": [ - "I81V", - "H132Y", - "L301T", - "I452V" - ], - "NS1": [ - "I93T", - "H256Y", - "N339S" - ], - "NS3": [ - "I115T", - "V356A", - "E568Q" - ], - "NS5": [ - "R422K", - "K585T", - "D835N", - "L864P" ] }, "labels": { - "aa": "2K: V21I; C: R35K, M108I, T112A; E: I81V, H132Y, L301T, I452V; NS1: I93T, H256Y, N339S; NS3: I115T, V356A, E568Q; NS5: R422K, K585T, D835N, L864P", "lineage": "3III" } }, @@ -14264,12 +12136,12 @@ { "name": "JQ922555.1|1966", "node_attrs": { - "div": 0.07201225, - "country": { - "value": "India" - }, + "div": 0.072, "clade_membership": { "value": "3III" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -14421,100 +12293,14 @@ "G9550A", "C9760T", "C10024T" - ], - "C": [ - "P60S" - ], - "E": [ - "V206G", - "W210M", - "F211L", - "L216T", - "A222T", - "P227S", - "T228A", - "L234P", - "L235F", - "A243T", - "I320V", - "K391R", - "A404S" - ], - "NS1": [ - "L178I", - "C223S", - "L237Q", - "V350A" - ], - "NS2A": [ - "H55R" - ], - "NS2B": [ - "D25G" - ], - "NS3": [ - "T120S", - "E491D", - "D497E", - "A519G", - "I520L", - "K557L" - ], - "NS4A": [ - "P14S", - "L28K", - "V29M", - "H36Y" - ], - "NS4B": [ - "M15V", - "T49A", - "L65M", - "S100F", - "Q101Y", - "L112F", - "Q134H", - "R136K", - "K143N", - "N144P", - "T146P", - "V147G", - "I201T" - ], - "NS5": [ - "R84K", - "T214R", - "H215N", - "P365L", - "G368R", - "T404P", - "N405I", - "E414Q", - "E415R", - "N416D", - "L433P", - "R438C", - "E439N", - "L440S", - "K442Q", - "I541N", - "N548M", - "E549K", - "D557G", - "E559G", - "R561S", - "Q562R" ] - }, - "labels": { - "aa": "C: P60S; E: V206G, W210M, F211L, L216T, A222T, P227S, T228A, L234P, L235F, A243T, I320V, K391R, A404S; NS1: L178I, C223S, L237Q, V350A; NS2A: H55R; NS2B: D25G; NS3: T120S, E491D, D497E, A519G, I520L, K557L; NS4A: P14S, L28K, V29M, H36Y; NS4B: M15V, T49A, L65M, S100F, Q101Y, L112F, Q134H, R136K, K143N, N144P, T146P, V147G, I201T; NS5: R84K, T214R, H215N, P365L, G368R, T404P, N405I, E414Q, E415R, N416D, L433P, R438C, E439N, L440S, K442Q, I541N, N548M, E549K, D557G, E559G, R561S, Q562R" } } }, { - "name": "NODE_0000085", + "name": "NODE_0000092", "node_attrs": { - "div": 0.07158534999999999, + "div": 0.0716, "clade_membership": { "value": "3III" } @@ -14641,31 +12427,14 @@ "C10165T", "G10219A", "A10249G" - ], - "E": [ - "S124P", - "A169T", - "K383N" - ], - "NS2A": [ - "L37F" - ], - "NS4A": [ - "D99E" - ], - "NS4B": [ - "V115I" ] - }, - "labels": { - "aa": "E: S124P, A169T, K383N; NS2A: L37F; NS4A: D99E; NS4B: V115I" } }, "children": [ { - "name": "NODE_0000086", + "name": "NODE_0000093", "node_attrs": { - "div": 0.07844269999999999, + "div": 0.0784, "clade_membership": { "value": "3III_A" } @@ -14746,19 +12515,9 @@ "C10105T", "T10201C", "G10240A" - ], - "E": [ - "T219A" - ], - "NS5": [ - "I72V", - "T553I", - "S629T", - "D820E" ] }, "labels": { - "aa": "E: T219A; NS5: I72V, T553I, S629T, D820E", "lineage": "3III_A" } }, @@ -14766,12 +12525,12 @@ { "name": "FJ882573.1|1993", "node_attrs": { - "div": 0.08348977999999999, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0835, "clade_membership": { "value": "3III_A" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -14829,33 +12588,14 @@ "T9625C", "C9856T", "T9937C" - ], - "2K": [ - "I20M" - ], - "E": [ - "S472P" - ], - "NS1": [ - "I94T" - ], - "NS3": [ - "F31L" - ], - "NS5": [ - "I280V", - "T649A" ] - }, - "labels": { - "aa": "2K: I20M; E: S472P; NS1: I94T; NS3: F31L; NS5: I280V, T649A" } } }, { - "name": "NODE_0000087", + "name": "NODE_0000094", "node_attrs": { - "div": 0.08309652, + "div": 0.0831, "clade_membership": { "value": "3III_A" } @@ -14910,23 +12650,14 @@ "T9268C", "A9358G", "C9884T" - ], - "NS1": [ - "N290S" - ], - "NS5": [ - "I50T" ] - }, - "labels": { - "aa": "NS1: N290S; NS5: I50T" } }, "children": [ { - "name": "NODE_0000088", + "name": "NODE_0000095", "node_attrs": { - "div": 0.08701244, + "div": 0.087, "clade_membership": { "value": "3III_A.2" } @@ -14973,16 +12704,9 @@ "A9657G", "G9736A", "C10210T" - ], - "NS2A": [ - "F19Y" - ], - "NS5": [ - "K698R" ] }, "labels": { - "aa": "NS2A: F19Y; NS5: K698R", "lineage": "3III_A.2" } }, @@ -14990,12 +12714,12 @@ { "name": "OP410993.1|2008-09", "node_attrs": { - "div": 0.09282217999999999, - "country": { - "value": "Singapore" - }, + "div": 0.0928, "clade_membership": { "value": "3III_A.2" + }, + "country": { + "value": "Singapore" } }, "branch_attrs": { @@ -15060,27 +12784,14 @@ "T10060C", "G10171A", "T10183C" - ], - "NS2A": [ - "V36F", - "I120V" - ], - "NS4B": [ - "A193V" - ], - "NS5": [ - "K595R" ] - }, - "labels": { - "aa": "NS2A: V36F, I120V; NS4B: A193V; NS5: K595R" } } }, { - "name": "NODE_0000089", + "name": "NODE_0000096", "node_attrs": { - "div": 0.08955503, + "div": 0.0896, "clade_membership": { "value": "3III_A.2" } @@ -15114,31 +12825,19 @@ "T9480C", "C9595T", "T9682C" - ], - "C": [ - "K35R" - ], - "NS2A": [ - "T195A" - ], - "NS5": [ - "L639P" ] - }, - "labels": { - "aa": "C: K35R; NS2A: T195A; NS5: L639P" } }, "children": [ { "name": "MG721059.2|2016", "node_attrs": { - "div": 0.09928142, - "country": { - "value": "India" - }, + "div": 0.0993, "clade_membership": { "value": "3III_A.2" + }, + "country": { + "value": "India" } }, "branch_attrs": { @@ -15241,44 +12940,14 @@ "A9985G", "T10000C", "C10158T" - ], - "2K": [ - "I20T" - ], - "NS1": [ - "T93S", - "T128I", - "S290N" - ], - "NS2A": [ - "V36A" - ], - "NS2B": [ - "I76V" - ], - "NS3": [ - "T436A", - "E469D", - "L480I" - ], - "NS4B": [ - "K211R" - ], - "NS5": [ - "Y482F", - "T585K", - "T865I" ] - }, - "labels": { - "aa": "2K: I20T; NS1: T93S, T128I, S290N; NS2A: V36A; NS2B: I76V; NS3: T436A, E469D, L480I; NS4B: K211R; NS5: Y482F, T585K, T865I" } } }, { - "name": "NODE_0000090", + "name": "NODE_0000097", "node_attrs": { - "div": 0.09182818, + "div": 0.0918, "clade_membership": { "value": "3III_A.2" } @@ -15307,25 +12976,19 @@ "C9112T", "C9386T", "T9904C" - ], - "NS2A": [ - "I158M" ] - }, - "labels": { - "aa": "NS2A: I158M" } }, "children": [ { "name": "LT996904.1|2007", "node_attrs": { - "div": 0.09476665, - "country": { - "value": "Malaysia" - }, + "div": 0.0948, "clade_membership": { "value": "3III_A.2" + }, + "country": { + "value": "Malaysia" } }, "branch_attrs": { @@ -15362,34 +13025,14 @@ "T9472C", "C9700T", "C9988G" - ], - "2K": [ - "L17M" - ], - "E": [ - "L234R", - "V249A", - "T471I" - ], - "NS3": [ - "K15R" - ], - "NS4B": [ - "K17R" - ], - "NS5": [ - "D808E" ] - }, - "labels": { - "aa": "2K: L17M; E: L234R, V249A, T471I; NS3: K15R; NS4B: K17R; NS5: D808E" } } }, { - "name": "NODE_0000091", + "name": "NODE_0000098", "node_attrs": { - "div": 0.09231152, + "div": 0.0923, "clade_membership": { "value": "3III_A.2" } @@ -15402,25 +13045,19 @@ "C7642T", "C9295T", "A10228G" - ], - "NS3": [ - "I506L" ] - }, - "labels": { - "aa": "NS3: I506L" } }, "children": [ { "name": "MH048677.1|2014-12", "node_attrs": { - "div": 0.09688111999999999, - "country": { - "value": "Malaysia" - }, + "div": 0.0969, "clade_membership": { "value": "3III_A.2" + }, + "country": { + "value": "Malaysia" } }, "branch_attrs": { @@ -15473,35 +13110,19 @@ "C9754T", "T9954C", "C10201T" - ], - "NS2A": [ - "G28W" - ], - "NS3": [ - "P106S" - ], - "NS4B": [ - "S23P" - ], - "NS5": [ - "T155I", - "I797T" ] - }, - "labels": { - "aa": "NS2A: G28W; NS3: P106S; NS4B: S23P; NS5: T155I, I797T" } } }, { "name": "KJ830751.1|2014-01-26", "node_attrs": { - "div": 0.09702717, - "country": { - "value": "Saudi Arabia" - }, + "div": 0.097, "clade_membership": { "value": "3III_A.2" + }, + "country": { + "value": "Saudi Arabia" } }, "branch_attrs": { @@ -15554,22 +13175,7 @@ "C9754A", "C10202T", "A10255G" - ], - "NS2A": [ - "D52N", - "E118D", - "S210N" - ], - "NS2B": [ - "T91I" - ], - "NS5": [ - "P636S", - "L679V" ] - }, - "labels": { - "aa": "NS2A: D52N, E118D, S210N; NS2B: T91I; NS5: P636S, L679V" } } } @@ -15582,9 +13188,9 @@ ] }, { - "name": "NODE_0000092", + "name": "NODE_0000099", "node_attrs": { - "div": 0.08443054, + "div": 0.0844, "clade_membership": { "value": "3III_A" } @@ -15612,10 +13218,7 @@ { "name": "DQ675533.1|1999", "node_attrs": { - "div": 0.08782409, - "country": { - "value": "Taiwan" - }, + "div": 0.0878, "clade_membership": { "value": "3III_A" } @@ -15660,32 +13263,14 @@ "T9493C", "T9503C", "C9605T" - ], - "E": [ - "T169H", - "I172L" - ], - "NS1": [ - "I94L" - ], - "NS2A": [ - "M23L", - "F207L" - ], - "NS3": [ - "Q568E", - "K589R" ] - }, - "labels": { - "aa": "E: T169H, I172L; NS1: I94L; NS2A: M23L, F207L; NS3: Q568E, K589R" } } }, { - "name": "NODE_0000093", + "name": "NODE_0000100", "node_attrs": { - "div": 0.08705376, + "div": 0.0871, "clade_membership": { "value": "3III_A.1" } @@ -15718,13 +13303,9 @@ "T7750C", "T10060C", "C10248T" - ], - "NS5": [ - "S895L" ] }, "labels": { - "aa": "NS5: S895L", "lineage": "3III_A.1" } }, @@ -15732,12 +13313,12 @@ { "name": "KU509283.1|2006", "node_attrs": { - "div": 0.09284721, - "country": { - "value": "Sri Lanka" - }, + "div": 0.0928, "clade_membership": { "value": "3III_A.1" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { @@ -15802,42 +13383,14 @@ "A9874G", "T9994C", "T10054C" - ], - "C": [ - "L103F" - ], - "E": [ - "K325R", - "G347S" - ], - "NS1": [ - "K170R" - ], - "NS2A": [ - "D66N", - "A79E" - ], - "NS3": [ - "M268I" - ], - "NS4B": [ - "L112F" - ], - "NS5": [ - "E500A", - "I567M", - "Y572N" ] - }, - "labels": { - "aa": "C: L103F; E: K325R, G347S; NS1: K170R; NS2A: D66N, A79E; NS3: M268I; NS4B: L112F; NS5: E500A, I567M, Y572N" } } }, { - "name": "NODE_0000094", + "name": "NODE_0000101", "node_attrs": { - "div": 0.08952769999999999, + "div": 0.0886, "clade_membership": { "value": "3III_A.1" } @@ -15845,22 +13398,14 @@ "branch_attrs": { "mutations": { "nuc": [ - "G388A", - "T511C", - "C520T", "G715A", "T905C", - "G1174A", "A1219C", "A2461G", "C2524T", - "T3160A", "T3502A", - "T3712C", - "T4198C", "G4201A", "A4912G", - "T5341C", "A5644G", "C5848T", "C6448T", @@ -15868,131 +13413,64 @@ "G7778A", "C7948T", "A8398G", - "G9247A", "G9388T" - ], - "NS5": [ - "V72I" ] - }, - "labels": { - "aa": "NS5: V72I" } }, "children": [ { - "name": "NODE_0000095", + "name": "OR389038.1|2004", "node_attrs": { - "div": 0.08972335999999999, + "div": 0.0893, "clade_membership": { "value": "3III_A.1" + }, + "country": { + "value": "Sri Lanka" } }, "branch_attrs": { "mutations": { "nuc": [ - "G5104A", - "G6340A" + "A2224G", + "T2901A", + "T6160C", + "G6874A", + "T6889C", + "G8638A", + "C9463T" ] } - }, - "children": [ - { - "name": "EU081210.1|2005", - "node_attrs": { - "div": 0.09070969999999999, - "country": { - "value": "Singapore" - }, - "clade_membership": { - "value": "3III_A.1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T271C", - "A486G", - "C1182T", - "T2310C", - "C6139T", - "T6490C", - "T7723C", - "C8455T", - "T9955C", - "A10075T" - ], - "E": [ - "P83L", - "V459A" - ], - "M": [ - "N17S" - ] - }, - "labels": { - "aa": "E: P83L, V459A; M: N17S" - } - } - }, - { - "name": "EU081217.1|2005", - "node_attrs": { - "div": 0.09071252999999999, - "country": { - "value": "Singapore" - }, - "clade_membership": { - "value": "3III_A.1" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T520C", - "G1627A", - "C3854T", - "G4228A", - "G4584A", - "C4588A", - "G4594A", - "G7009C", - "C7721T", - "G8614A" - ], - "NS3": [ - "R24K" - ], - "NS5": [ - "H53Y" - ] - }, - "labels": { - "aa": "NS3: R24K; NS5: H53Y" - } - } - } - ] + } }, { - "name": "NODE_0000096", + "name": "NODE_0000102", "node_attrs": { - "div": 0.08952869999999999, + "div": 0.0895, "clade_membership": { "value": "3III_A.1" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "G388A", + "T511C", + "C520T", + "G1174A", + "T3160A", + "T3712C", + "T4198C", + "T5341C", + "G9247A" + ] + } }, "children": [ { - "name": "EU081225.1|2005", + "name": "NODE_0000103", "node_attrs": { - "div": 0.09061254999999999, - "country": { - "value": "Singapore" - }, + "div": 0.0897, "clade_membership": { "value": "3III_A.1" } @@ -16000,64 +13478,141 @@ "branch_attrs": { "mutations": { "nuc": [ - "G201A", - "T235C", - "C1381T", - "C1410T", - "C2083T", - "G2422T", - "A6598G", - "T6994C", - "C8485G", - "A8962G", - "T9703C" - ], - "C": [ - "G36E" - ], - "E": [ - "T159M" + "G5104A", + "G6340A" ] + } + }, + "children": [ + { + "name": "EU081210.1|2005", + "node_attrs": { + "div": 0.0907, + "clade_membership": { + "value": "3III_A.1" + }, + "country": { + "value": "Singapore" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T271C", + "A486G", + "C1182T", + "T2310C", + "C6139T", + "T6490C", + "T7723C", + "C8455T", + "T9955C", + "A10075T" + ] + } + } }, - "labels": { - "aa": "C: G36E; E: T159M" + { + "name": "EU081217.1|2005", + "node_attrs": { + "div": 0.0907, + "clade_membership": { + "value": "3III_A.1" + }, + "country": { + "value": "Singapore" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T520C", + "G1627A", + "C3854T", + "G4228A", + "G4584A", + "C4588A", + "G4594A", + "G7009C", + "C7721T", + "G8614A" + ] + } + } } - } + ] }, { - "name": "EU081214.1|2005", + "name": "NODE_0000104", "node_attrs": { - "div": 0.09060925999999998, - "country": { - "value": "Singapore" - }, + "div": 0.0895, "clade_membership": { "value": "3III_A.1" } }, "branch_attrs": { - "mutations": { - "nuc": [ - "T2275C", - "C2416T", - "C3187T", - "C3194T", - "C3755T", - "C3850T", - "A5647G", - "G6358A", - "G6454A", - "T7675C", - "T9493C" - ], - "NS1": [ - "H261Y" - ] + "mutations": {} + }, + "children": [ + { + "name": "EU081225.1|2005", + "node_attrs": { + "div": 0.0906, + "clade_membership": { + "value": "3III_A.1" + }, + "country": { + "value": "Singapore" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G201A", + "T235C", + "C1381T", + "C1410T", + "C2083T", + "G2422T", + "A6598G", + "T6994C", + "C8485G", + "A8962G", + "T9703C" + ] + } + } }, - "labels": { - "aa": "NS1: H261Y" + { + "name": "EU081214.1|2005", + "node_attrs": { + "div": 0.0906, + "clade_membership": { + "value": "3III_A.1" + }, + "country": { + "value": "Singapore" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T2275C", + "C2416T", + "C3187T", + "C3194T", + "C3755T", + "C3850T", + "A5647G", + "G6358A", + "G6454A", + "T7675C", + "T9493C" + ] + } + } } - } + ] } ] } @@ -16072,9 +13627,9 @@ ] }, { - "name": "NODE_0000097", + "name": "NODE_0000105", "node_attrs": { - "div": 0.07424149, + "div": 0.0742, "clade_membership": { "value": "3III" } @@ -16105,4425 +13660,5006 @@ "T9979C", "A10018C", "T10060C" - ], - "NS2A": [ - "V150I" - ], - "NS4A": [ - "V100I" - ], - "NS5": [ - "L639P" ] - }, - "labels": { - "aa": "NS2A: V150I; NS4A: V100I; NS5: L639P" } }, "children": [ { - "name": "NODE_0000098", + "name": "NODE_0000106", "node_attrs": { - "div": 0.08187117, + "div": 0.0873, "clade_membership": { - "value": "3III_C" + "value": "3III_B" } }, "branch_attrs": { "mutations": { "nuc": [ - "C529T", - "T685C", - "A790G", - "C1055T", - "T1246A", - "T1357C", - "A1522G", - "A1606G", - "C1648T", - "C1718T", - "C1920T", - "C1984T", - "G2290A", - "T2308A", - "A2407G", - "C2428T", - "T2470C", - "T2612C", - "A2650G", - "C2691T", - "G2995A", - "C3100T", - "T3103C", - "A3202G", - "A3208G", - "C3220T", - "G3232A", - "G3334A", - "C3397T", - "A3571G", - "C3661A", - "C3685T", - "T3763C", - "G3910A", - "C4078T", - "G4201A", - "T4279C", - "C4447A", - "C4543T", - "C4691T", - "A5017G", - "G5047A", - "C5320T", - "T5321C", - "T5347C", - "G5371A", - "T5569A", - "G5704A", - "C6220T", - "C6427T", - "A6520G", - "G6586A", - "C6833T", - "G6904A", - "C7090A", - 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V59I; NS5: R382K, K468R, D520G" } } }, { - "name": "NODE_0000148", + "name": "OM417340.1|2021-09-21", "node_attrs": { - "div": 0.10307313, + "div": 0.105, "clade_membership": { - "value": "3III_B.3.2" + "value": "3III_C.2.1" + }, + "country": { + "value": "Mexico" } }, "branch_attrs": { - "mutations": {} - }, - "children": [ - { - "name": "OQ821520.1|2022-08-18", - "node_attrs": { - "div": 0.10500043, - "country": { - "value": "Cuba" - }, - "clade_membership": { - "value": "3III_B.3.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T784C", - "T1156C", - "G2542A", - "C3187A", - "T3662A", - "C3728T", - "T3961C", - "T4492C", - "T4819C", - "T5040C", - "T5665C", - "T7351C", - "A7402G", - "T8251C", - "A9886G", - "T9955C", - "T9958C" - ], - "NS2A": [ - "S65T" - ], - "NS3": [ - "M176T" - ] - }, - "labels": { - "aa": "NS2A: S65T; NS3: M176T" - } - } - }, - { - "name": "NODE_0000149", - "node_attrs": { - "div": 0.10335582, - "clade_membership": { - "value": "3III_B.3.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G2017A", - "G2203A" - ] - } - }, - "children": [ - { - "name": "OQ857506.1|2022-10-05", - "node_attrs": { - "div": 0.10508479, - "country": { - "value": "USA" - }, - "clade_membership": { - "value": "3III_B.3.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G451A", - "A1321G", - "T2056C", - "C3013T", - "A3643G", - "T4025A", - "C4339T", - "A4888G", - "C7193T", - "G7267A", - "A7891G", - "A8406G" - ], - "NS2A": [ - "I58M", - "L186M" - ], - "NS5": [ - "K281R" - ] - }, - "labels": { - "aa": "NS2A: I58M, L186M; NS5: K281R" - } - } - }, - { - "name": "OR150747.1|2022-12-23", - "node_attrs": { - "div": 0.10501596, - "country": { - "value": "USA" - }, - "clade_membership": { - "value": "3III_B.3.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "T1159C", - "T1825C", - "T2171C", - "C2314T", - "T2491C", - "A2734G", - "T4744C", - "G5173A", - "T5494A", - "T5671C", - "C6754T", - "C6857T", - "A9772G", - "C9841T", - "C10079T", - "G10243T" - ], - "NS5": [ - "E893D" - ] - }, - "labels": { - "aa": "NS5: E893D" - } - } - } + "mutations": { + "nuc": [ + "C407T", + "C431T", + "T1920C", + "T2005C", + "A2429G", + "G2674A", + "T2815C", + "C3061T", + "T3106C", + "G3454A", + "T3457C", + "T3578C", + "G3616A", + "T4087C", + "C4351T", + "A4564G", + "C4657T", + "C4903T", + "C5161T", + "C5602T", + "T5707C", + "C6295T", + "A6808G", + "T7021C", + "T7363C", + "T8101C", + "C8140T", + "T8191C", + "T9262C", + "C10006T", + "T10105C", + "C10138A" ] } - ] + } } ] } diff --git a/data/community/v-gen-lab/dengue/denv4/CHANGELOG.md b/data/community/v-gen-lab/dengue/denv4/CHANGELOG.md index a7d5f51a..8ab83a70 100644 --- a/data/community/v-gen-lab/dengue/denv4/CHANGELOG.md +++ b/data/community/v-gen-lab/dengue/denv4/CHANGELOG.md @@ -1,3 +1,7 @@ +## Unreleased + +- Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages. + ## 2024-08-31T20:44:06Z Initial release of a DENV-4 dataset for Lineage classification! diff --git a/data/community/v-gen-lab/dengue/denv4/README.md b/data/community/v-gen-lab/dengue/denv4/README.md index a0dab07b..edda9a70 100644 --- a/data/community/v-gen-lab/dengue/denv4/README.md +++ b/data/community/v-gen-lab/dengue/denv4/README.md @@ -18,9 +18,9 @@ This system is built on experience developing lineage systems for other viruses Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't necessarily always work like that—some minor lineages are very widespread, and some major lineages are geographically limited. -The source code is available at [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade). +The source code is available at [V-GEN-Lab/dengue-lineages-workflow](https://github.com/V-GEN-Lab/dengue-lineages-workflow). -For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues). +For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-workflow/issues). ## Maintainers and Contacts: diff --git a/data/community/v-gen-lab/dengue/denv4/tree.json b/data/community/v-gen-lab/dengue/denv4/tree.json index c632cdb5..578e4ee0 100644 --- a/data/community/v-gen-lab/dengue/denv4/tree.json +++ b/data/community/v-gen-lab/dengue/denv4/tree.json @@ -2,7 +2,7 @@ "version": "v2", "meta": { "title": "Dengue Lineages of DENV-4", - "updated": "2024-08-16", + "updated": "2024-09-10", "build_url": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade", "data_provenance": [ { @@ -24,86 +24,8 @@ "color_by": "country" }, "genome_annotations": { - "2K": { - "end": 6827, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 6759, - "strand": "+", - "type": "CDS" - }, - "C": { - "end": 440, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 102, - "strand": "+", - "type": "CDS" - }, - "E": { - "end": 2423, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 939, - "strand": "+", - "type": "CDS" - }, - "M": { - "end": 938, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 441, - "strand": "+", - "type": "CDS" - }, - "NS1": { - "end": 3479, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 2424, - "strand": "+", - "type": "CDS" - }, - "NS2A": { - "end": 4133, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 3480, - "strand": "+", - "type": "CDS" - }, - "NS2B": { - "end": 4523, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 4134, - "strand": "+", - "type": "CDS" - }, - "NS3": { - "end": 6377, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 4524, - "strand": "+", - "type": "CDS" - }, - "NS4A": { - "end": 6758, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 6378, - "strand": "+", - "type": "CDS" - }, - "NS4B": { - "end": 7562, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 6828, - "strand": "+", - "type": "CDS" - }, - "NS5": { - "end": 10262, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", - "start": 7563, - "strand": "+", - "type": "CDS" - }, "nuc": { "end": 10649, - "seqid": "/home/james_pereira/drdengue/pipelinePhyloReconstruction/reference_sequences/reference_dengue_denv4.gb", "start": 1, "strand": "+", "type": "source" @@ -136,113 +58,101 @@ { "key": "country", "demes": { - "Paraguay": { - "latitude": -23.33333, - "longitude": -58.0 - }, - "Mexico": { - "latitude": 19.4325301, - "longitude": -99.1332101 - }, - "New Caledonia": { - "latitude": -20.9043, - "longitude": 165.618 - }, - "El Salvador": { - "latitude": 13.68935, - "longitude": -89.18718 + "Malaysia": { + "latitude": 4.264153, + "longitude": 102.222436 }, - "India": { - "latitude": 22.3511148, - "longitude": 78.6677428 + "Pakistan": { + "latitude": 30.0, + "longitude": 70.0 }, - "Haiti": { - "latitude": 19.1399952, - "longitude": -72.3570971 + "Thailand": { + "latitude": 14.8971921, + "longitude": 100.83273 }, - "Philippines": { - "latitude": 12.8797, - "longitude": 121.774 + "China": { + "latitude": 33.394333, + "longitude": 104.689839 }, - "Vietnam": { - "latitude": 16.16667, - "longitude": 107.83333 + "Sri Lanka": { + "latitude": 7.8731, + "longitude": 80.7718 }, "Colombia": { "latitude": 2.893108, "longitude": -73.7845142 }, - "Ecuador": { - "latitude": -1.3397667, - "longitude": -79.3666964 - }, - "Senegal": { - "latitude": 14.5, - "longitude": -14.25 - }, - "Nicaragua": { - "latitude": 13.0, - "longitude": -85.0 + "Venezuela": { + "latitude": 7.838891, + "longitude": -65.916409 }, - "Indonesia": { - "latitude": -5.0, - "longitude": 120.0 + "Haiti": { + "latitude": 19.1399952, + "longitude": -72.3570972 }, - "Taiwan": { - "latitude": 23.6978, - "longitude": 120.9605 + "Paraguay": { + "latitude": -23.3165935, + "longitude": -58.1693445 }, - "Thailand": { - "latitude": 14.8971921, - "longitude": 100.83273 + "Mexico": { + "latitude": 19.4325301, + "longitude": -99.1332101 }, - "Venezuela": { - "latitude": 8.0, - "longitude": -66.0 + "USA": { + "latitude": 38.916963, + "longitude": -98.891372 }, - "Myanmar": { - "latitude": 21.0, - "longitude": 96.0 + "India": { + "latitude": 21.077353, + "longitude": 78.723951 }, - "China": { - "latitude": 35.000074, - "longitude": 104.999927 + "Senegal": { + "latitude": 14.5, + "longitude": -14.25 }, - "Sri Lanka": { - "latitude": 7.75, - "longitude": 80.75 + "Ecuador": { + "latitude": -1.0541, + "longitude": -78.1489 }, "Puerto Rico": { - "latitude": 18.2459121, - "longitude": -66.4164147 + "latitude": 18.2247706, + "longitude": -66.4858295 }, "Cambodia": { "latitude": 13.0, "longitude": 105.0 }, - "Pakistan": { - "latitude": 30.0, - "longitude": 70.0 - }, - "Singapore": { - "latitude": 1.2904527, - "longitude": 103.852038 - }, - "USA": { - "latitude": 39.7837304, - "longitude": -100.4458824 + "Australia": { + "latitude": -24.7761085, + "longitude": 134.755 }, "Jamaica": { - "latitude": 18.16667, - "longitude": -77.25 + "latitude": 18.1096, + "longitude": -77.2975 }, "Brazil": { "latitude": -10.3333332, "longitude": -53.1999999 }, - "Malaysia": { - "latitude": 2.3923759, - "longitude": 112.8471939 + "Nicaragua": { + "latitude": 12.6090157, + "longitude": -85.2936911 + }, + "Taiwan": { + "latitude": 23.8169, + "longitude": 121.031365 + }, + "Myanmar": { + "latitude": 20.600856, + "longitude": 96.287616 + }, + "Singapore": { + "latitude": 1.344189, + "longitude": 103.867546 + }, + "Indonesia": { + "latitude": -0.897599, + "longitude": 114.181602 } } } @@ -265,7 +175,6 @@ "branch_attrs": { "mutations": { "nuc": [ - "G77A", "G127A", "T176A", "T183A", @@ -1916,384 +1825,14 @@ "A10244C", "G10247A", "T10250G" - ], - "2K": [ - "T13G", - "T16I" - ], - "C": [ - "R9K", - "L28M", - "V29M", - "T34I", - "V55M", - "I81T", - "G82K", - "R84K", - "G96R", - "S100T", - "T101I", - "I102M", - "L104M", - "L105M" - ], - "E": [ - "A19T", - "T46I", - "T58S", - "G123E", - "L129M", - "I132V", - "T148A", - "H149N", - "M163T", - "S168A", - "T182I", - "L183M", - "N194K", - "K203R", - "S227E", - "E228K", - "V229I", - "H230Q", - "Y233D", - "S262T", - "A265T", - "S272A", - "D274N", - "A280T", - "S303T", - "A329T", - "V335I", - "V347I", - "L357F", - "A358V", - "T361R", - "V364I", - "V379M", - "V382T", - "N384D", - "S385R", - "A386T", - "L387I", - "L428V", - "I455V", - "F461L", - "M477I", - "T478S" - ], - "M": [ - "S2H", - "S4T", - "L11H", - "A15E", - "H17Q", - "P22S", - "T35M", - "L41V", - "L70A", - "S72A", - "M76T", - "T96A", - "S99T", - "A120V", - "T152I", - "F154I", - "V156I" - ], - "NS1": [ - "A6V", - "S9N", - "G10R", - "I19M", - "V22I", - "L42I", - "S44A", - "L86I", - "A90V", - "T98K", - "A103T", - "L104I", - "T105K", - "V108R", - "A128V", - "R129K", - "S131N", - "D139E", - "S141T", - "S152F", - "S175R", - "V178I", - "S185A", - "I188V", - "S205A", - "S246K", - "F251S", - "T264I", - "V265M", - "I275M", - "T286K", - "Q288E", - "D290N", - "D292G", - "V308I", - "L324M", - "L338S" - ], - "NS2A": [ - "Q2E", - "T4R", - "T7N", - "L15V", - "V19I", - "L34M", - "V36M", - "I38V", - "C41G", - "A42M", - "I44M", - "A56V", - "L57I", - "D62N", - "S65A", - "R67K", - "I68M", - "G69K", - "I72V", - "V79M", - "V87M", - "V90M", - "R98K", - "A101G", - "L113I", - "S114A", - "H117Q", - "D118N", - "L119V", - "L122I", - "S127A", - "L128M", - "I135M", - "V136I", - "T137V", - "T142E", - "V144M", - "L147V", - "L149M", - "S156T", - "T157I", - "V161N", - "R165K", - "A169T", - "V173I", - "S183R", - "C184K", - "Q188K", - "V192I", - "L199V", - "A201G", - "Q202E", - "V206I", - "G214E", - "A215K", - "S216T", - "R217K" - ], - "NS2B": [ - "A20T", - "L21I", - "L28M", - "L39I", - "V59M", - "Q60K", - "M64I", - "I73V", - "V74I", - "T92I", - "A102G", - "L112M", - "V126M" - ], - "NS3": [ - "A11T", - "A12T", - "K14Q", - "A17T", - "S19K", - "E20K", - "I40V", - "H41Q", - "C59S", - "H60Y", - "E61K", - "T62N", - "D94E", - "I100V", - "R142K", - "S158T", - "R170K", - "P174A", - "D179E", - "S206A", - "V208I", - "I240M", - "V247M", - "S249A", - "T267I", - "V282I", - "S292A", - "S301A", - "T322I", - "R337K", - "D349E", - "T400M", - "G420R", - "P435T", - "D469N", - "V473I", - "D477E", - "R513K", - "T516S", - "F523Y", - "T532N", - "S547R", - "S556T", - "E558K", - "R584K", - "R594K", - "D609E", - "S615R" - ], - "NS4A": [ - "L4M", - "I10M", - "L23Q", - "V58I", - "A63G", - "A66G", - "M83I", - "T87A", - "I100M" - ], - "NS4B": [ - "V18E", - "L45M", - "R83K", - "G87S", - "L112V", - "V113G", - "T148I", - "V168I", - "L191V", - "A194V", - "L199I", - "R208K" - ], - "NS5": [ - "R30K", - "L34I", - "S43I", - "A44G", - "D47K", - "S49E", - "S59T", - "V66M", - "N96K", - "T98S", - "K101R", - "Y103F", - "S128T", - "S150A", - "P170Q", - "S173T", - "S174*", - "V190I", - "H201Y", - "N204R", - "A224I", - "S225T", - "T235V", - "T245M", - "R246K", - "H247Y", - "D273N", - "T275K", - "L281I", - "Q285K", - "Q296K", - "Q365K", - "M372E", - "N379K", - "A383S", - "L384F", - "K387R", - "N390K", - "S401A", - "V412I", - "T420G", - "S421T", - "S429K", - "E433K", - "D436E", - "A440N", - "G499S", - "W504*", - "I518M", - "D523E", - "Q548M", - "T554M", - "A558G", - "P559T", - "H560E", - "H561Q", - "R586K", - "D632E", - "Q635K", - "L640V", - "R643K", - "C651Y", - "V653R", - "G676S", - "T677K", - "S678A", - "L680H", - "F718G", - "S724T", - "V726I", - "S764A", - "E787K", - "F789V", - "T807N", - "D821E", - "V831I", - "H832N", - "D836E", - "L846Q", - "S855N", - "H865Q", - "T866I", - "T869N", - "V881M", - "V886A", - "S891K", - "A892T", - "P893S", - "S894F", - "S896R" ] - }, - "labels": { - "aa": "2K: T13G, T16I; C: R9K, L28M, V29M, T34I, V55M, I81T, G82K, R84K, G96R, S100T, T101I, I102M, L104M, L105M; E: A19T, T46I, T58S, G123E, L129M, I132V, T148A, H149N, M163T, S168A, T182I, L183M, N194K, K203R, S227E, E228K, V229I, H230Q, Y233D, S262T, A265T, S272A, D274N, A280T, S303T, A329T, V335I, V347I, L357F, A358V, T361R, V364I, V379M, V382T, N384D, S385R, A386T, L387I, L428V, I455V, F461L, M477I, T478S; M: S2H, S4T, L11H, A15E, H17Q, P22S, T35M, L41V, L70A, S72A, M76T, T96A, S99T, A120V, T152I, F154I, V156I; NS1: A6V, S9N, G10R, I19M, V22I, L42I, S44A, L86I, A90V, T98K, A103T, L104I, T105K, V108R, A128V, R129K, S131N, D139E, S141T, S152F, S175R, V178I, S185A, I188V, S205A, S246K, F251S, T264I, V265M, I275M, T286K, Q288E, D290N, D292G, V308I, L324M, L338S; NS2A: Q2E, T4R, T7N, L15V, V19I, L34M, V36M, I38V, C41G, A42M, I44M, A56V, L57I, D62N, S65A, R67K, I68M, G69K, I72V, V79M, V87M, V90M, R98K, A101G, L113I, S114A, H117Q, D118N, L119V, L122I, S127A, L128M, I135M, V136I, T137V, T142E, V144M, L147V, L149M, S156T, T157I, V161N, R165K, A169T, V173I, S183R, C184K, Q188K, V192I, L199V, A201G, Q202E, V206I, G214E, A215K, S216T, R217K; NS2B: A20T, L21I, L28M, L39I, V59M, Q60K, M64I, I73V, V74I, T92I, A102G, L112M, V126M; NS3: A11T, A12T, K14Q, A17T, S19K, E20K, I40V, H41Q, C59S, H60Y, E61K, T62N, D94E, I100V, R142K, S158T, R170K, P174A, D179E, S206A, V208I, I240M, V247M, S249A, T267I, V282I, S292A, S301A, T322I, R337K, D349E, T400M, G420R, P435T, D469N, V473I, D477E, R513K, T516S, F523Y, T532N, S547R, S556T, E558K, R584K, R594K, D609E, S615R; NS4A: L4M, I10M, L23Q, V58I, A63G, A66G, M83I, T87A, I100M; NS4B: V18E, L45M, R83K, G87S, L112V, V113G, T148I, V168I, L191V, A194V, L199I, R208K; NS5: R30K, L34I, S43I, A44G, D47K, S49E, S59T, V66M, N96K, T98S, K101R, Y103F, S128T, S150A, P170Q, S173T, S174*, V190I, H201Y, N204R, A224I, S225T, T235V, T245M, R246K, H247Y, D273N, T275K, L281I, Q285K, Q296K, Q365K, M372E, N379K, A383S, L384F, K387R, N390K, S401A, V412I, T420G, S421T, S429K, E433K, D436E, A440N, G499S, W504*, I518M, D523E, Q548M, T554M, A558G, P559T, H560E, H561Q, R586K, D632E, Q635K, L640V, R643K, C651Y, V653R, G676S, T677K, S678A, L680H, F718G, S724T, V726I, S764A, E787K, F789V, T807N, D821E, V831I, H832N, D836E, L846Q, S855N, H865Q, T866I, T869N, V881M, V886A, S891K, A892T, P893S, S894F, S896R" } }, "children": [ { "name": "MZ215848.1|2007-05-21", "node_attrs": { - "div": 0.153118, - "country": { - "value": "Malaysia" - }, + "div": 0.153, "clade_membership": { "value": "Outgroup" } @@ -3320,291 +2859,9 @@ "A10256G", "T10259C", "G10262C" - ], - "2K": [ - "I16L", - "I17F", - "I21V", - "A23S" - ], - "C": [ - "T24S", - "K40R", - "K72R", - "K82N", - "K85R", - "N92A", - "I101V", - "M104I", - "M112L" - ], - "E": [ - "Q36P", - "I46T", - "I68T", - "A150S", - "I164V", - "I182L", - "K194S", - "R203S", - "T226A", - "K228N", - "I229T", - "D233A", - "T265A", - "I337V", - "S363A", - "I364L", - "T365A", - "N366S", - "M379T", - "R385G", - "V436L", - "M454I", - "T473A", - "I477L", - "I480L" - ], - "M": [ - "E43D", - "T59A", - "T73A", - "T81S", - "A134S", - "I144V", - "I149T", - "I152V" - ], - "NS1": [ - "R10S", - "M19V", - "I22M", - "A40S", - "A45S", - "V66L", - "I71V", - "T72S", - "K98E", - "K99R", - "K105N", - "R108S", - "T117S", - "M162V", - "T164S", - "K170R", - "R175V", - "I178T", - "K192L", - "K246Q", - "S251P", - "M265L", - "T284S", - "E289D", - "N290S", - "M318L", - "S339T", - "K341R", - "K347R" - ], - "NS2A": [ - "E2D", - "R4S", - "V35A", - "M36I", - "V37L", - "G41V", - "I43V", - "M44V", - "I57T", - "K69N", - "V72A", - "K81R", - "M87I", - "M103L", - "V112L", - "I123V", - "M144I", - "I154L", - "I157F", - "M158A", - "N161Y", - "M162T", - "I167V", - "V174A", - "T182S", - "R183T", - "K188T", - "S189P", - "I194L", - "I198L", - "V199A", - "E202G", - "Y207F", - "K217R" - ], - "NS2B": [ - "M44L", - "N58D", - "M59I", - "E63D", - "I64L", - "I67V", - "E75D", - "I92V", - "M94T", - "I95F", - "V106L", - "M112I", - "A113S", - "V116A", - "M123L", - "M126T" - ], - "NS3": [ - "T12P", - "K19E", - "K20T", - "K33R", - "T34S", - "S59T", - "Y60C", - "K61N", - "G86A", - "T127S", - "E169D", - "I171T", - "A197S", - "M240V", - "M247I", - "I267M", - "I322M", - "I335T", - "A372S", - "K381R", - "R420S", - "A466S", - "K480R", - "K513Q", - "R547A", - "K558A", - "K590S", - "K594R", - "M605V", - "R615G" - ], - "NS4A": [ - "I2P", - "M10V", - "Y16F", - "T34S", - "E50D", - "G62A", - "G63C", - "K76R", - "I83L", - "I86V", - "G93V", - "Q101P", - "I120V" - ], - "NS4B": [ - "M3L", - "I6L", - "K8R", - "T11A", - "F13L", - "Y16H", - "Q17H", - "K19R", - "T20A", - "T22P", - "M45I", - "M84L", - "M93I", - "G113C", - "V149A", - "V172A", - "F187L", - "I237V" - ], - "NS5": [ - "T4A", - "T5S", - "D21S", - "K23R", - "K42R", - "I43M", - "K46S", - "I51T", - "K52S", - "M66T", - "K74R", - "K96G", - "T137P", - "V168A", - "*174Q", - "T189S", - "K196R", - "R204G", - "I228V", - "K246T", - "M274L", - "K275E", - "K296N", - "I335V", - "K365R", - "K367Q", - "V373A", - "T375S", - "K379E", - "K388S", - "K390R", - "I400V", - "S423V", - "K429E", - "Q443L", - "*504Y", - "M518V", - "I522V", - "E523G", - "K524S", - "K525R", - "I553V", - "M554V", - "K562R", - "I563A", - "K566T", - "K596R", - "I629L", - "N636D", - "G639A", - "K641R", - "E642A", - "E645L", - "K649N", - "E650Q", - "Y651H", - "N703D", - "I717L", - "A758S", - "T786S", - "K787T", - "K812S", - "E820Q", - "N824S", - "T826P", - "N832T", - "E835D", - "I837V", - "I866V", - "M881I", - "K891E", - "E895Q", - "R896M" ] }, "labels": { - "aa": "2K: I16L, I17F, I21V, A23S; C: T24S, K40R, K72R, K82N, K85R, N92A, I101V, M104I, M112L; E: Q36P, I46T, I68T, A150S, I164V, I182L, K194S, R203S, T226A, K228N, I229T, D233A, T265A, I337V, S363A, I364L, T365A, N366S, M379T, R385G, V436L, M454I, T473A, I477L, I480L; M: E43D, T59A, T73A, T81S, A134S, I144V, I149T, I152V; NS1: R10S, M19V, I22M, A40S, A45S, V66L, I71V, T72S, K98E, K99R, K105N, R108S, T117S, M162V, T164S, K170R, R175V, I178T, K192L, K246Q, S251P, M265L, T284S, E289D, N290S, M318L, S339T, K341R, K347R; NS2A: E2D, R4S, V35A, M36I, V37L, G41V, I43V, M44V, I57T, K69N, V72A, K81R, M87I, M103L, V112L, I123V, M144I, I154L, I157F, M158A, N161Y, M162T, I167V, V174A, T182S, R183T, K188T, S189P, I194L, I198L, V199A, E202G, Y207F, K217R; NS2B: M44L, N58D, M59I, E63D, I64L, I67V, E75D, I92V, M94T, I95F, V106L, M112I, A113S, V116A, M123L, M126T; NS3: T12P, K19E, K20T, K33R, T34S, S59T, Y60C, K61N, G86A, T127S, E169D, I171T, A197S, M240V, M247I, I267M, I322M, I335T, A372S, K381R, R420S, A466S, K480R, K513Q, R547A, K558A, K590S, K594R, M605V, R615G; NS4A: I2P, M10V, Y16F, T34S, E50D, G62A, G63C, K76R, I83L, I86V, G93V, Q101P, I120V; NS4B: M3L, I6L, K8R, T11A, F13L, Y16H, Q17H, K19R, T20A, T22P, M45I, M84L, M93I, G113C, V149A, V172A, F187L, I237V; NS5: T4A, T5S, D21S, K23R, K42R, I43M, K46S, I51T, K52S, M66T, K74R, K96G, T137P, V168A, *174Q, T189S, K196R, R204G, I228V, K246T, M274L, K275E, K296N, I335V, K365R, K367Q, V373A, T375S, K379E, K388S, K390R, I400V, S423V, K429E, Q443L, *504Y, M518V, I522V, E523G, K524S, K525R, I553V, M554V, K562R, I563A, K566T, K596R, I629L, N636D, G639A, K641R, E642A, E645L, K649N, E650Q, Y651H, N703D, I717L, A758S, T786S, K787T, K812S, E820Q, N824S, T826P, N832T, E835D, I837V, I866V, M881I, K891E, E895Q, R896M", "lineage": "Outgroup" } } @@ -3612,7 +2869,7 @@ { "name": "NODE_0000001", "node_attrs": { - "div": 0.153117, + "div": 0.153, "clade_membership": { "value": "unassigned" } @@ -4281,7 +3538,7 @@ "T6500C", "G6509C", "G6542C", - "G6554C", + "G6554T", "A6563T", "G6565C", "G6574C", @@ -4673,312 +3930,14 @@ "A10238T", "T10239C", "G10250T" - ], - "2K": [ - "G13A", - "I16T" - ], - "C": [ - "K9R", - "M28L", - "M29V", - "I34T", - "M55V", - "K82G", - "K84R", - "R96G", - "T100S", - "I101T", - "M104L", - "M105L" - ], - "E": [ - "S58T", - "E123G", - "M129L", - "N149H", - "A168S", - "I182T", - "M183L", - "K194N", - "E227S", - "K228E", - "I229V", - "Q230H", - "D233Y", - "T262S", - "A272S", - "N274D", - "T280A", - "T303S", - "I347V", - "V358A", - "R361T", - "M379V", - "T382A", - "R385S", - "T386A", - "I387L", - "V428L", - "I477M" - ], - "M": [ - "T4S", - "H11L", - "E15A", - "Q17H", - "S22P", - "M35T", - "A70P", - "A72S", - "T99S", - "V120A", - "I152T", - "I154F", - "I156V" - ], - "NS1": [ - "N9S", - "R10G", - "M19I", - "I42L", - "A44S", - "I86L", - "V90A", - "K98T", - "T103A", - "K105T", - "R108V", - "V128A", - "K129R", - "E139D", - "T141S", - "R175S", - "I178V", - "A185S", - "A205S", - "K246T", - "I264T", - "K286T", - "E288Q", - "I308V", - "M324L", - "T351A" - ], - "NS2A": [ - "E2Q", - "R4T", - "N7T", - "V15L", - "I19M", - "M34L", - "M36V", - "V38A", - "G41C", - "M42A", - "M44I", - "V56A", - "N62D", - "A65S", - "K67R", - "K69G", - "M79V", - "M87V", - "M90V", - "K98R", - "G101A", - "I113F", - "A114S", - "Q117H", - "N118D", - "V119L", - "I122L", - "M128L", - "I136V", - "Q138H", - "E142A", - "M144V", - "V147L", - "M149L", - "I157T", - "N161I", - "K165R", - "T169A", - "I173V", - "R183S", - "K184C", - "K188Q", - "I192V", - "V199L", - "G201A", - "E202Q", - "I206V", - "E214G", - "K215A", - "T216S" - ], - "NS2B": [ - "T20A", - "I21L", - "M28L", - "I39L", - "M59V", - "K60Q", - "I64M", - "I92T", - "G102A", - "M112L", - "M126V" - ], - "NS3": [ - "T11A", - "T13A", - "K19T", - "K20E", - "Q41H", - "S59C", - "Y60H", - "K61E", - "N62T", - "E94D", - "T158S", - "A174P", - "E179D", - "A206S", - "I208V", - "M240I", - "M247V", - "I267T", - "I282V", - "A292S", - "A301S", - "K337R", - "E349D", - "M400T", - "R420G", - "N469D", - "I473V", - "E477D", - "K513R", - "S516T", - "Y523F", - "N532T", - "R547S", - "T556S", - "K584R", - "E609D", - "R615S" - ], - "NS4A": [ - "M4L", - "M10I", - "Q23L", - "G63A", - "G66A", - "I83M", - "M100I" - ], - "NS4B": [ - "M45L", - "K83R", - "V112L", - "G113V", - "I148T", - "I168V", - "V191L", - "V194A", - "I198V", - "I199L", - "K208R" - ], - "NS5": [ - "K30R", - "I34L", - "I43L", - "G44A", - "K47D", - "E49S", - "T59S", - "M66V", - "K96N", - "S98T", - "T128S", - "A150S", - "Q170P", - "T173S", - "*174S", - "I190V", - "R204S", - "I224A", - "T225S", - "M245T", - "Y247H", - "N273D", - "K275T", - "I281L", - "K285Q", - "K296Q", - "K365Q", - "E372V", - "K379N", - "S383A", - "K390N", - "A401S", - "I412V", - "G420A", - "T421S", - "K429S", - "E436D", - "N440A", - "S499G", - "*504W", - "M518I", - "E521D", - "E523D", - "M548L", - "M554T", - "G558A", - "T559P", - "E560D", - "Q561H", - "E632D", - "K635Q", - "V640L", - "Y651C", - "R653V", - "K677T", - "A678S", - "H680L", - "G718F", - "T724S", - "I726V", - "A764S", - "K787E", - "N807T", - "E821D", - "I831V", - "N832H", - "E836D", - "Q846L", - "N855T", - "I866T", - "N869T", - "M881V", - "K891S", - "T892A", - "S893P", - "R896S" ] - }, - "labels": { - "aa": "2K: G13A, I16T; C: K9R, M28L, M29V, I34T, M55V, K82G, K84R, R96G, T100S, I101T, M104L, M105L; E: S58T, E123G, M129L, N149H, A168S, I182T, M183L, K194N, E227S, K228E, I229V, Q230H, D233Y, T262S, A272S, N274D, T280A, T303S, I347V, V358A, R361T, M379V, T382A, R385S, T386A, I387L, V428L, I477M; M: T4S, H11L, E15A, Q17H, S22P, M35T, A70P, A72S, T99S, V120A, I152T, I154F, I156V; NS1: N9S, R10G, M19I, I42L, A44S, I86L, V90A, K98T, T103A, K105T, R108V, V128A, K129R, E139D, T141S, R175S, I178V, A185S, A205S, K246T, I264T, K286T, E288Q, I308V, M324L, T351A; NS2A: E2Q, R4T, N7T, V15L, I19M, M34L, M36V, V38A, G41C, M42A, M44I, V56A, N62D, A65S, K67R, K69G, M79V, M87V, M90V, K98R, G101A, I113F, A114S, Q117H, N118D, V119L, I122L, M128L, I136V, Q138H, E142A, M144V, V147L, M149L, I157T, N161I, K165R, T169A, I173V, R183S, K184C, K188Q, I192V, V199L, G201A, E202Q, I206V, E214G, K215A, T216S; NS2B: T20A, I21L, M28L, I39L, M59V, K60Q, I64M, I92T, G102A, M112L, M126V; NS3: T11A, T13A, K19T, K20E, Q41H, S59C, Y60H, K61E, N62T, E94D, T158S, A174P, E179D, A206S, I208V, M240I, M247V, I267T, I282V, A292S, A301S, K337R, E349D, M400T, R420G, N469D, I473V, E477D, K513R, S516T, Y523F, N532T, R547S, T556S, K584R, E609D, R615S; NS4A: M4L, M10I, Q23L, G63A, G66A, I83M, M100I; NS4B: M45L, K83R, V112L, G113V, I148T, I168V, V191L, V194A, I198V, I199L, K208R; NS5: K30R, I34L, I43L, G44A, K47D, E49S, T59S, M66V, K96N, S98T, T128S, A150S, Q170P, T173S, *174S, I190V, R204S, I224A, T225S, M245T, Y247H, N273D, K275T, I281L, K285Q, K296Q, K365Q, E372V, K379N, S383A, K390N, A401S, I412V, G420A, T421S, K429S, E436D, N440A, S499G, *504W, M518I, E521D, E523D, M548L, M554T, G558A, T559P, E560D, Q561H, E632D, K635Q, V640L, Y651C, R653V, K677T, A678S, H680L, G718F, T724S, I726V, A764S, K787E, N807T, E821D, I831V, N832H, E836D, Q846L, N855T, I866T, N869T, M881V, K891S, T892A, S893P, R896S" } }, "children": [ { "name": "NODE_0000002", "node_attrs": { - "div": 0.2183367, + "div": 0.218, "clade_membership": { "value": "4IV" } @@ -5404,6 +4363,7 @@ "G6484A", "C6515T", "A6551C", + "T6554C", "C6581T", "G6587A", "C6593T", @@ -5638,97 +4598,9 @@ "C10187T", "T10242C", "C10244A" - ], - "2K": [ - "I14L", - "G19S" - ], - "C": [ - "V8A", - "V111I" - ], - "E": [ - "D154S", - "A162T", - "R203G", - "R340K", - "V342M", - "T355I", - "V455I", - "L461I" - ], - "M": [ - "S4X", - "T5S", - "P70S", - "A107T" - ], - "NS1": [ - "K11R", - "I57V", - "A90T", - "A103V", - "T105A", - "E156D", - "F171L", - "K192R" - ], - "NS2A": [ - "T4P", - "L54V", - "S65F", - "V144L", - "R155K", - "A169V", - "L197I" - ], - "NS2B": [ - "M94L", - "T119A" - ], - "NS3": [ - "T17M", - "F31L", - "M42V", - "D87E", - "I190V", - "A321T", - "K558R" - ], - "NS4A": [ - "R36K", - "V97I" - ], - "NS4B": [ - "T20P", - "M93L", - "A194S", - "V198A", - "N205G", - "A240T" - ], - "NS5": [ - "V71I", - "M91V", - "V164I", - "K166R", - "S204N", - "V206I", - "I276V", - "V321I", - "F384L", - "E501D", - "D526E", - "D560G", - "F718L", - "R750K", - "T786V", - "H832Y", - "F894L" ] }, "labels": { - "aa": "2K: I14L, G19S; C: V8A, V111I; E: D154S, A162T, R203G, R340K, V342M, T355I, V455I, L461I; M: S4X, T5S, P70S, A107T; NS1: K11R, I57V, A90T, A103V, T105A, E156D, F171L, K192R; NS2A: T4P, L54V, S65F, V144L, R155K, A169V, L197I; NS2B: M94L, T119A; NS3: T17M, F31L, M42V, D87E, I190V, A321T, K558R; NS4A: R36K, V97I; NS4B: T20P, M93L, A194S, V198A, N205G, A240T; NS5: V71I, M91V, V164I, K166R, S204N, V206I, I276V, V321I, F384L, E501D, D526E, D560G, F718L, R750K, T786V, H832Y, F894L", "lineage": "4IV" } }, @@ -5736,7 +4608,7 @@ { "name": "NODE_0000003", "node_attrs": { - "div": 0.21919537, + "div": 0.219, "clade_membership": { "value": "4IV" } @@ -5753,24 +4625,14 @@ "A7681G", "C9131T", "G9788A" - ], - "M": [ - "K33R" - ], - "NS5": [ - "T4I", - "E40G" ] - }, - "labels": { - "aa": "M: K33R; NS5: T4I, E40G" } }, "children": [ { "name": "AP010|1975", "node_attrs": { - "div": 0.21929398, + "div": 0.219, "clade_membership": { "value": "4IV" } @@ -5779,20 +4641,14 @@ "mutations": { "nuc": [ "T2142C" - ], - "E": [ - "F402L" ] - }, - "labels": { - "aa": "E: F402L" } } }, { "name": "EF457906.1|1975", "node_attrs": { - "div": 0.21929308, + "div": 0.219, "country": { "value": "Malaysia" }, @@ -5813,7 +4669,7 @@ { "name": "NODE_0000004", "node_attrs": { - "div": 0.21946504, + "div": 0.219, "clade_membership": { "value": "4IV" } @@ -5832,20 +4688,14 @@ "C9164T", "A9227G", "T9885C" - ], - "NS3": [ - "I442V" ] - }, - "labels": { - "aa": "NS3: I442V" } }, "children": [ { "name": "AP009|1973", "node_attrs": { - "div": 0.21946604, + "div": 0.219, "clade_membership": { "value": "4IV" } @@ -5857,7 +4707,7 @@ { "name": "NODE_0000005", "node_attrs": { - "div": 0.21946919, + "div": 0.219, "clade_membership": { "value": "4IV" } @@ -5869,7 +4719,7 @@ { "name": "JF262780.1|1973", "node_attrs": { - "div": 0.21947019, + "div": 0.219, "country": { "value": "Malaysia" }, @@ -5884,7 +4734,7 @@ { "name": "NODE_0000006", "node_attrs": { - "div": 0.21965677, + "div": 0.22, "clade_membership": { "value": "4IV" } @@ -5894,20 +4744,14 @@ "nuc": [ "T7162C", "T7730G" - ], - "NS4B": [ - "L112S" ] - }, - "labels": { - "aa": "NS4B: L112S" } }, "children": [ { "name": "JF262779.1|1975", "node_attrs": { - "div": 0.21965777, + "div": 0.22, "country": { "value": "Malaysia" }, @@ -5922,7 +4766,7 @@ { "name": "AP011|1975", "node_attrs": { - "div": 0.21965777, + "div": 0.22, "clade_membership": { "value": "4IV" } @@ -5942,7 +4786,7 @@ { "name": "NODE_0000007", "node_attrs": { - "div": 0.2015104, + "div": 0.202, "clade_membership": { "value": "unassigned" } @@ -6382,92 +5226,14 @@ "C10219T", "C10241T", "A10247G" - ], - "C": [ - "M102I" - ], - "E": [ - "T19A", - "V132I", - "A148T", - "R203K", - "I335V", - "I364V", - "A382V", - "S478T" - ], - "M": [ - "V41L", - "P70L", - "T76M", - "A96T" - ], - "NS1": [ - "I104L", - "S109N", - "N131S", - "V188I", - "T246A", - "S251F", - "M275I", - "N290D", - "G292D", - "S338L", - "A351S" - ], - "NS2A": [ - "A38T", - "V72I", - "L122F", - "A127S", - "V137T", - "A142T", - "T156S" - ], - "NS2B": [ - "V73I" - ], - "NS3": [ - "V40I", - "V100I", - "K170R", - "A249S", - "I322T" - ], - "NS4A": [ - "I58V" - ], - "NS4B": [ - "E18V", - "S87G" - ], - "NS5": [ - "L43S", - "R101K", - "F103Y", - "Y201H", - "V235T", - "K246R", - "F384L", - "A420T", - "K433E", - "D560H", - "K643R", - "V789F", - "T855S", - "Q865H", - "A886V" ] - }, - "labels": { - "aa": "C: M102I; E: T19A, V132I, A148T, R203K, I335V, I364V, A382V, S478T; M: V41L, P70L, T76M, A96T; NS1: I104L, S109N, N131S, V188I, T246A, S251F, M275I, N290D, G292D, S338L, A351S; NS2A: A38T, V72I, L122F, A127S, V137T, A142T, T156S; NS2B: V73I; NS3: V40I, V100I, K170R, A249S, I322T; NS4A: I58V; NS4B: E18V, S87G; NS5: L43S, R101K, F103Y, Y201H, V235T, K246R, F384L, A420T, K433E, D560H, K643R, V789F, T855S, Q865H, A886V" } }, "children": [ { "name": "NODE_0000008", "node_attrs": { - "div": 0.2481403, + "div": 0.248, "clade_membership": { "value": "4III" } @@ -6774,7 +5540,6 @@ "G6437A", "C6458T", "C6500T", - "C6554T", "C6581A", "C6584T", "C6593T", @@ -6944,78 +5709,9 @@ "A10225G", "T10238C", "T10243C" - ], - "2K": [ - "I21V" - ], - "C": [ - "T34I", - "N74T", - "I102V" - ], - "E": [ - "V4I", - "K174E", - "T182S", - "K202E", - "Y233H", - "K310R", - "S474P" - ], - "M": [ - "S83N" - ], - "NS1": [ - "S9T", - "I22T", - "K33Q", - "T98V", - "R129K", - "N166S", - "K341R" - ], - "NS2A": [ - "T4S", - "M19I", - "R26K", - "L40F", - "S65L", - "G66S", - "M68V", - "I72T", - "A78I", - "F122L", - "I161T", - "V173A", - "L197I" - ], - "NS2B": [ - "K55R", - "V116I", - "K127R" - ], - "NS3": [ - "F31L", - "R538K" - ], - "NS4A": [ - "M83V" - ], - "NS4B": [ - "T11A" - ], - "NS5": [ - "V206I", - "P368L", - "K524R", - "K562R", - "R750K", - "K888R", - "F894S" ] }, "labels": { - "aa": "2K: I21V; C: T34I, N74T, I102V; E: V4I, K174E, T182S, K202E, Y233H, K310R, S474P; M: S83N; NS1: S9T, I22T, K33Q, T98V, R129K, N166S, K341R; NS2A: T4S, M19I, R26K, L40F, S65L, G66S, M68V, I72T, A78I, F122L, I161T, V173A, L197I; NS2B: K55R, V116I, K127R; NS3: F31L, R538K; NS4A: M83V; NS4B: T11A; NS5: V206I, P368L, K524R, K562R, R750K, K888R, F894S", "lineage": "4III" } }, @@ -7023,7 +5719,7 @@ { "name": "NODE_0000009", "node_attrs": { - "div": 0.25036376, + "div": 0.25, "clade_membership": { "value": "4III" } @@ -7053,22 +5749,14 @@ "G8741A", "G9575A", "C10175T" - ], - "NS1": [ - "H50Y", - "A90V", - "L217F" ] - }, - "labels": { - "aa": "NS1: H50Y, A90V, L217F" } }, "children": [ { "name": "MW945493.1|1999", "node_attrs": { - "div": 0.25193265, + "div": 0.252, "country": { "value": "Thailand" }, @@ -7094,23 +5782,14 @@ "G8033A", "T8255A", "C8846T" - ], - "M": [ - "T81A" - ], - "NS3": [ - "T34A" ] - }, - "labels": { - "aa": "M: T81A; NS3: T34A" } } }, { "name": "KY586945.1|1998", "node_attrs": { - "div": 0.25106146, + "div": 0.251, "country": { "value": "Thailand" }, @@ -7138,7 +5817,7 @@ { "name": "NODE_0000010", "node_attrs": { - "div": 0.24889128000000002, + "div": 0.249, "clade_membership": { "value": "4III" } @@ -7154,23 +5833,14 @@ "A7667G", "T10058C", "C10240T" - ], - "NS5": [ - "P893L" ] - }, - "labels": { - "aa": "NS5: P893L" } }, "children": [ { "name": "MW945667.1|1997", "node_attrs": { - "div": 0.25018337, - "country": { - "value": "Thailand" - }, + "div": 0.25, "clade_membership": { "value": "4III" } @@ -7190,20 +5860,14 @@ "T8285C", "T8291C", "C9701T" - ], - "E": [ - "N360S" ] - }, - "labels": { - "aa": "E: N360S" } } }, { "name": "NODE_0000011", "node_attrs": { - "div": 0.24937339000000003, + "div": 0.249, "clade_membership": { "value": "4III" } @@ -7223,7 +5887,7 @@ { "name": "MW945727.1|2005", "node_attrs": { - "div": 0.25154119, + "div": 0.252, "country": { "value": "Thailand" }, @@ -7255,23 +5919,14 @@ "C7871T", "T8363C", "A9941G" - ], - "E": [ - "L387I" - ], - "NS3": [ - "R170K" ] - }, - "labels": { - "aa": "E: L387I; NS3: R170K" } } }, { "name": "NODE_0000012", "node_attrs": { - "div": 0.24947015000000003, + "div": 0.249, "clade_membership": { "value": "4III" } @@ -7288,7 +5943,7 @@ { "name": "MW945619.1|1996", "node_attrs": { - "div": 0.24996376000000003, + "div": 0.25, "country": { "value": "Thailand" }, @@ -7311,7 +5966,7 @@ { "name": "NODE_0000013", "node_attrs": { - "div": 0.25293095000000004, + "div": 0.253, "clade_membership": { "value": "4III" } @@ -7354,23 +6009,14 @@ "T10136C", "C10181T", "A10253G" - ], - "C": [ - "R9K" - ], - "M": [ - "T81A" ] - }, - "labels": { - "aa": "C: R9K; M: T81A" } }, "children": [ { "name": "KY586944.1|2001", "node_attrs": { - "div": 0.25421433000000004, + "div": 0.254, "country": { "value": "Thailand" }, @@ -7394,26 +6040,14 @@ "A7269G", "T8354C", "C9524T" - ], - "E": [ - "N157S" - ], - "NS1": [ - "I275M" - ], - "NS4B": [ - "T148A" ] - }, - "labels": { - "aa": "E: N157S; NS1: I275M; NS4B: T148A" } } }, { "name": "MW945621.1|2001", "node_attrs": { - "div": 0.25381666, + "div": 0.254, "country": { "value": "Thailand" }, @@ -7433,16 +6067,7 @@ "A7058G", "T7169C", "C7351T" - ], - "NS2A": [ - "I123V" - ], - "NS4B": [ - "A175V" ] - }, - "labels": { - "aa": "NS2A: I123V; NS4B: A175V" } } } @@ -7459,7 +6084,7 @@ { "name": "NODE_0000014", "node_attrs": { - "div": 0.219397, + "div": 0.219, "clade_membership": { "value": "unassigned" } @@ -7616,46 +6241,17 @@ "T9671C", "T9863C", "C9965T", + "C9989T", "C10034T", "A10172G" - ], - "2K": [ - "A13T" - ], - "E": [ - "T329A", - "L461F" - ], - "NS1": [ - "M265V" - ], - "NS2A": [ - "M19V", - "I57L", - "F113L", - "I161V" - ], - "NS3": [ - "T12A" - ], - "NS4B": [ - "V198I" - ], - "NS5": [ - "V372M", - "R387K", - "M530I" ] - }, - "labels": { - "aa": "2K: A13T; E: T329A, L461F; NS1: M265V; NS2A: M19V, I57L, F113L, I161V; NS3: T12A; NS4B: V198I; NS5: V372M, R387K, M530I" } }, "children": [ { "name": "NODE_0000015", "node_attrs": { - "div": 0.22859781, + "div": 0.229, "clade_membership": { "value": "4II" } @@ -7744,6 +6340,7 @@ "T9278C", "A9413T", "T9560C", + "C9857T", "T9866C", "C9962T", "T10113C", @@ -7751,36 +6348,9 @@ "G10190A", "T10202C", "T10243C" - ], - "C": [ - "T81I" - ], - "E": [ - "I46T", - "T265A" - ], - "NS1": [ - "I22V", - "A246S", - "S351T" - ], - "NS2A": [ - "T38I", - "M68I", - "F122L", - "M135I", - "K217R" - ], - "NS3": [ - "A13T", - "T19S" - ], - "NS5": [ - "F894S" ] }, "labels": { - "aa": "C: T81I; E: I46T, T265A; NS1: I22V, A246S, S351T; NS2A: T38I, M68I, F122L, M135I, K217R; NS3: A13T, T19S; NS5: F894S", "lineage": "4II" } }, @@ -7788,7 +6358,7 @@ { "name": "NODE_0000016", "node_attrs": { - "div": 0.23670433000000002, + "div": 0.237, "clade_membership": { "value": "4II_A" } @@ -7879,34 +6449,10 @@ "A9530G", "G9722A", "T9749C", - "C9857T", "T9968C" - ], - "E": [ - "S120L" - ], - "NS2A": [ - "L40F" - ], - "NS2B": [ - "T119A" - ], - "NS3": [ - "K381R" - ], - "NS4A": [ - "R20K", - "R36K" - ], - "NS4B": [ - "A175V" - ], - "NS5": [ - "K200R" ] }, "labels": { - "aa": "E: S120L; NS2A: L40F; NS2B: T119A; NS3: K381R; NS4A: R20K, R36K; NS4B: A175V; NS5: K200R", "lineage": "4II_A" } }, @@ -7914,7 +6460,7 @@ { "name": "FJ196849.1|1978", "node_attrs": { - "div": 0.25909993000000003, + "div": 0.259, "country": { "value": "China" }, @@ -8049,7 +6595,6 @@ "C6425T", "G6443A", "G6527A", - "C6554T", "C6593T", "G6636A", "G6655C", @@ -8144,100 +6689,18 @@ "T9884C", "G9971A", "A9986G", - "C9989T", "A10067G", "G10085A", "A10158G", "C10202T" - ], - "C": [ - "N74S", - "I93F", - "V111A" - ], - "E": [ - "T58A", - "T155I", - "K174E", - "Y233H", - "E403G", - "S470T", - "M477V" - ], - "M": [ - "R86Q", - "R87G", - "W126R" - ], - "NS1": [ - "L13S", - "V22I", - "L47V", - "Q70R", - "K94T", - "K101N", - "F160L", - "M198V", - "E289K", - "R322K", - "T351M" - ], - "NS2A": [ - "L45I", - "V112E", - "L113V" - ], - "NS3": [ - "K117R", - "T120N", - "I147V", - "E180V", - "D192V", - "K248E", - "K357E", - "T400M", - "V449I" - ], - "NS4A": [ - "A87T", - "G93A", - "I109V" - ], - "NS4B": [ - "E2G", - "F13L", - "T22A", - "I44L", - "V71I", - "N100D", - "L112S", - "E189G" - ], - "NS5": [ - "Q16L", - "K95E", - "E111A", - "N122S", - "C145Y", - "V206I", - "F349Y", - "N390K", - "E433G", - "A440T", - "R595G", - "Q635H", - "T866A" ] - }, - "labels": { - "aa": "C: N74S, I93F, V111A; E: T58A, T155I, K174E, Y233H, E403G, S470T, M477V; M: R86Q, R87G, W126R; NS1: L13S, V22I, L47V, Q70R, K94T, K101N, F160L, M198V, E289K, R322K, T351M; NS2A: L45I, V112E, L113V; NS3: K117R, T120N, I147V, E180V, D192V, K248E, K357E, T400M, V449I; NS4A: A87T, G93A, I109V; NS4B: E2G, F13L, T22A, I44L, V71I, N100D, L112S, E189G; NS5: Q16L, K95E, E111A, N122S, C145Y, V206I, F349Y, N390K, E433G, A440T, R595G, Q635H, T866A" } } }, { "name": "NODE_0000017", "node_attrs": { - "div": 0.25460603000000004, + "div": 0.255, "clade_membership": { "value": "4II_A" } @@ -8337,6 +6800,7 @@ "T6182C", "T6188C", "A6323G", + "T6554C", "T6555C", "A6575C", "A6599G", @@ -8405,49 +6869,14 @@ "T10031C", "C10181T", "G10199A" - ], - "C": [ - "G96R", - "K98R", - "I102M" - ], - "NS1": [ - "S9N", - "L153F", - "K245R" - ], - "NS2A": [ - "L113F", - "M158I", - "L171F" - ], - "NS2B": [ - "M123I" - ], - "NS3": [ - "S292C" - ], - "NS4B": [ - "F187L", - "L199M" - ], - "NS5": [ - "T235I", - "V373I", - "N390S", - "G499S", - "I563T" ] - }, - "labels": { - "aa": "C: G96R, K98R, I102M; NS1: S9N, L153F, K245R; NS2A: L113F, M158I, L171F; NS2B: M123I; NS3: S292C; NS4B: F187L, L199M; NS5: T235I, V373I, N390S, G499S, I563T" } }, "children": [ { "name": "NODE_0000018", "node_attrs": { - "div": 0.26872553000000005, + "div": 0.269, "clade_membership": { "value": "4II_A" } @@ -8564,47 +6993,18 @@ "G9845A", "C9905T", "A9941G", + "T9989C", "A10010G", "T10124C", "G10247A" - ], - "C": [ - "I77V" - ], - "E": [ - "Y233H", - "D384E" - ], - "M": [ - "S83N" - ], - "NS1": [ - "T286A", - "Q288R" - ], - "NS3": [ - "R584K" - ], - "NS4B": [ - "M93I", - "I198A" - ], - "NS5": [ - "H201Y", - "I276V", - "K525Q", - "K649T" ] - }, - "labels": { - "aa": "C: I77V; E: Y233H, D384E; M: S83N; NS1: T286A, Q288R; NS3: R584K; NS4B: M93I, I198A; NS5: H201Y, I276V, K525Q, K649T" } }, "children": [ { "name": "MN018396.1|2015-11-12", "node_attrs": { - "div": 0.30032443000000003, + "div": 0.3, "country": { "value": "China" }, @@ -8871,89 +7271,14 @@ "G10160A", "G10161C", "A10199C" - ], - "C": [ - "V8A" - ], - "E": [ - "A329T" - ], - "M": [ - "M39K", - "I144V", - "T152I" - ], - "NS1": [ - "T72A" - ], - "NS2A": [ - "L34F", - "V35T", - "V36T", - "V37T", - "I68M", - "V90I", - "F113L", - "L122F", - "I135M", - "R155K", - "I158M", - "F171L", - "R217K" - ], - "NS2B": [ - "A119T", - "I123M" - ], - "NS3": [ - "T13A", - "S19T", - "F31L", - "I40V", - "M42T", - "T62S", - "E285R", - "R426W", - "Q467P", - "E468Y", - "R538K" - ], - "NS4A": [ - "A59L", - "F72S", - "M73A" - ], - "NS4B": [ - "V18E", - "T20Q", - "I24N", - "R30G", - "L37S", - "V175A" - ], - "NS5": [ - "A54V", - "G69R", - "K72Q", - "V124A", - "D526E", - "I568H", - "A660E", - "H865X", - "T866A", - "A867P", - "E879D" ] - }, - "labels": { - "aa": "C: V8A; E: A329T; M: M39K, I144V, T152I; NS1: T72A; NS2A: L34F, V35T, V36T, V37T, I68M, V90I, F113L, L122F, I135M, R155K, I158M, F171L, R217K; NS2B: A119T, I123M; NS3: T13A, S19T, F31L, I40V, M42T, T62S, E285R, R426W, Q467P, E468Y, R538K; NS4A: A59L, F72S, M73A; NS4B: V18E, T20Q, I24N, R30G, L37S, V175A; NS5: A54V, G69R, K72Q, V124A, D526E, I568H, A660E, H865X, T866A, A867P, E879D" } } }, { "name": "MN018393.1|2015-07-25", "node_attrs": { - "div": 0.28753343000000003, + "div": 0.288, "country": { "value": "China" }, @@ -9170,89 +7495,7 @@ "A10067G", "T10098C", "A10225G" - ], - "2K": [ - "L7F" - ], - "C": [ - "V29G" - ], - "E": [ - "G78R", - "E79P", - "P80T", - "Y81R", - "L82P", - "E85L", - "I132V", - "V287E", - "R288H", - "E290V" - ], - "M": [ - "R21G", - "T27I" - ], - "NS1": [ - "S141P", - "F153L" - ], - "NS2A": [ - "I154L" - ], - "NS3": [ - "N74S", - "R170K", - "L188K", - "N277A", - "Y278C", - "L385M", - "S386L", - "R387W", - "K388W", - "T389S", - "E528N", - "Q529K" - ], - "NS4A": [ - "T65G", - "A66S" - ], - "NS4B": [ - "L104S", - "M110S", - "V113R", - "M199L", - "G207X", - "R208-", - "F209-", - "W210X", - "N211R", - "T212K" - ], - "NS5": [ - "L34Q", - "V164A", - "K166S", - "M167K", - "V168E", - "P170T", - "V182I", - "V206I", - "I235V", - "R279T", - "R280M", - "L281D", - "Q282W", - "S390N", - "N427S", - "L755S", - "H832R", - "K888R" ] - }, - "labels": { - "aa": "2K: L7F; C: V29G; E: G78R, E79P, P80T, Y81R, L82P, E85L, I132V, V287E, R288H, E290V; M: R21G, T27I; NS1: S141P, F153L; NS2A: I154L; NS3: N74S, R170K, L188K, N277A, Y278C, L385M, S386L, R387W, K388W, T389S, E528N, Q529K; NS4A: T65G, A66S; NS4B: L104S, M110S, V113R, M199L, G207X, R208-, F209-, W210X, N211R, T212K; NS5: L34Q, V164A, K166S, M167K, V168E, P170T, V182I, V206I, I235V, R279T, R280M, L281D, Q282W, S390N, N427S, L755S, H832R, K888R" } } } @@ -9261,7 +7504,7 @@ { "name": "NODE_0000019", "node_attrs": { - "div": 0.25672466000000005, + "div": 0.257, "clade_membership": { "value": "4II_A" } @@ -9301,24 +7544,14 @@ "T9113C", "C9587T", "T9704C" - ], - "NS3": [ - "T322I" - ], - "NS5": [ - "K46R", - "V71I" ] - }, - "labels": { - "aa": "NS3: T322I; NS5: K46R, V71I" } }, "children": [ { "name": "OL314740.1|2019-05-30", "node_attrs": { - "div": 0.2820317600000001, + "div": 0.282, "country": { "value": "Indonesia" }, @@ -9538,57 +7771,20 @@ "T9965A", "C9968T", "G9971A", + "T9989C", "T10034C", "T10040A", "T10154C", "C10182T", "G10205A" - ], - "2K": [ - "I21V" - ], - "E": [ - "N469S" - ], - "NS1": [ - "N24S", - "H50P", - "V66I", - "F153L" - ], - "NS2A": [ - "Q2E", - "V27I", - "V37I", - "R181K", - "S183T" - ], - "NS4A": [ - "K20R", - "I78M", - "A87S" - ], - "NS5": [ - "S49F", - "H201Y", - "H247Y", - "T420A", - "P637Q", - "K646R", - "V726A", - "T786A", - "H801Q" ] - }, - "labels": { - "aa": "2K: I21V; E: N469S; NS1: N24S, H50P, V66I, F153L; NS2A: Q2E, V27I, V37I, R181K, S183T; NS4A: K20R, I78M, A87S; NS5: S49F, H201Y, H247Y, T420A, P637Q, K646R, V726A, T786A, H801Q" } } }, { "name": "NODE_0000020", "node_attrs": { - "div": 0.26742286000000004, + "div": 0.267, "clade_membership": { "value": "4II_A" } @@ -9676,45 +7872,19 @@ "T9884C", "T9885C", "G9920A", - "C9989T", "C9995T", "C10025T", "T10098C", "T10219C", "C10243T" - ], - "E": [ - "V455I" - ], - "NS1": [ - "V265A" - ], - "NS2A": [ - "I158T" - ], - "NS3": [ - "A321S" - ], - "NS4A": [ - "S12T" - ], - "NS5": [ - "V886A", - "S894F" ] - }, - "labels": { - "aa": "E: V455I; NS1: V265A; NS2A: I158T; NS3: A321S; NS4A: S12T; NS5: V886A, S894F" } }, "children": [ { "name": "MH888334.1|2013-01-04", "node_attrs": { - "div": 0.28024996, - "country": { - "value": "Malaysia" - }, + "div": 0.28, "clade_membership": { "value": "4II_A" } @@ -9851,56 +8021,14 @@ "T10034C", "G10160A", "T10204A" - ], - "C": [ - "K72R", - "I77V", - "V111A" - ], - "E": [ - "Q88R", - "Y233N", - "S363G", - "V382A", - "S385G" - ], - "M": [ - "L55I", - "T96A" - ], - "NS1": [ - "N9T" - ], - "NS2A": [ - "F171L" - ], - "NS4A": [ - "I2V", - "I86V" - ], - "NS4B": [ - "V18A", - "T22I", - "A63T" - ], - "NS5": [ - "S225T", - "H247Y", - "A383T", - "N703D", - "V726I", - "V881E" ] - }, - "labels": { - "aa": "C: K72R, I77V, V111A; E: Q88R, Y233N, S363G, V382A, S385G; M: L55I, T96A; NS1: N9T; NS2A: F171L; NS4A: I2V, I86V; NS4B: V18A, T22I, A63T; NS5: S225T, H247Y, A383T, N703D, V726I, V881E" } } }, { "name": "NODE_0000021", "node_attrs": { - "div": 0.26752522000000006, + "div": 0.268, "clade_membership": { "value": "4II_A" } @@ -9910,20 +8038,14 @@ "nuc": [ "G7796A", "A8416G" - ], - "NS5": [ - "Q285R" ] - }, - "labels": { - "aa": "NS5: Q285R" } }, "children": [ { "name": "NODE_0000022", "node_attrs": { - "div": 0.27238110000000004, + "div": 0.272, "clade_membership": { "value": "4II_A.2" } @@ -9983,19 +8105,9 @@ "C9614T", "C9635T", "T10106C" - ], - "NS2B": [ - "I123V" - ], - "NS4B": [ - "I198V" - ], - "NS5": [ - "H53Y" ] }, "labels": { - "aa": "NS2B: I123V; NS4B: I198V; NS5: H53Y", "lineage": "4II_A.2" } }, @@ -10003,7 +8115,7 @@ { "name": "KC762698.1|2008-04-30", "node_attrs": { - "div": 0.27605557000000003, + "div": 0.276, "country": { "value": "Indonesia" }, @@ -10051,36 +8163,14 @@ "G9767A", "C9842T", "C9853T" - ], - "E": [ - "V382A" - ], - "M": [ - "D65V" - ], - "NS3": [ - "R381K" - ], - "NS4B": [ - "T22N" - ], - "NS5": [ - "T269I", - "Q296H", - "V324I", - "K657E", - "S764L" ] - }, - "labels": { - "aa": "E: V382A; M: D65V; NS3: R381K; NS4B: T22N; NS5: T269I, Q296H, V324I, K657E, S764L" } } }, { "name": "NODE_0000023", "node_attrs": { - "div": 0.27285796000000007, + "div": 0.273, "clade_membership": { "value": "4II_A.2" } @@ -10093,20 +8183,14 @@ "A5825G", "C8735T", "A8933G" - ], - "C": [ - "T34I" ] - }, - "labels": { - "aa": "C: T34I" } }, "children": [ { "name": "NODE_0000024", "node_attrs": { - "div": 0.2779473500000001, + "div": 0.278, "clade_membership": { "value": "4II_A.2" } @@ -10166,31 +8250,14 @@ "C10151T", "C10163T", "C10202T" - ], - "E": [ - "D147N" - ], - "NS2A": [ - "V35A", - "A56V" - ], - "NS4B": [ - "T20P" - ], - "NS5": [ - "S49T", - "I276V" ] - }, - "labels": { - "aa": "E: D147N; NS2A: V35A, A56V; NS4B: T20P; NS5: S49T, I276V" } }, "children": [ { "name": "KP723482.1|2010", "node_attrs": { - "div": 0.27824185000000007, + "div": 0.278, "country": { "value": "China" }, @@ -10204,20 +8271,14 @@ "C2840T", "G4554T", "T8732C" - ], - "NS3": [ - "A11S" ] - }, - "labels": { - "aa": "NS3: A11S" } } }, { "name": "JF741967.1|2010-09-26", "node_attrs": { - "div": 0.2785401300000001, + "div": 0.279, "country": { "value": "China" }, @@ -10234,19 +8295,7 @@ "T4671G", "G4706A", "C4732G" - ], - "NS2B": [ - "D88E" - ], - "NS3": [ - "Q14H", - "M49V", - "W50G", - "A70G" ] - }, - "labels": { - "aa": "NS2B: D88E; NS3: Q14H, M49V, W50G, A70G" } } } @@ -10255,7 +8304,7 @@ { "name": "NODE_0000025", "node_attrs": { - "div": 0.2741013500000001, + "div": 0.274, "clade_membership": { "value": "4II_A.2" } @@ -10282,7 +8331,7 @@ { "name": "KC762699.1|2008-03-28", "node_attrs": { - "div": 0.27557787000000006, + "div": 0.276, "country": { "value": "Indonesia" }, @@ -10308,20 +8357,14 @@ "G9098A", "C9353T", "C9785T" - ], - "NS2A": [ - "D118E" ] - }, - "labels": { - "aa": "NS2A: D118E" } } }, { "name": "KC762696.1|2007-08-13", "node_attrs": { - "div": 0.2756797100000001, + "div": 0.276, "country": { "value": "Indonesia" }, @@ -10348,16 +8391,7 @@ "C8687T", "T9515C", "A9757C" - ], - "NS2A": [ - "L132I" - ], - "NS5": [ - "Q732P" ] - }, - "labels": { - "aa": "NS2A: L132I; NS5: Q732P" } } } @@ -10370,7 +8404,7 @@ { "name": "NODE_0000026", "node_attrs": { - "div": 0.26880965000000007, + "div": 0.269, "clade_membership": { "value": "4II_A" } @@ -10388,23 +8422,14 @@ "G7256T", "G7445A", "C7553T" - ], - "NS2A": [ - "M51V" ] - }, - "labels": { - "aa": "NS2A: M51V" } }, "children": [ { "name": "JQ915085.1|2008-02-20", "node_attrs": { - "div": 0.27505264000000007, - "country": { - "value": "New Caledonia" - }, + "div": 0.275, "clade_membership": { "value": "4II_A" } @@ -10475,34 +8500,14 @@ "T9338C", "A9575G", "G9629A" - ], - "C": [ - "I93T" - ], - "E": [ - "M454I" - ], - "NS2A": [ - "H117R", - "A169V" - ], - "NS3": [ - "T13I", - "R381K" - ], - "NS4A": [ - "T34A" ] - }, - "labels": { - "aa": "C: I93T; E: M454I; NS2A: H117R, A169V; NS3: T13I, R381K; NS4A: T34A" } } }, { "name": "NODE_0000027", "node_attrs": { - "div": 0.27112945000000005, + "div": 0.271, "clade_membership": { "value": "4II_A.1" } @@ -10510,14 +8515,13 @@ "branch_attrs": { "mutations": { "nuc": [ - "A1391G", "G1913A", "A2045G", "A2390G", + "C2474T", "T3315C", "T3764C", "G3866A", - "A4373G", "T5184C", "C5798T", "C5933T", @@ -10531,22 +8535,11 @@ "A8565G", "C8627T", "C9050T", - "T9725C", "T9962C", "G10178A" - ], - "2K": [ - "I21V" - ], - "NS4B": [ - "M93I" - ], - "NS5": [ - "I335V" ] }, "labels": { - "aa": "2K: I21V; NS4B: M93I; NS5: I335V", "lineage": "4II_A.1" } }, @@ -10554,7 +8547,7 @@ { "name": "NODE_0000028", "node_attrs": { - "div": 0.27287089000000003, + "div": 0.272, "clade_membership": { "value": "4II_A.1" } @@ -10562,43 +8555,26 @@ "branch_attrs": { "mutations": { "nuc": [ - "T722A", - "T2336C", - "C2474T", - "C2651T", - "A3548G", - "G4610A", - "A4886G", - "G4925A", - "T4961A", - "C5342T", - "T6014C", - "G6347A", - "C6638T", - "T6792C", - "T7403C", - "T8132C", - "A8388G", - "C9461T", - "A9636G", - "T9761C" - ], - "NS5": [ - "I276V", - "I692V" + "T1670C", + "T2675C", + "A3239G", + "A4658G", + "G6032A", + "C6335T", + "C6968T", + "C8426T", + "T9047C", + "C10235T" ] - }, - "labels": { - "aa": "NS5: I276V, I692V" } }, "children": [ { - "name": "OP600512.1|2022-07", + "name": "KY921909.1|2016-03", "node_attrs": { - "div": 0.28804549, + "div": 0.281, "country": { - "value": "Malaysia" + "value": "Singapore" }, "clade_membership": { "value": "4II_A.1" @@ -10607,185 +8583,104 @@ "branch_attrs": { "mutations": { "nuc": [ - "G314A", - "A467G", - "C470T", - "C554T", - "C606T", - "G842T", - "G848A", - "T872C", - "C887T", - "A920G", - "A1013G", - "C1043T", - "T1088C", - "T1277C", - "G1391T", - "C1406T", - "G1418T", - "G1427A", - "C1505T", + "C212T", + "T343C", + "G407C", + "G500A", + "C671T", + "C846T", + "G890A", + "G993A", + "C1076T", + "T1232C", + "A1265G", + "T1277A", + "T1589C", "A1601G", - "A1661G", - "G1748A", "G1838A", - "T2264C", - "T2319C", - "G2372A", - "A2672G", - "C2797T", - "G2815A", - "C2853T", - "C2936T", - "T3074C", - "C3107T", - "C3132T", - "G3290C", - "G3350C", - "C3522T", - "A3638G", - "C3707T", - "A3755G", - "G3782A", - "C3828A", + "C1994T", + "C2003T", + "C2225T", + "T2322C", + "G2453A", + "G2498A", + "G2564A", + "T2621C", + "C2646T", + "T2795C", + "T2813C", + "T2912C", + "C3093T", + "T3231C", + "T3563C", + "T3589C", + "T3752C", "T3830C", - "A3941G", - "G4097A", - "C4190T", - "G4202A", - "A4244G", - "T4271C", - "A4451G", - "C4575T", - "G4613C", - "A4658G", - "C4697T", - "G4712A", - "A4715G", - "T4745C", - "G4766A", - "A4832G", - "G4856A", - "T4937C", - "A4997G", - "T5072C", - "T5456C", - "T5468A", - "T5642C", - "C5696T", - "C5822T", - "T5846A", - "A5867T", - "T5873C", - "A5879T", - "T5909A", - "T6149C", - "T6185C", - "A6242G", - "A6275G", - "G6494A", - "A6503G", - "C6531T", - "G6533A", - "G6602A", - "T6629C", - "T6716C", + "T3990C", + "C4007T", + "A4040G", + "A4061T", + "C4154T", + "C4304T", + "C4397T", + "C4544T", + "C4553T", + "G4577A", + "G4694A", + "A4985G", + "T5003C", + "C5210T", + "T5249C", + "T5387C", + "T5399C", + "C5750T", + "C5807T", + "T5882C", + "A6302G", + "G6344A", + "A6560G", + "T6698C", "T6722C", - "G6734A", - "A6881G", - "C7019T", - "A7145G", - "T7166C", - "C7281T", - "T7385C", - "T7454C", - "A7523G", - "G7559A", - "C7611T", - "C7625T", - "T7709G", - "A7712G", - "C7793T", - "T7829C", - "T7871C", - "C7985T", - "T8018C", - "C8195T", - "T8252C", - "T8280C", - "A8375G", - "A8552G", - "T8561C", - "T8579C", - "T8583C", - "T8681C", - "A8693G", + "C6797T", + "C6950T", + "C7085T", + "A7109G", + "A7163G", + "G7265C", + "A7283G", + "C7343T", + "A7376G", + "C7466T", + "T7490C", + "T7707A", + "T7883C", + "A7889G", + "A8129C", + "C8285T", "C8711T", - "C8717A", - "A8722G", - "C8762T", - "G8848A", - "G8885A", - "G9083A", - "C9188T", - "A9215G", - "G9326C", - "A9349G", - "C9521T", - "A9575T", - "T9587C", - "A9670G", - "C9671T", - "C9692T", - "G9809A", - "A9872G", - "C9885T", - "C9899A", - "T9914C", - "C10007T", - "G10046A", - "G10053A", - "C10139G", - "C10202T", - "G10205A", - "A10217G" - ], - "E": [ - "F461L" - ], - "NS1": [ - "T125I", - "S131N", - "P144S", - "E289D" - ], - "NS2A": [ - "H117N", - "I154M" - ], - "NS3": [ - "L30F" - ], - "NS5": [ - "K387R", - "S429N", - "K596R", - "N703S", - "V831I" + "G8741A", + "A8825G", + "T8946C", + "G8999A", + "C9068T", + "C9252T", + "A9259G", + "G9317A", + "T9387C", + "T9548C", + "T9995C", + "T10034C", + "C10232T" ] - }, - "labels": { - "aa": "E: F461L; NS1: T125I, S131N, P144S, E289D; NS2A: H117N, I154M; NS3: L30F; NS5: K387R, S429N, K596R, N703S, V831I" } } }, { - "name": "OQ821649.1|2016-03-21", + "name": "MH382789.1|2016", "node_attrs": { - "div": 0.28235482, + "div": 0.279, "country": { - "value": "Jamaica" + "value": "Australia" }, "clade_membership": { "value": "4II_A.1" @@ -10794,116 +8689,74 @@ "branch_attrs": { "mutations": { "nuc": [ - "T210C", - "A322G", - "G383A", - "C431T", - "G590A", - "A1136G", - "G1148A", - "T1178A", - "G1238A", - "T1277A", - "A1508G", - "C1590T", - "A1599G", - "T1637C", - "C1739T", - "G1871A", - "G1964A", - "G1977T", - "T2201C", - "C2375T", - "C2411T", - "C2754T", - "A2774G", - "C2937A", - "T2970C", - "T3188C", - "G3218A", - "C3266T", - "C3274T", - "G3431A", + "G127A", + "T209G", + "G674C", + "A726G", + "A956G", + "G986A", + "C1037T", + "C1112T", + "C1184T", + "G1377A", + "C2135T", + "A2477G", + "A2783G", + "A2969G", + "G3056A", + "T3152C", + "C3160T", + "A3298G", + "T3302C", + "A3497G", "A3578G", - "T3579G", - "T3605C", - "T3668C", - "G3785C", - "A3791G", - "T3873C", - "A3880G", - "A3887T", - "T4148C", - "G4439A", + "C3635T", + "C3930T", + "A4127G", + "A4184G", "T4481C", - "G4619A", - "T4763C", - "T4988C", - "C5169T", - "T5249C", - "T5357C", - "T5477C", - "G5834A", - "T5846C", - "C5917T", - "C6164T", - "T6342C", - "C6506T", - "T6644A", - "C6656T", - "A6674G", - "T6698A", - "C6782T", - "T6788C", - "C6840T", - "T6956C", - "T6959C", - "C7338T", - "C7421T", - "C7685T", - "A7706G", - "C7730T", - "T7874A", - "C7907T", - "A7937G", - "C8111T", - "C8207T", - "G8234C", - "C8759T", - "G8774A", - "A8900G", + "A4604G", + "G4606A", + "C4778T", + "T4847C", + "G4925A", + "T4961C", + "T5069C", + "A5087G", + "A5102G", + "A5138G", + "A5867T", + "T5915C", + "T6240C", + "A6488G", + "G6549A", + "C6593T", + "A6755G", + "A7007G", + "T7709C", + "G7745A", + "A7769G", + "C7832T", + "T7913C", + "T7928C", + "C8096T", + "C8117T", + "T8132A", + "G8258A", + "C8277T", + "G8282A", + "G8321A", + "T8579C", + "T8677A", + "C8888T", + "C9173T", + "C9273T", + "T9338C", "G9347A", - "T9413A", - "G9644A", - "A9653G", - "C9716T", - "A9800T", - "A9911T", - "C9938T", - "C9962T" - ], - "C": [ - "F37L", - "N74S" - ], - "E": [ - "T221A", - "V347L" - ], - "NS1": [ - "T284I" - ], - "NS2A": [ - "I33M", - "L34V", - "K134R" - ], - "NS3": [ - "P465L" + "T9413C", + "T9587C", + "C9878T" ] - }, - "labels": { - "aa": "C: F37L, N74S; E: T221A, V347L; NS1: T284I; NS2A: I33M, L34V, K134R; NS3: P465L" } } } @@ -10912,7 +8765,7 @@ { "name": "NODE_0000029", "node_attrs": { - "div": 0.27218886000000003, + "div": 0.271, "clade_membership": { "value": "4II_A.1" } @@ -10920,32 +8773,17 @@ "branch_attrs": { "mutations": { "nuc": [ - "C1994T", - "G2619A", - "C2906T", - "C3596T", - "A4985G", - "T5735C", - "G6221A", - "A8981G", - "A10190G" - ], - "NS1": [ - "V66I" + "A1391G", + "A4373G", + "T9725C" ] - }, - "labels": { - "aa": "NS1: V66I" } }, "children": [ { - "name": "OP411002.1|2019-07", + "name": "NODE_0000030", "node_attrs": { - "div": 0.28410306, - "country": { - "value": "Singapore" - }, + "div": 0.273, "clade_membership": { "value": "4II_A.1" } @@ -10953,145 +8791,301 @@ "branch_attrs": { "mutations": { "nuc": [ - "T125C", - "T323C", - "A402G", - "G482A", - "T734C", - "C839T", - "T857C", - "G1040A", - "T1115C", - "C1250T", - "T1253C", - "T1286C", - "A1331G", - "A1346G", - "C1406T", - "A1538G", - "A1571G", - "C1787T", - "T1820C", - "T1931C", - "T1937C", - "T2270C", - "A2462G", - "T2562C", - "G2609A", - "A2672T", - "T2712C", - "C2717T", - "T2762C", - "A2972G", - "C3114T", - "G3116A", - "G3182A", - "G3242A", - "T3393C", - "A3497G", - "C3698T", - "C3876T", - "A3880G", - "G4175A", - "A4343G", - "A4411G", - "G4439A", - "A4462T", - "T4481C", - "G4640A", - "C4700T", - "C4793T", - "G4856A", - "T4961C", - "G5021A", - "C5027T", - "T5132C", - "C5184T", - "C5231T", - "C5255T", - "T5387C", - "A5427T", - "T5606C", - "G5702A", - "T5771C", - "A5962G", - "C6020T", - "A6044G", - "T6119C", - "T6230C", - "C6558T", - "A6560G", - "T6722C", - "T6956C", - "G6989A", - "T7115C", - "T7137C", - "T7232C", - "G7325C", - "A7397G", - "A7565T", - "C7793T", - "G7838A", - "C7961T", + "T722A", + "T2336C", + "C2651T", + "A3548G", + "G4610A", + "A4886G", + "G4925A", + "T4961A", + "C5342T", + "T6014C", + "G6347A", + "C6638T", + "T6792C", + "T7403C", "T8132C", - "T8210C", - "T8231C", - "C8277T", - "T8393A", - "G8414A", - "C8516T", - "T8642C", - "C8666T", - "G8678A", - "T8703C", - "G8815A", - "C9344T", - "C9419T", - "C9425T", - "C9458T", - "T9480C", - "A9542T", - "A9662G", - "G9737T", - "G9794A", - "T9857C", - "G9875A", - "G10001A", - "C10028T", - "G10145A", - "C10187T" - ], - "C": [ - "T101A" - ], - "E": [ - "M34I" - ], - "NS2A": [ - "K134R" - ], - "NS2B": [ - "N93S", - "Y110F" - ], - "NS3": [ - "T302S", - "K480R" - ], - "NS5": [ - "M372I", - "G418E" + "A8388G", + "C9461T", + "A9636G", + "T9761C" ] + } + }, + "children": [ + { + "name": "OP600512.1|2022-07", + "node_attrs": { + "div": 0.288, + "country": { + "value": "Malaysia" + }, + "clade_membership": { + "value": "4II_A.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G314A", + "A467G", + "C470T", + "C554T", + "C606T", + "G842T", + "G848A", + "T872C", + "C887T", + "A920G", + "A1013G", + "C1043T", + "T1088C", + "T1277C", + "G1391T", + "C1406T", + "G1418T", + "G1427A", + "C1505T", + "A1601G", + "A1661G", + "G1748A", + "G1838A", + "T2264C", + "T2319C", + "G2372A", + "A2672G", + "C2797T", + "G2815A", + "C2853T", + "C2936T", + "T3074C", + "C3107T", + "C3132T", + "G3290C", + "G3350C", + "C3522T", + "A3638G", + "C3707T", + "A3755G", + "G3782A", + "C3828A", + "T3830C", + "A3941G", + "G4097A", + "C4190T", + "G4202A", + "A4244G", + "T4271C", + "A4451G", + "C4575T", + "G4613C", + "A4658G", + "C4697T", + "G4712A", + "A4715G", + "T4745C", + "G4766A", + "A4832G", + "G4856A", + "T4937C", + "A4997G", + "T5072C", + "T5456C", + "T5468A", + "T5642C", + "C5696T", + "C5822T", + "T5846A", + "A5867T", + "T5873C", + "A5879T", + "T5909A", + "T6149C", + "T6185C", + "A6242G", + "A6275G", + "G6494A", + "A6503G", + "C6531T", + "G6533A", + "G6602A", + "T6629C", + "T6716C", + "T6722C", + "G6734A", + "A6881G", + "C7019T", + "A7145G", + "T7166C", + "C7281T", + "T7385C", + "T7454C", + "A7523G", + "G7559A", + "C7611T", + "C7625T", + "T7709G", + "A7712G", + "C7793T", + "T7829C", + "T7871C", + "C7985T", + "T8018C", + "C8195T", + "T8252C", + "T8280C", + "A8375G", + "A8552G", + "T8561C", + "T8579C", + "T8583C", + "T8681C", + "A8693G", + "C8711T", + "C8717A", + "A8722G", + "C8762T", + "G8848A", + "G8885A", + "G9083A", + "C9188T", + "A9215G", + "G9326C", + "A9349G", + "C9521T", + "A9575T", + "T9587C", + "A9670G", + "C9671T", + "C9692T", + "G9809A", + "A9872G", + "C9885T", + "C9899A", + "T9914C", + "C10007T", + "G10046A", + "G10053A", + "C10139G", + "C10202T", + "G10205A", + "A10217G" + ] + } + } }, - "labels": { - "aa": "C: T101A; E: M34I; NS2A: K134R; NS2B: N93S, Y110F; NS3: T302S, K480R; NS5: M372I, G418E" + { + "name": "OQ821649.1|2016-03-21", + "node_attrs": { + "div": 0.282, + "country": { + "value": "Jamaica" + }, + "clade_membership": { + "value": "4II_A.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T210C", + "A322G", + "G383A", + "C431T", + "G590A", + "A1136G", + "G1148A", + "T1178A", + "G1238A", + "T1277A", + "A1508G", + "C1590T", + "A1599G", + "T1637C", + "C1739T", + "G1871A", + "G1964A", + "G1977T", + "T2201C", + "C2375T", + "C2411T", + "C2754T", + "A2774G", + "C2937A", + "T2970C", + "T3188C", + "G3218A", + "C3266T", + "C3274T", + "G3431A", + "A3578G", + "T3579G", + "T3605C", + "T3668C", + "G3785C", + "A3791G", + "T3873C", + "A3880G", + "A3887T", + "T4148C", + "G4439A", + "T4481C", + "G4619A", + "T4763C", + "T4988C", + "C5169T", + "T5249C", + "T5357C", + "T5477C", + "G5834A", + "T5846C", + "C5917T", + "C6164T", + "T6342C", + "C6506T", + "T6644A", + "C6656T", + "A6674G", + "T6698A", + "C6782T", + "T6788C", + "C6840T", + "T6956C", + "T6959C", + "C7338T", + "C7421T", + "C7685T", + "A7706G", + "C7730T", + "T7874A", + "C7907T", + "A7937G", + "C8111T", + "C8207T", + "G8234C", + "C8759T", + "G8774A", + "A8900G", + "G9347A", + "T9413A", + "G9644A", + "A9653G", + "C9716T", + "A9800T", + "A9911T", + "C9938T", + "C9962T" + ] + } + } } - } + ] }, { - "name": "NODE_0000030", + "name": "NODE_0000031", "node_attrs": { - "div": 0.27575780000000005, + "div": 0.272, "clade_membership": { "value": "4II_A.1" } @@ -11099,58 +9093,26 @@ "branch_attrs": { "mutations": { "nuc": [ - "T365C", - "C461T", - "T515C", - "C846T", - "C1733T", - "G1790A", - "T1982C", - "A2153G", - "T2213C", - "T2618C", - "T2621C", - "A2687G", - "T3203C", - "C3347A", - "C3516T", - "C3521T", - "C3665T", - "C4850T", - "T4937C", - "A5102G", - "C5108T", - "C5567T", - "G6104A", - "C6251T", - "T6329C", - "C6872T", - "C6893T", - "C6938T", - "G7589A", - "T7714C", - "T8266C", - "C8666A", - "T8837C", - "C9905T", - "C10163T" - ], - "NS5": [ - "I51T", - "I235T" + "C1994T", + "T2474C", + "G2619A", + "C2906T", + "C3596T", + "A4985G", + "T5735C", + "G6221A", + "A8981G", + "A10190G" ] - }, - "labels": { - "aa": "NS5: I51T, I235T" } }, "children": [ { - "name": "OL314741.1|2019-06-20", + "name": "OP411002.1|2019-07", "node_attrs": { - "div": 0.28523848000000007, + "div": 0.284, "country": { - "value": "Indonesia" + "value": "Singapore" }, "clade_membership": { "value": "4II_A.1" @@ -11159,126 +9121,121 @@ "branch_attrs": { "mutations": { "nuc": [ - "G237A", - "C473T", - "G883C", - "C983T", - "T1088C", - "T1247C", - "T1297C", - "C1323T", + "T125C", + "T323C", + "A402G", + "G482A", + "T734C", + "C839T", + "T857C", + "G1040A", + "T1115C", + "C1250T", + "T1253C", + "T1286C", "A1331G", + "A1346G", + "C1406T", "A1538G", "A1571G", - "C1727T", - "T1751C", "C1787T", - "C1922T", - "C1943T", - "C1991T", - "A2099G", - "C2177T", - "A2513G", - "G2564A", - "A2572C", - "G2645A", - "C2660T", + "T1820C", + "T1931C", + "T1937C", + "T2270C", + "A2462G", + "T2562C", + "G2609A", + "A2672T", "T2712C", - "A2804G", - "G2805C", - "T3008C", - "G3470A", - "A3548G", - "T3605C", - "G3630A", - "G3740A", - "T4014C", - "G4016A", - "T4070C", - "T4145A", - "G4202A", - "T4532C", - "A4679G", - "A4829G", - "A4832G", - "T5036C", - "T5100C", - "C5342T", - "C5513T", - "C5672T", - "G5789A", - "C5984T", - "A6128G", - "A6242G", - "T6309C", - "G6947A", + "C2717T", + "T2762C", + "A2972G", + "C3114T", + "G3116A", + "G3182A", + "G3242A", + "T3393C", + "A3497G", + "C3698T", + "C3876T", + "A3880G", + "G4175A", + "A4343G", + "A4411G", + "G4439A", + "A4462T", + "T4481C", + "G4640A", + "C4700T", + "C4793T", + "G4856A", + "T4961C", + "G5021A", + "C5027T", + "T5132C", + "C5184T", + "C5231T", + "C5255T", + "T5387C", + "A5427T", + "T5606C", + "G5702A", + "T5771C", + "A5962G", + "C6020T", + "A6044G", + "T6119C", + "T6230C", + "C6558T", + "A6560G", + "T6722C", "T6956C", - "T6959C", - "G6974A", "G6989A", - "A6998T", - "C7085T", - "A7121G", - "C7262T", - "A7328G", - "A7412G", - "C7505T", - "T7721C", - "G7847A", - "T7871C", - "T7874C", - "T7973A", - "C8114T", - "G8130A", - "G8156A", - "A8162G", - "G8234A", - "G8501A", - "A8662G", - "C8717T", - "C8762T", - "C9269T", - "A9329G", - "C9449T", - "G9569A", - "A9677G", - "T9701C", - "C9830T", - "C10220T" - ], - "C": [ - "V46M" - ], - "E": [ - "L120S" - ], - "M": [ - "G148A" - ], - "NS1": [ - "H50P", - "A128P" - ], - "NS2A": [ - "V51M" - ], - "NS5": [ - "V190I", - "K367R" + "T7115C", + "T7137C", + "T7232C", + "G7325C", + "A7397G", + "A7565T", + "C7793T", + "G7838A", + "C7961T", + "T8132C", + "T8210C", + "T8231C", + "C8277T", + "T8393A", + "G8414A", + "C8516T", + "T8642C", + "C8666T", + "G8678A", + "T8703C", + "G8815A", + "C9344T", + "C9419T", + "C9425T", + "C9458T", + "T9480C", + "A9542T", + "A9662G", + "G9737T", + "G9794A", + "T9857C", + "G9875A", + "G10001A", + "C10028T", + "G10145A", + "C10187T" ] - }, - "labels": { - "aa": "C: V46M; E: L120S; M: G148A; NS1: H50P, A128P; NS2A: V51M; NS5: V190I, K367R" } } }, { - "name": "OP600478.1|2020-08", + "name": "NODE_0000032", "node_attrs": { - "div": 0.28715510000000005, - "country": { - "value": "Malaysia" - }, + "div": 0.276, "clade_membership": { "value": "4II_A.1" } @@ -11286,115 +9243,260 @@ "branch_attrs": { "mutations": { "nuc": [ - "C248T", - "A263G", - "G278A", - "C339T", - "C554T", - "T734C", - "A794G", - "A854G", - "T872C", - "C887T", - "C1043T", - "A1154T", - "C1244T", - "A1451G", - "G1532A", - "A1697G", - "C1799T", - "G1841A", - "A1919G", - "C2036T", - "C2310T", - "C2393T", - "C2480T", - "C2501T", - "C2547T", - "A2549G", - "T2741C", - "T2753C", - "A2807G", - "T2823C", - "T3092C", - "T3435C", - "T3488C", - "T3563C", - "A3842G", - "T3899C", - "T3926C", - "C3930T", - "C4046T", - "C4112T", - "C4290T", - "A4394G", - "T4499C", - "G4586A", - "C4697A", - "C4784G", - "T5090C", - "G5165A", - "C5255T", - "C5315T", - "T5357C", - "T5399C", - "C5558T", - "T5646C", - "A5721G", - "G5900A", - "C6095T", - "C6118A", - "G6443A", - "C6464T", - "C6506T", - "T6566C", - "T6722C", - "T6809C", - "T6830C", - "C6972T", - "C6980T", - "C7019T", - "A7145G", - "T7166C", - "C7281T", - "T7385C", - "T7403C", - "A7523G", - "A7542G", - "A7628G", - "T8393C", - "C8441T", - "A8465G", - "T8495C", - "A8537G", - "C8541T", - "T8771C", - "C9101T", - "C9161T", - "C9252T", - "A9260G", - "G9317A", - "T9548C", - "T9587C", - "G9644A", - "T10076C" - ], - "E": [ - "M301I" - ], - "NS3": [ - "D87E", - "T400A", - "T532N" - ], - "NS4B": [ - "N239D" + "T365C", + "C461T", + "T515C", + "C846T", + "C1733T", + "G1790A", + "T1982C", + "A2153G", + "T2213C", + "T2618C", + "T2621C", + "A2687G", + "T3203C", + "C3347A", + "C3516T", + "C3521T", + "C3665T", + "C4850T", + "T4937C", + "A5102G", + "C5108T", + "C5567T", + "G6104A", + "C6251T", + "T6329C", + "C6872T", + "C6893T", + "C6938T", + "G7589A", + "T7714C", + "T8266C", + "C8666A", + "T8837C", + "C9905T", + "C10163T" ] + } + }, + "children": [ + { + "name": "OL314741.1|2019-06-20", + "node_attrs": { + "div": 0.285, + "country": { + "value": "Indonesia" + }, + "clade_membership": { + "value": "4II_A.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G237A", + "C473T", + "G883C", + "C983T", + "T1088C", + "T1247C", + "T1297C", + "C1323T", + "A1331G", + "A1538G", + "A1571G", + "C1727T", + "T1751C", + "C1787T", + "C1922T", + "C1943T", + "C1991T", + "A2099G", + "C2177T", + "A2513G", + "G2564A", + "A2572C", + "G2645A", + "C2660T", + "T2712C", + "A2804G", + "G2805C", + "T3008C", + "G3470A", + "A3548G", + "T3605C", + "G3630A", + "G3740A", + "T4014C", + "G4016A", + "T4070C", + "T4145A", + "G4202A", + "T4532C", + "A4679G", + "A4829G", + "A4832G", + "T5036C", + "T5100C", + "C5342T", + "C5513T", + "C5672T", + "G5789A", + "C5984T", + "A6128G", + "A6242G", + "T6309C", + "G6947A", + "T6956C", + "T6959C", + "G6974A", + "G6989A", + "A6998T", + "C7085T", + "A7121G", + "C7262T", + "A7328G", + "A7412G", + "C7505T", + "T7721C", + "G7847A", + "T7871C", + "T7874C", + "T7973A", + "C8114T", + "G8130A", + "G8156A", + "A8162G", + "G8234A", + "G8501A", + "A8662G", + "C8717T", + "C8762T", + "C9269T", + "A9329G", + "C9449T", + "G9569A", + "A9677G", + "T9701C", + "C9830T", + "C10220T" + ] + } + } }, - "labels": { - "aa": "E: M301I; NS3: D87E, T400A, T532N; NS4B: N239D" + { + "name": "OP600478.1|2020-08", + "node_attrs": { + "div": 0.287, + "country": { + "value": "Malaysia" + }, + "clade_membership": { + "value": "4II_A.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C248T", + "A263G", + "G278A", + "C339T", + "C554T", + "T734C", + "A794G", + "A854G", + "T872C", + "C887T", + "C1043T", + "A1154T", + "C1244T", + "A1451G", + "G1532A", + "A1697G", + "C1799T", + "G1841A", + "A1919G", + "C2036T", + "C2310T", + "C2393T", + "C2480T", + "C2501T", + "C2547T", + "A2549G", + "T2741C", + "T2753C", + "A2807G", + "T2823C", + "T3092C", + "T3435C", + "T3488C", + "T3563C", + "A3842G", + "T3899C", + "T3926C", + "C3930T", + "C4046T", + "C4112T", + "C4290T", + "A4394G", + "T4499C", + "G4586A", + "C4697A", + "C4784G", + "T5090C", + "G5165A", + "C5255T", + "C5315T", + "T5357C", + "T5399C", + "C5558T", + "T5646C", + "A5721G", + "G5900A", + "C6095T", + "C6118A", + "G6443A", + "C6464T", + "C6506T", + "T6566C", + "T6722C", + "T6809C", + "T6830C", + "C6972T", + "C6980T", + "C7019T", + "A7145G", + "T7166C", + "C7281T", + "T7385C", + "T7403C", + "A7523G", + "A7542G", + "A7628G", + "T8393C", + "C8441T", + "A8465G", + "T8495C", + "A8537G", + "C8541T", + "T8771C", + "C9101T", + "C9161T", + "C9252T", + "A9260G", + "G9317A", + "T9548C", + "T9587C", + "G9644A", + "T10076C" + ] + } + } } - } + ] } ] } @@ -11415,9 +9517,9 @@ ] }, { - "name": "NODE_0000031", + "name": "NODE_0000033", "node_attrs": { - "div": 0.23880241000000002, + "div": 0.239, "clade_membership": { "value": "4II_B" } @@ -11439,6 +9541,7 @@ "T1628C", "A1697G", "C1733T", + "G1964A", "C1988T", "T2000C", "T2009G", @@ -11454,13 +9557,13 @@ "T3410C", "G3512T", "A3518G", + "G3581A", "C3596T", "T3620C", "T3650C", "A3659G", "T3695C", "T3867C", - "T3935C", "C3980T", "C4175T", "C4193T", @@ -11512,11 +9615,13 @@ "G8546A", "G8618A", "C8717T", + "G8720A", "T8882C", "T8960C", "A9152G", "A9194G", "T9205A", + "C9236T", "T9239C", "A9319G", "C9335T", @@ -11527,27 +9632,9 @@ "G10199A", "C10220A", "C10244A" - ], - "E": [ - "F357L", - "D384N" - ], - "NS3": [ - "T17A", - "K142R" - ], - "NS4A": [ - "A87T" - ], - "NS5": [ - "S204N", - "I530M", - "L548Q", - "K586R" ] }, "labels": { - "aa": "E: F357L, D384N; NS3: T17A, K142R; NS4A: A87T; NS5: S204N, I530M, L548Q, K586R", "lineage": "4II_B" } }, @@ -11555,7 +9642,7 @@ { "name": "OK469362.1|1995", "node_attrs": { - "div": 0.26563111, + "div": 0.266, "country": { "value": "Singapore" }, @@ -11608,7 +9695,6 @@ "C1835T", "T1844C", "A1956C", - "G1964A", "C1967T", "A1989G", "T2007C", @@ -11655,7 +9741,6 @@ "G3524T", "G3534A", "T3546C", - "G3581A", "A3641G", "T3657C", "T3668C", @@ -11665,6 +9750,7 @@ "T3818C", "A3901G", "G3932A", + "T3935C", "A3944T", "G4016A", "G4053A", @@ -11738,6 +9824,7 @@ "G6484A", "G6494A", "C6500T", + "T6554C", "A6557G", "T6578C", "T6580C", @@ -11787,7 +9874,6 @@ "A8621G", "G8639A", "G8709A", - "G8720A", "A8729G", "C8762T", "C8888T", @@ -11798,7 +9884,6 @@ "T8946C", "G8954A", "T9047C", - "C9236T", "C9273T", "G9317A", "A9350G", @@ -11816,7 +9901,9 @@ "A9809G", "C9825T", "A9833G", + "T9857C", "G9881A", + "T9989C", "C10025T", "C10043T", "T10049C", @@ -11827,64 +9914,14 @@ "T10118C", "C10182T", "A10253G" - ], - "C": [ - "I102M" - ], - "E": [ - "D95N", - "K200E", - "I351V" - ], - "M": [ - "L3F", - "S4T" - ], - "NS1": [ - "V22A", - "T125A" - ], - "NS2A": [ - "V19M", - "I72V", - "V104I", - "N141S", - "R155S", - "V192I" - ], - "NS2B": [ - "A40T" - ], - "NS3": [ - "M42I", - "A321T" - ], - "NS4A": [ - "R36K", - "I68T", - "I100L" - ], - "NS4B": [ - "M84V" - ], - "NS5": [ - "L34I", - "K101R", - "Y103F", - "A383T", - "K446R", - "I837V" ] - }, - "labels": { - "aa": "C: I102M; E: D95N, K200E, I351V; M: L3F, S4T; NS1: V22A, T125A; NS2A: V19M, I72V, V104I, N141S, R155S, V192I; NS2B: A40T; NS3: M42I, A321T; NS4A: R36K, I68T, I100L; NS4B: M84V; NS5: L34I, K101R, Y103F, A383T, K446R, I837V" } } }, { - "name": "NODE_0000032", + "name": "NODE_0000034", "node_attrs": { - "div": 0.24494798, + "div": 0.245, "clade_membership": { "value": "4II_B" } @@ -11899,7 +9936,6 @@ "C1301T", "G1361A", "A1622G", - "C1658T", "T1751C", "C2270T", "G2301A", @@ -11907,9 +9943,7 @@ "A2366T", "A2465G", "T2741C", - "T2795C", "G2978A", - "C2987T", "T3488C", "G3869A", "C3872T", @@ -11927,6 +9961,7 @@ "T6389C", "C6455T", "G6710A", + "A6740G", "T6956A", "T7112C", "G7247A", @@ -11939,34 +9974,23 @@ "A8192G", "T8231A", "A8510T", + "C8669T", "G8774A", "G8885A", "C9125G", "G9149A", "T9242C", "A9588G", - "T9824C" - ], - "E": [ - "V455I" - ], - "NS3": [ - "K594R" - ], - "NS5": [ - "D521E", - "S676G" + "T9824C", + "G10178A" ] - }, - "labels": { - "aa": "E: V455I; NS3: K594R; NS5: D521E, S676G" } }, "children": [ { - "name": "KX812530.1|1976", + "name": "OK605767.1|1976", "node_attrs": { - "div": 0.24800589, + "div": 0.248, "country": { "value": "Indonesia" }, @@ -11977,60 +10001,54 @@ "branch_attrs": { "mutations": { "nuc": [ - "A334G", - "C603T", - "T2029C", - "A2042G", - "T2322C", - "A2531G", - "C2651T", - "A3279G", - "T3605C", - "A3887G", - "G4775A", - "T4862C", - "G5345A", - "C6353T", - "C6365T", - "C6554T", - "A6740G", - "A7034G", - "A7340C", - "T7506C", - "C7546T", - "C7748T", - "A7841G", - "A8420G", - "A8565G", - "C8669T", - "C9989T", - "G10178A" - ], - "C": [ - "K78R" - ], - "E": [ - "V364A" - ], - "NS1": [ - "T286A" - ], - "NS4B": [ - "A240V" - ], - "NS5": [ - "I335V" - ] - }, - "labels": { - "aa": "C: K78R; E: V364A; NS1: T286A; NS4B: A240V; NS5: I335V" - } + "G218T", + "G500A", + "G653A", + "G1355A", + "T1409C", + "G1439A", + "G2318C", + "C2501T", + "C3044T", + "A3080G", + "G3116A", + "C3278T", + "A3689G", + "C3695T", + "C3707T", + "T3990C", + "C4481T", + "C4871T", + "T4910C", + "C5027T", + "G5032A", + "C5558T", + "T5669C", + "A5936G", + "C6011T", + "C6023T", + "G6299A", + "C6449T", + "C6875T", + "C6983T", + "A7190G", + "G7773A", + "G7838A", + "T8003A", + "T9032C", + "C9147T", + "G9644A", + "A9662T", + "C10025T", + "C10163T" + ] + } } }, { - "name": "NODE_0000033", + "name": "NODE_0000035", "node_attrs": { - "div": 0.25391434, + "div": 0.245, "clade_membership": { "value": "4II_B" } @@ -12038,122 +10056,19 @@ "branch_attrs": { "mutations": { "nuc": [ - "A299G", - "T647C", - "T1004C", - "C1145T", - "A1184G", - "A1196G", - "T1323C", - "T1529C", - "G1532A", - "T1559C", - "A1586G", - "A1592T", - "C1856T", - "G1964A", - "T1988C", - "A1989G", - "C1991T", - "T2093C", - "T2366C", - "A2423G", - "A2455G", - "T2525C", - "G2564A", - "C2642T", - "C2678T", - "A2749G", - "T2813C", - "C2846T", - "T2878C", - "G2981T", - "T3114C", - "C3359T", - "A3473G", - "G3581A", - "A3614G", - "G3815A", - "G3863A", - "G3866A", - "T3893G", - "C3923T", - "C3935T", - "T4271C", - "G4367A", - "T4616C", - "T4703C", - "T4805C", - "C4820T", - "T4841C", - "C5177T", - "C5363T", - "T5399C", - "C5423T", - "T5732C", - "C5768T", - "G5801A", - "G6227A", - "G6293A", - "A6296G", - "C6380T", - "C6500T", - "C6521T", - "T6542C", - "C6818A", - "T7022C", - "T7136C", - "T7184C", - "C7250T", - "G7256A", - "C8360T", - "T8390C", - "C8435A", - "A8534G", - "A8537G", - "T8555C", - "C8579T", - "C8597T", - "C8666A", - "G8720A", - "C8918T", - "A9212G", - "C9236T", - "A9508G", - "G9575A", - "C9716T", - "C9857T", - "T9968C", - "C10130T", - "C10169T", - "C10235T" - ], - "E": [ - "I351V" - ], - "NS1": [ - "K11R", - "N109S", - "F152S" - ], - "NS2A": [ - "H138Q" - ], - "NS5": [ - "K649R" + "C1658T", + "T2795C", + "C2987T" ] - }, - "labels": { - "aa": "E: I351V; NS1: K11R, N109S, F152S; NS2A: H138Q; NS5: K649R" } }, "children": [ { - "name": "OR389346.1|1987", + "name": "KX812530.1|1976", "node_attrs": { - "div": 0.25530333, + "div": 0.248, "country": { - "value": "El Salvador" + "value": "Indonesia" }, "clade_membership": { "value": "4II_B" @@ -12162,36 +10077,43 @@ "branch_attrs": { "mutations": { "nuc": [ - "G341A", - "T461C", - "T1059C", - "A1346G", - "G1871A", - "T2381A", - "T3393C", - "T3926C", - "T4676C", - "G5186A", - "A5483C", - "A5867T", - "T6809C", - "C9287T", - "G9589C", - "A9737G" - ], - "NS5": [ - "G676A" + "A334G", + "C603T", + "A1964G", + "T2029C", + "A2042G", + "T2322C", + "A2531G", + "C2651T", + "A3279G", + "A3581G", + "T3605C", + "A3887G", + "T3935C", + "G4775A", + "T4862C", + "G5345A", + "C6353T", + "C6365T", + "A7034G", + "A7340C", + "T7506C", + "C7546T", + "C7748T", + "A7841G", + "A8420G", + "A8565G", + "A8720G", + "T9236C", + "T9857C" ] - }, - "labels": { - "aa": "NS5: G676A" } } }, { - "name": "NODE_0000034", + "name": "NODE_0000036", "node_attrs": { - "div": 0.25820641, + "div": 0.254, "clade_membership": { "value": "4II_B" } @@ -12199,81 +10121,189 @@ "branch_attrs": { "mutations": { "nuc": [ - "C414T", - "C839T", - "T1211C", - "G1238A", - "G1451A", - "C2114T", - "C2403T", - "A2801T", - "C2876T", - "T3240C", - "T3380C", - "T3583C", - "A3638G", - "T3694C", - "G3813A", - "T3814C", - "C3954T", - "C4304T", - "C4346T", - "A4373G", - "A4679T", - "C4940T", - "A4985G", - "T5249C", - "G5534A", - "A5537G", - "G5702A", - "A6218T", - "T6455C", - "A6710G", - "T6845A", - "A6944G", - "G7238A", - "A8654G", - "G8705A", - "A8885T", - "T9113C", - "G9971A", - "T10031C", - "C10039T" - ], - "NS2A": [ - "V35A", - "I72T", - "V112T", - "P159S" - ], - "NS5": [ - "T826I" + "A299G", + "T647C", + "T1004C", + "C1145T", + "A1184G", + "A1196G", + "T1323C", + "T1529C", + "G1532A", + "T1559C", + "A1586G", + "A1592T", + "C1856T", + "T1988C", + "A1989G", + "C1991T", + "T2093C", + "T2366C", + "A2423G", + "A2455G", + "T2525C", + "G2564A", + "C2642T", + "C2678T", + "A2749G", + "T2813C", + "C2846T", + "T2878C", + "G2981T", + "T3114C", + "C3359T", + "A3473G", + "A3614G", + "G3815A", + "G3863A", + "G3866A", + "T3893G", + "C3923T", + "T4271C", + "G4367A", + "T4616C", + "T4703C", + "T4805C", + "C4820T", + "T4841C", + "C5177T", + "C5363T", + "T5399C", + "C5423T", + "T5732C", + "C5768T", + "G5801A", + "G6227A", + "G6293A", + "A6296G", + "C6380T", + "C6500T", + "C6521T", + "T6542C", + "T6554C", + "G6740A", + "C6818A", + "T7022C", + "T7136C", + "T7184C", + "C7250T", + "G7256A", + "C8360T", + "T8390C", + "C8435A", + "A8534G", + "A8537G", + "T8555C", + "C8579T", + "C8597T", + "C8666A", + "T8669C", + "C8918T", + "A9212G", + "A9508G", + "G9575A", + "C9716T", + "T9968C", + "T9989C", + "C10130T", + "C10169T", + "A10178G", + "C10235T" ] - }, - "labels": { - "aa": "NS2A: V35A, I72T, V112T, P159S; NS5: T826I" } }, "children": [ { - "name": "NODE_0000035", + "name": "OR389346.1|1987", + "node_attrs": { + "div": 0.255, + "clade_membership": { + "value": "4II_B" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "G341A", + "T461C", + "T1059C", + "A1346G", + "G1871A", + "T2381A", + "T3393C", + "T3926C", + "T4676C", + "G5186A", + "A5483C", + "A5867T", + "T6809C", + "C9287T", + "G9589C", + "A9737G" + ] + } + } + }, + { + "name": "NODE_0000037", "node_attrs": { - "div": 0.25830068, + "div": 0.258, "clade_membership": { "value": "4II_B" } }, "branch_attrs": { - "mutations": {} + "mutations": { + "nuc": [ + "C414T", + "C839T", + "T1211C", + "G1238A", + "G1451A", + "C2114T", + "C2403T", + "A2801T", + "C2876T", + "T3240C", + "T3380C", + "T3583C", + "G3590A", + "A3638G", + "T3694C", + "G3813A", + "T3814C", + "C3954T", + "C4304T", + "C4346T", + "A4373G", + "A4679T", + "C4940T", + "A4985G", + "T5249C", + "G5534A", + "A5537G", + "G5702A", + "A6218T", + "T6455C", + "A6710G", + "T6845A", + "A6944G", + "G7238A", + "A8654G", + "G8705A", + "A8885T", + "T9113C", + "G9971A", + "T10031C", + "C10039T" + ] + } }, "children": [ { - "name": "KT276273.1|2014-09-08", + "name": "NODE_0000038", "node_attrs": { - "div": 0.28193558, - "country": { - "value": "Haiti" - }, + "div": 0.258, "clade_membership": { "value": "4II_B" } @@ -12281,548 +10311,231 @@ "branch_attrs": { "mutations": { "nuc": [ - "C203A", - "C266T", - "C332T", - "T343C", - "A434G", - "C554T", - "A725G", - "A911T", - "A1051G", - "C1088T", - "C1118T", - "T1145C", - "C1199T", - "C1244T", - "A1394G", - "C1406T", - "A1458G", - "T1461C", - "C1499T", - "A1544C", - "C1559T", - "G1586A", - "T1635A", - "C1673T", - "C1715T", - "T1724A", - "G1823A", - "G1980A", - "C2000T", - "C2002T", - "A2030G", - "T2144C", - "A2189G", - "A2192G", - "C2210T", - "T2270C", - "C2310T", - "T2384C", - "T2402C", - "A2459G", - "G2465A", - "G2487A", - "C2681T", - "T2746C", - "G2747A", - "A2837C", - "C2840T", - "G2955A", - "C2966T", - "C3014T", - "G3095A", - "C3107T", - "T3188C", - "C3194T", - "C3214T", - "T3217C", - "G3218A", - "T3302C", - "A3341G", - "C3342T", - "C3455T", - "A3474G", - "C3583T", - "C3597T", - "G3638A", - "C3694T", - "C3699T", - "G3743A", - "A3813G", - "C3814T", - "C3828T", - "T3873C", - "T3954C", - "C4073T", - "T4145C", - "T4170C", - "A4199G", - "T4220A", - "G4232A", - "G4394A", - "A4433G", - "C4440T", - "T4491C", - "C4499T", - "C4646T", - "A4658G", - "T4661C", - "C4703T", - "C4814T", - "A4832G", - "T4862A", - "T4940C", - "T4988C", - "C5009T", - "C5015T", - "A5075G", - "A5123G", - "T5157C", - "G5165A", - "T5184C", - "G5213A", - "C5342T", - "T5363C", - "G5369A", - "T5375C", - "A5378G", - "G5447A", - "A5450G", - "T5477C", - "C5567T", - "C5570T", - "C5585T", - "C5633T", - "T5669C", - "C5672T", - "T5696C", - "A5708G", - "T5771C", - "C5958T", - "T6045C", - "C6095T", - "A6131G", - "G6152A", - "T6176A", - "T6230C", - "C6233T", - "A6281G", - "C6326T", - "A6383T", - "C6395T", - "C6425T", - "C6455T", - "C6506T", - "T6578C", - "T6677C", - "C6683T", - "G6713A", - "T6812A", - "A6884G", - "C6911T", - "A6926G", - "G6944A", - "G6995A", - "C7011T", - "C7022T", - "T7098C", - "A7100G", - "A7286G", - "T7344C", - "T7365C", - "C7481A", - "G7508A", - "G7643A", - "A7664G", - "C7685T", - "A7727G", - "T7904A", - "C7907T", - "C7964T", - "T8055C", - "C8102A", - "G8144A", - 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"G5109A", + "T5177C", + "C5360T", + "C5468T", + "C5488T", + "T5681C", + "G5714A", + "A5786G", + "C6020T", + "A6227G", + "C6332T", + "T6463C", + "T6866C", + "T6992C", + "C7005T", + "A7130G", + "G7445A", + "T7748C", + "T7856C", + "A7859G", + "G7901T", + "T7913C", + "T8111C", + "C8114T", + "A8546G", + "T8699C", + "A8948G", + "G8951A", + "G9326T", + "C9353T", + "G9738A", + "A9827G", + "C10163T" + ] + } + } + } + ] + } + ] } - } + ] } ] } @@ -15471,9 +13222,9 @@ ] }, { - "name": "NODE_0000057", + "name": "NODE_0000065", "node_attrs": { - "div": 0.22215376, + "div": 0.222, "clade_membership": { "value": "4I" } @@ -15505,24 +13256,17 @@ "A8027G", "C9605T", "C9806T" - ], - "E": [ - "Q494H" - ], - "NS1": [ - "V5A" ] }, "labels": { - "aa": "E: Q494H; NS1: V5A", "lineage": "4I" } }, "children": [ { - "name": "NODE_0000058", + "name": "NODE_0000066", "node_attrs": { - "div": 0.24606896, + "div": 0.246, "clade_membership": { "value": "4I" } @@ -15690,6 +13434,7 @@ "C6449T", "A6482G", "T6548A", + "T6554C", "A6635G", "C6722T", "T6727C", @@ -15770,55 +13515,14 @@ "G10172A", "G10205A", "T10241C" - ], - "C": [ - "I102V" - ], - "E": [ - "S120L", - "H230Q", - "F461L", - "V482I" - ], - "NS1": [ - "V265I", - "D292N" - ], - "NS2A": [ - "A75T", - "M103I", - "T137A" - ], - "NS3": [ - "G420R", - "T516I" - ], - "NS4A": [ - "I86M", - "V117A" - ], - "NS4B": [ - "L112S", - "V172A" - ], - "NS5": [ - "Q285R", - "N390S", - "K562R" ] - }, - "labels": { - "aa": "C: I102V; E: S120L, H230Q, F461L, V482I; NS1: V265I, D292N; NS2A: A75T, M103I, T137A; NS3: G420R, T516I; NS4A: I86M, V117A; NS4B: L112S, V172A; NS5: Q285R, N390S, K562R" } }, "children": [ { "name": "JF262783.1|1961", "node_attrs": { - "div": 0.25095615, - "country": { - "value": "India" - }, + "div": 0.251, "clade_membership": { "value": "4I" } @@ -15873,45 +13577,15 @@ "C8918T", "C9273T", "T9807C", - "C9989T", "T10124C" - ], - "C": [ - "V29M" - ], - "E": [ - "A54T", - "A150V", - "N153K" - ], - "M": [ - "T50M" - ], - "NS1": [ - "T164A", - "G235E" - ], - "NS2B": [ - "T119A" - ], - "NS3": [ - "K145R", - "V154I", - "I190V" - ], - "NS5": [ - "D257N" ] - }, - "labels": { - "aa": "C: V29M; E: A54T, A150V, N153K; M: T50M; NS1: T164A, G235E; NS2B: T119A; NS3: K145R, V154I, I190V; NS5: D257N" } } }, { "name": "JQ922558.1|1962", "node_attrs": { - "div": 0.26071596, + "div": 0.261, "country": { "value": "India" }, @@ -16060,94 +13734,19 @@ "C9311T", "G9329A", "G9722A", + "T9989C", "A10071G", "T10242A" - ], - "C": [ - "Q3R", - "R4P", - "G35E", - "L36F", - "V102L" - ], - "E": [ - "S122L", - "T155I", - "F213V", - "T221A", - "E228K", - "N360H" - ], - "NS1": [ - "I22V", - "T209P", - "E213G", - "K214N" - ], - "NS2B": [ - "Q60H" - ], - "NS3": [ - "E173D", - "T267A", - "R268N", - "L269P", - "F288L", - "T289Q", - "P291L", - "S293I" - ], - "NS4A": [ - "L115S" - ], - "NS4B": [ - "T134S", - "A215P" - ], - "NS5": [ - "L34F", - "T39H", - "A41I", - "S43Y", - "A44T", - "K52N", - "V55M", - "R57T", - "S60I", - "W64G", - "V66D", - "L80Q", - "Y89H", - "M91T", - "L94A", - "N96K", - "A224V", - "T267I", - "V354E", - "D360Y", - "R362S", - "Q365H", - "G369W", - "L385G", - "R396W", - "Q574H", - "N575S", - "V578M", - "I837V", - "F894I" ] - }, - "labels": { - "aa": "C: Q3R, R4P, G35E, L36F, V102L; E: S122L, T155I, F213V, T221A, E228K, N360H; NS1: I22V, T209P, E213G, K214N; NS2B: Q60H; NS3: E173D, T267A, R268N, L269P, F288L, T289Q, P291L, S293I; NS4A: L115S; NS4B: T134S, A215P; NS5: L34F, T39H, A41I, S43Y, A44T, K52N, V55M, R57T, S60I, W64G, V66D, L80Q, Y89H, M91T, L94A, N96K, A224V, T267I, V354E, D360Y, R362S, Q365H, G369W, L385G, R396W, Q574H, N575S, V578M, I837V, F894I" } } } ] }, { - "name": "NODE_0000059", + "name": "NODE_0000067", "node_attrs": { - "div": 0.23323636, + "div": 0.233, "clade_membership": { "value": "4I" } @@ -16230,7 +13829,6 @@ "T6389C", "G6493A", "G6533A", - "C6554T", "C6585T", "T6677C", "T6923C", @@ -16261,43 +13859,16 @@ "C9572T", "G9791A", "C9869T", - "C9989T", "C10055T", "A10133G" - ], - "E": [ - "F429L" - ], - "M": [ - "T73A" - ], - "NS1": [ - "T98S", - "T105A" - ], - "NS2A": [ - "V90I" - ], - "NS3": [ - "K142R" - ], - "NS4A": [ - "R39K" - ], - "NS5": [ - "A224V", - "Q635H" ] - }, - "labels": { - "aa": "E: F429L; M: T73A; NS1: T98S, T105A; NS2A: V90I; NS3: K142R; NS4A: R39K; NS5: A224V, Q635H" } }, "children": [ { - "name": "NODE_0000060", + "name": "NODE_0000068", "node_attrs": { - "div": 0.24219383, + "div": 0.242, "clade_membership": { "value": "4I" } @@ -16388,38 +13959,14 @@ "G9920A", "G10085A", "G10094A" - ], - "C": [ - "I102M" - ], - "E": [ - "T221A" - ], - "NS1": [ - "M2T", - "V66I", - "R129K" - ], - "NS2B": [ - "V89I" - ], - "NS3": [ - "I171T", - "T516N" - ], - "NS4B": [ - "I198V" ] - }, - "labels": { - "aa": "C: I102M; E: T221A; NS1: M2T, V66I, R129K; NS2B: V89I; NS3: I171T, T516N; NS4B: I198V" } }, "children": [ { "name": "KY670635.1|2003-10", "node_attrs": { - "div": 0.27648713, + "div": 0.276, "country": { "value": "Taiwan" }, @@ -16723,70 +14270,14 @@ "T10238A", "T10241C", "C10244T" - ], - "C": [ - "K6R" - ], - "E": [ - "Y233H", - "I351V", - "H494Q" - ], - "M": [ - "A15G", - "I127V", - "T152A" - ], - "NS1": [ - "H84Y", - "A128T", - "V178L", - "K214R", - "I287V" - ], - "NS2A": [ - "S5P", - "T38A", - "A78T", - "V79M", - "K94R", - "L113F", - "I126L" - ], - "NS2B": [ - "S48A", - "T119A" - ], - "NS3": [ - "A12V", - "L85F", - "K143R", - "A466T", - "N516S" - ], - "NS4B": [ - "T22I", - "Q68H", - "L112F" - ], - "NS5": [ - "H201Y", - "P312L", - "N390K", - "A440T", - "D526E", - "V881T" ] - }, - "labels": { - "aa": "C: K6R; E: Y233H, I351V, H494Q; M: A15G, I127V, T152A; NS1: H84Y, A128T, V178L, K214R, I287V; NS2A: S5P, T38A, A78T, V79M, K94R, L113F, I126L; NS2B: S48A, T119A; NS3: A12V, L85F, K143R, A466T, N516S; NS4B: T22I, Q68H, L112F; NS5: H201Y, P312L, N390K, A440T, D526E, V881T" } } }, { - "name": "NODE_0000061", + "name": "NODE_0000069", "node_attrs": { - "div": 0.24296504, + "div": 0.243, "clade_membership": { "value": "4I" } @@ -16823,10 +14314,7 @@ { "name": "KR011349.2|1956-08-28", "node_attrs": { - "div": 0.24365093999999998, - "country": { - "value": "Philippines" - }, + "div": 0.244, "clade_membership": { "value": "4I" } @@ -16841,31 +14329,14 @@ "A6493G", "C7141T", "C8541T" - ], - "E": [ - "T155I", - "N360Y", - "F402L" - ], - "M": [ - "K52E" - ], - "NS4A": [ - "K39R" - ], - "NS4B": [ - "T105I" ] - }, - "labels": { - "aa": "E: T155I, N360Y, F402L; M: K52E; NS4A: K39R; NS4B: T105I" } } }, { "name": "OK469357.1|1963", "node_attrs": { - "div": 0.24355663, + "div": 0.244, "country": { "value": "Puerto Rico" }, @@ -16882,17 +14353,7 @@ "G449C", "T450A", "C1552A" - ], - "E": [ - "T205K" - ], - "M": [ - "H2P", - "S4T" ] - }, - "labels": { - "aa": "E: T205K; M: H2P, S4T" } } } @@ -16901,9 +14362,9 @@ ] }, { - "name": "NODE_0000062", + "name": "NODE_0000070", "node_attrs": { - "div": 0.25002166, + "div": 0.25, "clade_membership": { "value": "4I" } @@ -17080,45 +14541,14 @@ "C9962T", "T10124C", "C10130T" - ], - "2K": [ - "I21V" - ], - "E": [ - "Y233H", - "T478S" - ], - "M": [ - "V156I" - ], - "NS1": [ - "A128T" - ], - "NS2A": [ - "G66S", - "R155K" - ], - "NS3": [ - "T62S", - "A321T", - "K480R" - ], - "NS5": [ - "H53Y", - "S59T", - "V256A", - "Q631R" ] - }, - "labels": { - "aa": "2K: I21V; E: Y233H, T478S; M: V156I; NS1: A128T; NS2A: G66S, R155K; NS3: T62S, A321T, K480R; NS5: H53Y, S59T, V256A, Q631R" } }, "children": [ { - "name": "NODE_0000063", + "name": "NODE_0000071", "node_attrs": { - "div": 0.2511267, + "div": 0.251, "clade_membership": { "value": "4I" } @@ -17144,7 +14574,7 @@ { "name": "AP012|1971-05-17", "node_attrs": { - "div": 0.25498067999999996, + "div": 0.255, "clade_membership": { "value": "4I" } @@ -17189,32 +14619,14 @@ "A9887G", "G10061T", "T10130C" - ], - "E": [ - "F402L" - ], - "NS1": [ - "V21I" - ], - "NS2A": [ - "I194L" - ], - "NS4B": [ - "L112S" - ], - "NS5": [ - "A383T" ] - }, - "labels": { - "aa": "E: F402L; NS1: V21I; NS2A: I194L; NS4B: L112S; NS5: A383T" } } }, { - "name": "NODE_0000064", + "name": "NODE_0000072", "node_attrs": { - "div": 0.25360870999999996, + "div": 0.254, "clade_membership": { "value": "4I_B" } @@ -17247,13 +14659,9 @@ "C8246T", "T9245C", "T9884C" - ], - "NS3": [ - "L434I" ] }, "labels": { - "aa": "NS3: L434I", "lineage": "4I_B" } }, @@ -17261,7 +14669,7 @@ { "name": "JQ922559.1|1979", "node_attrs": { - "div": 0.27278490999999994, + "div": 0.273, "country": { "value": "India" }, @@ -17467,93 +14875,14 @@ "G10223A", "A10227T", "A10229G" - ], - "E": [ - "S120L", - "T155I", - "N157I", - "H230Q", - "H233Y", - "N362Y", - "V379I", - "F461L" - ], - "NS1": [ - "V88I", - "K341R" - ], - "NS2A": [ - "V144M" - ], - "NS3": [ - "K248L", - "E412V" - ], - "NS4A": [ - "K80E", - "V90G", - "V97G", - "A98T", - "E99K", - "I100T", - "Q101P", - "Q103P", - "I105G", - "I109N" - ], - "NS4B": [ - "T105I" - ], - "NS5": [ - "T4V", - "Y53Q", - "G129R", - "R246K", - "K289Q", - "S308G", - "F413S", - "A422S", - "S423F", - "I522L", - "K525R", - "D528X", - "I530V", - "Y531F", - "I542F", - "T543X", - "N549K", - "E551K", - "L552P", - "T554P", - "E555G", - "Q556P", - "H561Q", - "K562R", - "L564P", - "K566R", - "P583L", - "T584K", - "P585L", - "D597E", - "K657E", - "K877I", - "E879G", - "M884F", - "P885L", - "V886L", - "M887I", - "R889W" ] - }, - "labels": { - "aa": "E: S120L, T155I, N157I, H230Q, H233Y, N362Y, V379I, F461L; NS1: V88I, K341R; NS2A: V144M; NS3: K248L, E412V; NS4A: K80E, V90G, V97G, A98T, E99K, I100T, Q101P, Q103P, I105G, I109N; NS4B: T105I; NS5: T4V, Y53Q, G129R, R246K, K289Q, S308G, F413S, A422S, S423F, I522L, K525R, D528X, I530V, Y531F, I542F, T543X, N549K, E551K, L552P, T554P, E555G, Q556P, H561Q, K562R, L564P, K566R, P583L, T584K, P585L, D597E, K657E, K877I, E879G, M884F, P885L, V886L, M887I, R889W" } } }, { - "name": "NODE_0000065", + "name": "NODE_0000073", "node_attrs": { - "div": 0.25545077999999993, + "div": 0.255, "clade_membership": { "value": "4I_B" } @@ -17591,7 +14920,7 @@ { "name": "OK605769.1|1983", "node_attrs": { - "div": 0.26625987999999995, + "div": 0.266, "country": { "value": "Senegal" }, @@ -17704,43 +15033,14 @@ "C9890T", "T10031C", "T10238C" - ], - "C": [ - "I102L" - ], - "E": [ - "D95N", - "K200T", - "K325R", - "A329T" - ], - "NS2A": [ - "V37M", - "V173A" - ], - "NS2B": [ - "L109I" - ], - "NS3": [ - "A12P" - ], - "NS4B": [ - "M110I" - ], - "NS5": [ - "K23R", - "K76R" ] - }, - "labels": { - "aa": "C: I102L; E: D95N, K200T, K325R, A329T; NS2A: V37M, V173A; NS2B: L109I; NS3: A12P; NS4B: M110I; NS5: K23R, K76R" } } }, { - "name": "NODE_0000066", + "name": "NODE_0000074", "node_attrs": { - "div": 0.27385237999999995, + "div": 0.274, "clade_membership": { "value": "4I_B" } @@ -17921,48 +15221,14 @@ "G9971A", "T10034C", "C10043T" - ], - "E": [ - "V130I", - "K174E", - "K202N" - ], - "NS1": [ - "V21I" - ], - "NS2A": [ - "D62N" - ], - "NS2B": [ - "N58T" - ], - "NS3": [ - "I100V", - "I383V", - "M605V" - ], - "NS4A": [ - "I78M", - "V117A" - ], - "NS4B": [ - "A240T" - ], - "NS5": [ - "H247Y", - "T275A", - "V373I" ] - }, - "labels": { - "aa": "E: V130I, K174E, K202N; NS1: V21I; NS2A: D62N; NS2B: N58T; NS3: I100V, I383V, M605V; NS4A: I78M, V117A; NS4B: A240T; NS5: H247Y, T275A, V373I" } }, "children": [ { - "name": "NODE_0000067", + "name": "NODE_0000075", "node_attrs": { - "div": 0.27927409999999997, + "div": 0.279, "clade_membership": { "value": "4I_B.1" } @@ -18024,18 +15290,9 @@ "T10169C", "G10190A", "G10196A" - ], - "NS1": [ - "V265M" - ], - "NS3": [ - "A13T", - "R73K", - "Y499H" ] }, "labels": { - "aa": "NS1: V265M; NS3: A13T, R73K, Y499H", "lineage": "4I_B.1" } }, @@ -18043,7 +15300,7 @@ { "name": "KF041260.1|2009", "node_attrs": { - "div": 0.28146994999999997, + "div": 0.281, "country": { "value": "Pakistan" }, @@ -18071,26 +15328,14 @@ "A7121G", "T8354C", "C10070T" - ], - "E": [ - "I164V" - ], - "NS2A": [ - "I72T" - ], - "NS3": [ - "S249T" ] - }, - "labels": { - "aa": "E: I164V; NS2A: I72T; NS3: S249T" } } }, { - "name": "NODE_0000068", + "name": "NODE_0000076", "node_attrs": { - "div": 0.29393929999999996, + "div": 0.294, "clade_membership": { "value": "4I_B.1" } @@ -18253,46 +15498,14 @@ "T10043C", "G10061A", "A10121G" - ], - "E": [ - "I130V", - "I132V", - "E174K", - "K200T", - "N202K", - "T265A", - "N366S", - "H494Q" - ], - "M": [ - "A15T", - "M158I" - ], - "NS1": [ - "F171L" - ], - "NS2A": [ - "F122L", - "V136A" - ], - "NS3": [ - "V383I", - "A466T" - ], - "NS5": [ - "H201Y", - "R246K" ] - }, - "labels": { - "aa": "E: I130V, I132V, E174K, K200T, N202K, T265A, N366S, H494Q; M: A15T, M158I; NS1: F171L; NS2A: F122L, V136A; NS3: V383I, A466T; NS5: H201Y, R246K" } }, "children": [ { "name": "MG272272.1|2016", "node_attrs": { - "div": 0.29623383999999997, + "div": 0.296, "country": { "value": "India" }, @@ -18322,26 +15535,14 @@ "C7472T", "A9152G", "G10085A" - ], - "E": [ - "E62K" - ], - "NS2A": [ - "C184R" - ], - "NS5": [ - "I530M" ] - }, - "labels": { - "aa": "E: E62K; NS2A: C184R; NS5: I530M" } } }, { - "name": "NODE_0000069", + "name": "NODE_0000077", "node_attrs": { - "div": 0.31548519999999997, + "div": 0.315, "clade_membership": { "value": "4I_B.1" } @@ -18515,38 +15716,14 @@ "C10169T", "A10196G", "A10205G" - ], - "C": [ - "V111A" - ], - "E": [ - "K202E" - ], - "NS2B": [ - "T58N" - ], - "NS3": [ - "T13A", - "K73R", - "H499Y" - ], - "NS4A": [ - "M78I", - "A117V" - ], - "NS4B": [ - "T240A" ] - }, - "labels": { - "aa": "C: V111A; E: K202E; NS2B: T58N; NS3: T13A, K73R, H499Y; NS4A: M78I, A117V; NS4B: T240A" } }, "children": [ { "name": "MN018398.1|2016-08-16", "node_attrs": { - "div": 0.33457119999999996, + "div": 0.335, "country": { "value": "China" }, @@ -18711,63 +15888,14 @@ "G10145A", "G10199C", "T10204C" - ], - "C": [ - "T81A" - ], - "E": [ - "T200K", - "A263P", - "V348I" - ], - "M": [ - "M140W" - ], - "NS1": [ - "D139N", - "A246V", - "G328E" - ], - "NS2A": [ - "G70R", - "K81R", - "R93K", - "L122I", - "Q202R", - "Y207H" - ], - "NS2B": [ - "I95K", - "T105P" - ], - "NS3": [ - "T34A" - ], - "NS4B": [ - "K19N" - ], - "NS5": [ - "S49L", - "Y53H", - "S60G", - "G159E", - "Y201H", - "N406I", - "H635D", - "E835K", - "E879D", - "V881A" ] - }, - "labels": { - "aa": "C: T81A; E: T200K, A263P, V348I; M: M140W; NS1: D139N, A246V, G328E; NS2A: G70R, K81R, R93K, L122I, Q202R, Y207H; NS2B: I95K, T105P; NS3: T34A; NS4B: K19N; NS5: S49L, Y53H, S60G, G159E, Y201H, N406I, H635D, E835K, E879D, V881A" } } }, { - "name": "NODE_0000070", + "name": "NODE_0000078", "node_attrs": { - "div": 0.31577769999999994, + "div": 0.316, "clade_membership": { "value": "4I_B.1" } @@ -18781,20 +15909,14 @@ "A5204G", "G9479C", "A9918G" - ], - "NS5": [ - "T786A" ] - }, - "labels": { - "aa": "NS5: T786A" } }, "children": [ { "name": "OM639995.1|2021-11-16", "node_attrs": { - "div": 0.3494051999999999, + "div": 0.349, "country": { "value": "India" }, @@ -19172,112 +16294,14 @@ "G10172A", "A10190G", "T10208C" - ], - "C": [ - "V7A", - "V8R", - "R9N", - "P10T", - "P25V", - "G27Q", - "V29T", - "T34L", - "L36M", - "F37L", - "S38A", - "K40R", - "R44K", - "M45L", - "V46F", - "L47M", - "I50V", - "T51A" - ], - "E": [ - "V4I", - "V6I", - "G7S", - "A19S", - "L23I", - "G29S", - "Q36K", - "G37N", - "K174N" - ], - "M": [ - "L70S", - "A73T", - "M76T", - "Q82H", - "S83R", - "I158L", - "M159T", - "L160A", - "V161I", - "Y165M", - "G166T" - ], - "NS1": [ - "Q191N", - "K192R", - "S205A", - "K206L", - "Q208D", - "Q211K", - "L217F", - "T222S", - "L224H", - "T228S", - "Q240E", - "L242I", - "A246N", - "Y247F", - "F251V" - ], - "NS2A": [ - "K81R", - "V104A", - "C184R" - ], - "NS3": [ - "A12T", - "V100I" - ], - "NS5": [ - "S449T", - "R467K", - "G499S", - "W504L", - "R514K", - "I553V", - "K579R", - "L581Q", - "K586R", - "A588T", - "K596R", - "E673D", - "S676G", - "T677A", - "S678X", - "L679Q", - "F681-", - "L682X", - "P693Q", - "K702N", - "A758S", - "S777A", - "M778N" ] - }, - "labels": { - "aa": "C: V7A, V8R, R9N, P10T, P25V, G27Q, V29T, T34L, L36M, F37L, S38A, K40R, R44K, M45L, V46F, L47M, I50V, T51A; E: V4I, V6I, G7S, A19S, L23I, G29S, Q36K, G37N, K174N; M: L70S, A73T, M76T, Q82H, S83R, I158L, M159T, L160A, V161I, Y165M, G166T; NS1: Q191N, K192R, S205A, K206L, Q208D, Q211K, L217F, T222S, L224H, T228S, Q240E, L242I, A246N, Y247F, F251V; NS2A: K81R, V104A, C184R; NS3: A12T, V100I; NS5: S449T, R467K, G499S, W504L, R514K, I553V, K579R, L581Q, K586R, A588T, K596R, E673D, S676G, T677A, S678X, L679Q, F681-, L682X, P693Q, K702N, A758S, S777A, M778N" } } }, { "name": "OP984198.1|2018", "node_attrs": { - "div": 0.3304407999999999, + "div": 0.33, "country": { "value": "India" }, @@ -19425,30 +16449,7 @@ "G10199A", "T10202C", "C10220A" - ], - "M": [ - "H2S" - ], - "NS1": [ - "D292G", - "S351T" - ], - "NS2A": [ - "T38I", - "N62D", - "S66G", - "M68I", - "I90V", - "H138Q", - "K217R" - ], - "NS3": [ - "A12T", - "V100I" ] - }, - "labels": { - "aa": "M: H2S; NS1: D292G, S351T; NS2A: T38I, N62D, S66G, M68I, I90V, H138Q, K217R; NS3: A12T, V100I" } } } @@ -19461,9 +16462,9 @@ ] }, { - "name": "NODE_0000071", + "name": "NODE_0000079", "node_attrs": { - "div": 0.27719235999999997, + "div": 0.277, "clade_membership": { "value": "4I_B.2" } @@ -19506,17 +16507,9 @@ "A8753G", "C9059T", "G9788A" - ], - "E": [ - "T221A", - "I351V" - ], - "NS2A": [ - "I123V" ] }, "labels": { - "aa": "E: T221A, I351V; NS2A: I123V", "lineage": "4I_B.2" } }, @@ -19524,7 +16517,7 @@ { "name": "KU509287.1|2009", "node_attrs": { - "div": 0.28526049, + "div": 0.285, "country": { "value": "India" }, @@ -19616,57 +16609,14 @@ "G9662A", "C9695T", "G9722A" - ], - "E": [ - "V242I", - "S478T" - ], - "M": [ - "R88P" - ], - "NS2A": [ - "T38I" - ], - "NS2B": [ - "T58S" - ], - "NS3": [ - "V126L" - ], - "NS4A": [ - "V90K", - "E99Q" - ], - "NS4B": [ - "P101L" - ], - "NS5": [ - "G1R", - "T245P", - "Y247H", - "A275T", - "R279G", - "E290D", - "D333H", - "Q365K", - "N575I", - "K586R", - "K638Q", - "K649T", - "R658K", - "T677P", - "D691V" ] - }, - "labels": { - "aa": "E: V242I, S478T; M: R88P; NS2A: T38I; NS2B: T58S; NS3: V126L; NS4A: V90K, E99Q; NS4B: P101L; NS5: G1R, T245P, Y247H, A275T, R279G, E290D, D333H, Q365K, N575I, K586R, K638Q, K649T, R658K, T677P, D691V" } } }, { - "name": "NODE_0000072", + "name": "NODE_0000080", "node_attrs": { - "div": 0.27746977999999994, + "div": 0.277, "clade_membership": { "value": "4I_B.2" } @@ -19675,268 +16625,16 @@ "mutations": { "nuc": [ "C8393T", + "A8565G", "A10205G" ] } }, "children": [ { - "name": "NODE_0000073", + "name": "NODE_0000081", "node_attrs": { - "div": 0.28152031999999994, - "clade_membership": { - "value": "4I_B.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A355G", - "C680T", - "A854C", - "G1892A", - "C1910T", - "C2339A", - "T2397C", - "C2660T", - "T2897C", - "C3107T", - "C3251G", - "G3473A", - "G3515A", - "T3546C", - "T3836C", - "G3960A", - "T4010C", - "A4244G", - "G4430A", - "A4550G", - "T4943C", - "A5153G", - "C5169T", - "C5342T", - "G5657A", - "T6005C", - "T6230C", - "T6446G", - "G6833A", - "A7208G", - "C7526T", - "C7940T", - "T7973C", - "G8141A", - "G8564-", - "C8642T", - "G9005A", - "G9029A", - "C9216T", - "C9245T", - "T9281C", - "G9307A", - "T9374A", - "A9530G", - "G9758A", - "A9944G", - "G10053A", - "C10112T" - ], - "C": [ - "K85R" - ], - "NS1": [ - "D276E" - ], - "NS2A": [ - "V161I" - ], - "NS5": [ - "V334X", - "R582K", - "V831I" - ] - }, - "labels": { - "aa": "C: K85R; NS1: D276E; NS2A: V161I; NS5: V334X, R582K, V831I" - } - }, - "children": [ - { - "name": "KX059029.1|2012-08", - "node_attrs": { - "div": 0.2860894299999999, - "country": { - "value": "Sri Lanka" - }, - "clade_membership": { - "value": "4I_B.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "G956A", - "T1424G", - "T3584C", - "A3591G", - "G3710A", - "C4194T", - "G4206T", - "T4210C", - "A4217C", - "C4225A", - "C4304T", - "C4352T", - "G4848A", - "C5243T", - "G5684A", - "G6056A", - "G6170A", - "A7027G", - "A7031G", - "C7070T", - "G7523A", - "A8534G", - "T8536A", - "A8565-", - "T8566-", - "A9608T", - "A9657C", - "T9806C" - ], - "NS2A": [ - "T38A", - "M77I" - ], - "NS2B": [ - "L21F", - "D25Y", - "V26A", - "P31Q" - ], - "NS3": [ - "V109I" - ], - "NS4B": [ - "N67S" - ], - "NS5": [ - "V325D", - "I335X", - "L682F", - "K699Q" - ] - }, - "labels": { - "aa": "NS2A: T38A, M77I; NS2B: L21F, D25Y, V26A, P31Q; NS3: V109I; NS4B: N67S; NS5: V325D, I335X, L682F, K699Q" - } - } - }, - { - "name": "KX059015.1|2012-07", - "node_attrs": { - "div": 0.2877917199999999, - "country": { - "value": "Sri Lanka" - }, - "clade_membership": { - "value": "4I_B.2" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "C175T", - "G2889A", - "G2938C", - "G2952T", - "A2953T", - "A2954G", - "G2955A", - "G3056A", - "G3518A", - "T4208G", - "G4209C", - "T4214C", - "T4763G", - "G4856A", - "A5042G", - "A5141T", - "A5159G", - "A5471G", - "C5478T", - "T7521C", - "T7544C", - "G7558A", - "T7696G", - "G7697A", - "C8528T", - "G8531A", - "T8536C", - "T8537C", - "A8538G", - "A8539C", - "A8540T", - "T8542C", - "C8548A", - "A8549T", - "A8550G", - "A8551G", - "G8559T", - "A8560G", - "C8561T", - "T8563C", - "-8564C", - "T8566C", - "C8568T", - "A8571T", - "A9644T", - "T9968C" - ], - "C": [ - "P25L" - ], - "NS1": [ - "E156K", - "R172P", - "E177L", - "V178M" - ], - "NS2B": [ - "D25E", - "V26L" - ], - "NS3": [ - "P319S" - ], - "NS4B": [ - "R244K" - ], - "NS5": [ - "L45R", - "V325A", - "K326A", - "L327P", - "T329N", - "K330G", - "D333C", - "X334A", - "I335T", - "P336S", - "M337L", - "Q694H" - ] - }, - "labels": { - "aa": "C: P25L; NS1: E156K, R172P, E177L, V178M; NS2B: D25E, V26L; NS3: P319S; NS4B: R244K; NS5: L45R, V325A, K326A, L327P, T329N, K330G, D333C, X334A, I335T, P336S, M337L, Q694H" - } - } - } - ] - }, - { - "name": "NODE_0000074", - "node_attrs": { - "div": 0.27844489999999994, + "div": 0.278, "clade_membership": { "value": "4I_B.2" } @@ -19953,22 +16651,15 @@ "A4985G", "T5864C", "A6293G", - "C7662T", - "A8565G" - ], - "NS5": [ - "I335V" + "C7662T" ] - }, - "labels": { - "aa": "NS5: I335V" } }, "children": [ { "name": "KX845005.1|2015", "node_attrs": { - "div": 0.28439624999999996, + "div": 0.284, "country": { "value": "India" }, @@ -20039,36 +16730,14 @@ "T9929C", "T10031C", "G10172T" - ], - "C": [ - "I102T" - ], - "E": [ - "L429F" - ], - "NS3": [ - "V208I" - ], - "NS4B": [ - "V18A" - ], - "NS5": [ - "H201Y", - "G226R", - "R631Q", - "K638E", - "Q870H" ] - }, - "labels": { - "aa": "C: I102T; E: L429F; NS3: V208I; NS4B: V18A; NS5: H201Y, G226R, R631Q, K638E, Q870H" } } }, { "name": "MK858146.2|2016-07-03", "node_attrs": { - "div": 0.28352543999999996, + "div": 0.284, "country": { "value": "India" }, @@ -20130,214 +16799,498 @@ "C9731T", "A9986G", "C10070T" - ], - "E": [ - "I378V" - ], - "NS2A": [ - "S156T" - ], - "NS2B": [ - "K127R" - ], - "NS3": [ - "I123V" - ], - "NS4B": [ - "T56A", - "A175V" - ], - "NS5": [ - "A275T" ] - }, - "labels": { - "aa": "E: I378V; NS2A: S156T; NS2B: K127R; NS3: I123V; NS4B: T56A, A175V; NS5: A275T" } } } ] - } - ] - } - ] - } - ] - } - ] - } - ] - } - ] - }, - { - "name": "NODE_0000075", - "node_attrs": { - "div": 0.25603609, - "clade_membership": { - "value": "4I_A" - } - }, - "branch_attrs": { - "mutations": { - "nuc": [ - "A200G", - "A335G", - "G341A", - "C464T", - "C536T", - "G692A", - "T800C", - "T872C", - "G974A", - "C1232T", - "T1247C", - "A1388T", - "C1487T", - "T1559C", - "C1793T", - "C2054T", - "T2126C", - "T2261C", - "T2408C", - "A2459G", - "T2555G", - "A2888G", - "C3362T", - "G3389A", - "T3410C", - "T3428C", - "G3476A", - "C3611T", - "C3623T", - "A3644T", - "C3861T", - "G3875A", - "A4418T", - "A4583G", - "A4880T", - "T4961C", - "C5420T", - "C5462T", - "T5540C", - "G5669C", - "T5681C", - "C6011T", - "G6056A", - "C6380T", - "C6396T", - "A6668G", - "A6735G", - "C6960T", - "T7161C", - "C7428T", - "G7436A", - "A8049C", - "G8057A", - "A8138G", - "C8252T", - "T8555C", - "C9117T", - "C10039T", - "G10046A" - ], - "NS4A": [ - "I120V" - ], - "NS5": [ - "T826I" - ] - }, - "labels": { - "aa": "NS4A: I120V; NS5: T826I", - "lineage": "4I_A" - } - }, - "children": [ - { - "name": "OK469358.1|1976", 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"C7442T", + "C7535T", + "A7575T", + "A7577G", + "G7736T", + "G7768A", + "T7988A", + "T8046C", + "C8102T", + "G8173A", + "C8312T", + "C8393T", + "A8502T", + "C8689T", + "A8834G", + "G8999A", + "G9038A", + "T9257C", + "C9524T", + "T9545C", + "C9554T", + "T9560C", + "T9572C", + "T9593C", + "T9605C", + "C9614T", + "T9638C", + "A9644G", + "G9811A", + "A9812G", + "A9918G", + "T9962C", + "C10070T", + "T10145C" + ] + } + } + } + ] } ] } @@ -22844,9 +19487,9 @@ ] }, { - "name": "NODE_0000088", + "name": "NODE_0000102", "node_attrs": { - "div": 0.2711532, + "div": 0.271, "clade_membership": { "value": "4I_A" } @@ -22874,10 +19517,7 @@ { "name": "MW945663.1|1994", "node_attrs": { - "div": 0.27470562, - "country": { - "value": "Thailand" - }, + "div": 0.275, "clade_membership": { "value": "4I_A" } @@ -22921,28 +19561,14 @@ "A9809G", "A9872G", "T9899C" - ], - "E": [ - "T155S", - "I485V" - ], - "M": [ - "I149V" - ], - "NS5": [ - "E616G", - "R631Q" ] - }, - "labels": { - "aa": "E: T155S, I485V; M: I149V; NS5: E616G, R631Q" } } }, { - "name": "NODE_0000089", + "name": "NODE_0000103", "node_attrs": { - "div": 0.27363867, + "div": 0.274, "clade_membership": { "value": "4I_A.1" } @@ -22974,21 +19600,17 @@ "C7739T", "A9413G", "T10031C" - ], - "E": [ - "V160E" ] }, "labels": { - "aa": "E: V160E", "lineage": "4I_A.1" } }, "children": [ { - "name": "NODE_0000090", + "name": "NODE_0000104", "node_attrs": { - "div": 0.27894877999999995, + "div": 0.279, "clade_membership": { "value": "4I_A.1" } @@ -23049,34 +19671,14 @@ "A9662G", "C9779T", "C9785T" - ], - "E": [ - "V382A", - "A481V" - ], - "NS1": [ - "A5V", - "I251T" - ], - "NS2A": [ - "V79M" - ], - "NS3": [ - "V22A" - ], - "NS4A": [ - "I78M" ] - }, - "labels": { - "aa": "E: V382A, A481V; NS1: A5V, I251T; NS2A: V79M; NS3: V22A; NS4A: I78M" } }, "children": [ { "name": "MW945498.1|2010", "node_attrs": { - "div": 0.29032568, + "div": 0.29, "country": { "value": "Thailand" }, @@ -23199,38 +19801,14 @@ "G9788A", "T10154C", "C10220G" - ], - "E": [ - "I132V" - ], - "NS1": [ - "V350A" - ], - "NS2A": [ - "V104A", - "I167V", - "K217R" - ], - "NS3": [ - "T17I" - ], - "NS4B": [ - "I147L" - ], - "NS5": [ - "H201Y", - "A558T" ] - }, - "labels": { - "aa": "E: I132V; NS1: V350A; NS2A: V104A, I167V, K217R; NS3: T17I; NS4B: I147L; NS5: H201Y, A558T" } } }, { "name": "KY586942.1|2006", "node_attrs": { - "div": 0.28627646999999995, + "div": 0.286, "country": { "value": "Thailand" }, @@ -23316,40 +19894,16 @@ "T10098A", "A10240-", "T10241C" - ], - "C": [ - "V111A" - ], - "NS1": [ - "T128I", - "S141P" - ], - "NS2A": [ - "A42V" - ], - "NS3": [ - "E561D" - ], - "NS5": [ - "R279K", - "N390K", - "A558G", - "I563N", - "L846M", - "H893X" ] - }, - "labels": { - "aa": "C: V111A; NS1: T128I, S141P; NS2A: A42V; NS3: E561D; NS5: R279K, N390K, A558G, I563N, L846M, H893X" } } } ] }, { - "name": "NODE_0000091", + "name": "NODE_0000105", "node_attrs": { - "div": 0.28347957999999995, + "div": 0.283, "clade_membership": { "value": "4I_A.1" } @@ -23454,37 +20008,14 @@ "C10058T", "A10067G", "G10094A" - ], - "C": [ - "I102M" - ], - "E": [ - "M96V" - ], - "NS1": [ - "K192R", - "V265M" - ], - "NS2A": [ - "T38I", - "D62N", - "F122L" - ], - "NS3": [ - "S249A", - "F509Y", - "G510A" ] - }, - "labels": { - "aa": "C: I102M; E: M96V; NS1: K192R, V265M; NS2A: T38I, D62N, F122L; NS3: S249A, F509Y, G510A" } }, "children": [ { - "name": "NODE_0000092", + "name": "NODE_0000106", "node_attrs": { - "div": 0.28565510999999993, + "div": 0.286, "clade_membership": { "value": "4I_A.1.1" } @@ -23496,51 +20027,30 @@ "T428C", "T431G", "T593C", - "C839T", "C1214T", "G2441A", - "T3281C", - "T3867C", "C4073T", "C4181T", "A4238G", - "C4340T", "G4560A", "A4916G", - "C5072T", "T5090C", - "A5417G", "T5642C", "G5684A", "T5819A", - "C6092T", - "C6797T", + "C6455T", "A6929G", - "G6995A", - "C7397T", "A7664G", "C7685T", "C7695T", "T8018C", "C8132T", "T8201C", - "G8562A", "G9005A", - "T9155C", - "A9319G", - "T9605C", - "A9662T" - ], - "NS3": [ - "A13T" - ], - "NS5": [ - "V334M", - "K586R" + "A9319G" ] }, "labels": { - "aa": "NS3: A13T; NS5: V334M, K586R", "lineage": "4I_A.1.1" } }, @@ -23548,9 +20058,9 @@ { "name": "OQ426982.1|2018-12-18", "node_attrs": { - "div": 0.2899671199999999, + "div": 0.29, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.1" @@ -23560,45 +20070,50 @@ "mutations": { "nuc": [ "T312C", + "C839T", "C1754A", "T2054C", "A2234G", "T3185C", "A3248G", + "T3281C", "T3516C", "G3551A", + "T3867C", + "C4340T", "C4397T", "C4865T", "C4970T", + "C5072T", + "A5417G", + "C6092T", "T6380C", "A6551G", "C6677T", + "C6797T", + "G6995A", "G7247A", "C7331T", + "C7397T", "C7573T", "T8231C", + "G8562A", + "T9155C", "A9284G", "C9419T", "C9524T", + "T9605C", + "A9662T", "A9809G", "A9881G" - ], - "NS1": [ - "I275M" - ], - "NS5": [ - "T4I" ] - }, - "labels": { - "aa": "NS1: I275M; NS5: T4I" } } }, { - "name": "NODE_0000093", + "name": "NODE_0000107", "node_attrs": { - "div": 0.2900225899999999, + "div": 0.287, "clade_membership": { "value": "4I_A.1.1" } @@ -23606,56 +20121,27 @@ "branch_attrs": { "mutations": { "nuc": [ - "G707A", - "C1184T", "A1787G", "G1853A", - "C2066T", "A2117G", - "G2222A", - "C2309T", - "A3569G", "C3977T", "T4376C", - "G4442A", - "C4466T", - "A4821G", - "G4856A", - "T4880C", - "A4925G", "C5882T", "A5996G", "T6179C", - "C6455T", "G6686A", - "C6809T", "C7280T", - "G7589A", - "C9068T", - "T9095C", - "T9458G", - "G9490A", - "T9885C" - ], - "NS3": [ - "I100V" - ], - "NS5": [ - "D632E", - "R643K" + "C9068T" ] - }, - "labels": { - "aa": "NS3: I100V; NS5: D632E, R643K" } }, "children": [ { - "name": "OQ427042.1|2019-01-08", + "name": "PP269983.1|2011-12-29", "node_attrs": { - "div": 0.2942647899999999, + "div": 0.289, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.1" @@ -23664,74 +20150,35 @@ "branch_attrs": { "mutations": { "nuc": [ - "C542T", - "T1487C", - "T1799C", - "T1812C", - "C2225T", - "A2312G", - "T2579A", - "T2712C", - "C2717A", - "T2844C", - "T2948C", - "G2998A", - "T3203C", - "C3526T", - "T3695C", - "C3867T", - "A3920G", - "T4088C", - "C4418T", - "G4712A", - "C4784T", - "G4916A", - "C4940T", - "T4943C", - "G5032A", - "G5145A", - "A5159G", - "C5501T", - "T5885A", - "A6128G", - "A6290G", - "C6446T", - "A6737G", - "C7095T", - "C7344T", - "G7664A", - "T7695C", - "T8315C", + "T210C", + "C902T", + "T1397C", + "A2828G", + "A3845G", + "C4491T", + "C4573T", + "T4588C", + "G4791A", + "C5978T", + "G6869T", + "C6911T", + "T7404C", + "T7481C", + "G7796A", + "G7838A", "C8426T", - "G8999A", - "A9110T", - "C9596A", - "C9740T", - "T9962C", - "G10196A" - ], - "NS1": [ - "D52E", - "S141P", - "R192K" - ], - "NS2A": [ - "T16I" - ], - "NS3": [ - "R170K", - "V208I" + "G8840A", + "A9071T", + "A9212G", + "A9764G" ] - }, - "labels": { - "aa": "NS1: D52E, S141P, R192K; NS2A: T16I; NS3: R170K, V208I" } } }, { - "name": "NODE_0000094", + "name": "NODE_0000108", "node_attrs": { - "div": 0.2903989799999999, + "div": 0.29, "clade_membership": { "value": "4I_A.1.1" } @@ -23739,17 +20186,46 @@ "branch_attrs": { "mutations": { "nuc": [ - "C9735T" + "C839T", + "C1184T", + "C2066T", + "G2222A", + "C2309T", + "T3281C", + "A3569G", + "C4340T", + "G4442A", + "C4466T", + "A4821G", + "G4856A", + "T4880C", + "A4925G", + "C5072T", + "A5417G", + "C6092T", + "C6797T", + "C6809T", + "G6995A", + "C7397T", + "G7589A", + "G8562A", + "T9095C", + "T9155C", + "T9458G", + "G9490A", + "T9605C", + "A9662T", + "T9885C" ] } }, "children": [ { - "name": "OQ427061.1|2018-12-24", + "name": "OQ427042.1|2019-01-08", "node_attrs": { - "div": 0.29533860999999995, + "div": 0.294, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.1" @@ -23758,83 +20234,59 @@ "branch_attrs": { "mutations": { "nuc": [ - "A319G", - "T506C", - "T536C", - "C575T", - "A707G", - "G749A", - "T1064C", - "G1097A", - "C1351T", - "A1619G", - "C1754A", - "A2219G", - "G2327A", - "C2474T", - "G2714A", - "A3239G", - "C3359T", - "T3623C", - "C3647T", - "T3836C", - "C3872T", - "T4019C", - "G4040A", - "T4178C", - "T4440C", - "G4613A", - "C4784A", - "A4859G", - "C5582T", - "C6077T", - "C6188T", - "A6671T", - "A6740G", - "T6792C", - "A6858G", - "T7052C", - "C7073T", - "G7091T", - "G7226A", - "C7472T", - "A7971T", - "C8714T", - "C8921T", - "T9557C", - "T9572C", - "G9575A", - "C9785T", - "G9845A", - "C9938T", - "C10112T", - "C10136T" - ], - "C": [ - "K73R" - ], - "E": [ - "T138M" - ], - "NS3": [ - "D87E" - ], - "NS4B": [ - "T11A" - ], - "NS5": [ - "T137S" + "C542T", + "G707A", + "T1487C", + "T1799C", + "T1812C", + "C2225T", + "A2312G", + "T2579A", + "T2712C", + "C2717A", + "T2844C", + "T2948C", + "G2998A", + "T3203C", + "C3526T", + "T3695C", + "A3920G", + "T4088C", + "C4418T", + "G4712A", + "C4784T", + "G4916A", + "C4940T", + "T4943C", + "G5032A", + "G5145A", + "A5159G", + "C5501T", + "T5885A", + "A6128G", + "A6290G", + "C6446T", + "A6737G", + "C7095T", + "C7344T", + "G7664A", + "T7695C", + "T8315C", + "C8426T", + "G8999A", + "A9110T", + "C9596A", + "C9740T", + "T9962C", + "G10196A" ] - }, - "labels": { - "aa": "C: K73R; E: T138M; NS3: D87E; NS4B: T11A; NS5: T137S" } } }, { - "name": "NODE_0000095", + "name": "NODE_0000109", "node_attrs": { - "div": 0.2909639799999999, + "div": 0.29, "clade_membership": { "value": "4I_A.1.1" } @@ -23842,28 +20294,18 @@ "branch_attrs": { "mutations": { "nuc": [ - "G959A", - "G2084A", - "A5559G", - "T5639C", - "A6551G", - "G7247A" - ], - "NS3": [ - "T346A" + "T3867C", + "C9735T" ] - }, - "labels": { - "aa": "NS3: T346A" } }, "children": [ { - "name": "OQ427048.1|2019-01-15", + "name": "OQ427061.1|2018-12-24", "node_attrs": { - "div": 0.2970172099999999, + "div": 0.295, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.1" @@ -23872,95 +20314,64 @@ "branch_attrs": { "mutations": { "nuc": [ - "T381C", - "G482A", + "A319G", "T506C", - "A707T", - "C1076T", - "T1214C", - "C1247T", - "G1316A", - "T1487C", - "T1625C", - "T1634C", - "C1766T", - "G1886A", - "T2018C", - "C2069T", - "T2081C", - "C2375T", - "T2795C", - "A2861G", - "A2939G", - "A3057C", - "A3248G", - "T3435C", - "G3590C", - "T3977C", - "T4370C", - "C4573T", - "C4716T", - "G4766A", - "T4820C", + "T536C", + "C575T", + "G749A", + "T1064C", + "G1097A", + "C1351T", + "A1619G", + "C1754A", + "A2219G", + "G2327A", + "C2474T", + "G2714A", + "A3239G", + "C3359T", + "T3623C", + "C3647T", + "T3836C", + "C3872T", + "T4019C", + "G4040A", + "T4178C", + "T4440C", + "G4613A", + "C4784A", "A4859G", - "C4865T", - "C4940T", - "C5114T", - "C5318T", - "A5378G", - "G5600A", - "G5657A", - "A5675G", - "T5882C", - "T6380C", - "T6732C", - "G6734A", - "T6806C", - "T6809C", - "C6896T", - "G7094A", - "C7349T", - "C7427T", - "C7493T", - "C7573T", - "A7595G", - "A7682G", - "C7694A", - "A8349C", - "G8679A", - "G9038A", - "C9095T", - "C9236T", - "A9284G", - "T9899C" - ], - "M": [ - "E89D" - ], - "NS1": [ - "I212L", - "I275M" - ], - "NS3": [ - "T17I" - ], - "NS5": [ - "T4I", - "V373I" + "C5582T", + "C6077T", + "C6188T", + "A6671T", + "A6740G", + "T6792C", + "A6858G", + "T7052C", + "C7073T", + "G7091T", + "G7226A", + "C7472T", + "A7971T", + "C8714T", + "C8921T", + "T9557C", + "T9572C", + "G9575A", + "C9785T", + "G9845A", + "C9938T", + "C10112T", + "C10136T" ] - }, - "labels": { - "aa": "M: E89D; NS1: I212L, I275M; NS3: T17I; NS5: T4I, V373I" } } }, { - "name": "MZ976860.1|2020-08-03", + "name": "NODE_0000110", "node_attrs": { - "div": 0.2960654999999999, - "country": { - "value": "Cambodia" - }, + "div": 0.291, "clade_membership": { "value": "4I_A.1.1" } @@ -23968,75 +20379,162 @@ "branch_attrs": { "mutations": { "nuc": [ - "C203A", - "T433C", - "T551C", - "C560T", - "G578A", - "C830T", - "C1423T", - "G1643A", - "C1673T", - "C1733T", - "T1751C", - "A1883G", - "G1919A", - "C2380T", - "T3092C", - "C3563T", - "A3845G", - "T4109C", - "G4250A", - "T4625A", - "C4919T", - "A4955G", - "G4959A", - "T4964C", - "C4970T", - "T5354C", - "T5741C", - "T5846C", - "T6149C", - "C6365T", - "A6420G", - "T6662C", - "A7031G", - "G7196A", - "G7559A", - "G7619A", - "C7721T", - "C7955T", - "A8159G", - "C8390T", - "C8603T", - "C8849T", - "A9152G", - "T9401C", - "C9596T", - "C9701T", - "T9716C" - ], - "C": [ - "V111A" - ], - "E": [ - "A162V", - "A481V" - ], - "NS3": [ - "V146I" - ], - "NS4A": [ - "T15A" - ], - "NS5": [ - "I530M" + "G959A", + "G2084A", + "A5559G", + "T5639C", + "A6551G", + "G7247A" ] + } + }, + "children": [ + { + "name": "OQ427048.1|2019-01-15", + "node_attrs": { + "div": 0.297, + "country": { + "value": "Viet Nam" + }, + "clade_membership": { + "value": "4I_A.1.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "T381C", + "G482A", + "T506C", + "G707T", + "C1076T", + "T1214C", + "C1247T", + "G1316A", + "T1487C", + "T1625C", + "T1634C", + "C1766T", + "G1886A", + "T2018C", + "C2069T", + "T2081C", + "C2375T", + "T2795C", + "A2861G", + "A2939G", + "A3057C", + "A3248G", + "T3435C", + "G3590C", + "T3977C", + "T4370C", + "C4573T", + "C4716T", + "G4766A", + "T4820C", + "A4859G", + "C4865T", + "C4940T", + "C5114T", + "C5318T", + "A5378G", + "G5600A", + "G5657A", + "A5675G", + "T5882C", + "T6380C", + "T6732C", + "G6734A", + "T6806C", + "T6809C", + "C6896T", + "G7094A", + "C7349T", + "C7427T", + "C7493T", + "C7573T", + "A7595G", + "A7682G", + "C7694A", + "A8349C", + "G8679A", + "G9038A", + "C9095T", + "C9236T", + "A9284G", + "T9899C" + ] + } + } }, - "labels": { - "aa": "C: V111A; E: A162V, A481V; NS3: V146I; NS4A: T15A; NS5: I530M" + { + "name": "MZ976860.1|2020-08-03", + "node_attrs": { + "div": 0.296, + "country": { + "value": "Cambodia" + }, + "clade_membership": { + "value": "4I_A.1.1" + } + }, + "branch_attrs": { + "mutations": { + "nuc": [ + "C203A", + "T433C", + "T551C", + "C560T", + "G578A", + "G707A", + "C830T", + "C1423T", + "G1643A", + "C1673T", + "C1733T", + "T1751C", + "A1883G", + "G1919A", + "C2380T", + "T3092C", + "C3563T", + "A3845G", + "T4109C", + "G4250A", + "T4625A", + "C4919T", + "A4955G", + "G4959A", + "T4964C", + "C4970T", + "T5354C", + "T5741C", + "T5846C", + "T6149C", + "C6365T", + "A6420G", + "T6662C", + "A7031G", + "G7196A", + "G7559A", + "G7619A", + "C7721T", + "C7955T", + "A8159G", + "C8390T", + "C8603T", + "C8849T", + "A9152G", + "T9401C", + "C9596T", + "C9701T", + "T9716C" + ] + } + } } - } + ] } ] } @@ -24047,9 +20545,9 @@ ] }, { - "name": "NODE_0000096", + "name": "NODE_0000111", "node_attrs": { - "div": 0.28542127999999994, + "div": 0.285, "clade_membership": { "value": "4I_A.1" } @@ -24074,26 +20572,14 @@ "T8177C", "C8441T", "T8669C" - ], - "E": [ - "H494R" - ], - "NS1": [ - "E146D" ] - }, - "labels": { - "aa": "E: H494R; NS1: E146D" } }, "children": [ { "name": "KP792537.2|2011-06", "node_attrs": { - "div": 0.28822260999999993, - "country": { - "value": "Singapore" - }, + "div": 0.288, "clade_membership": { "value": "4I_A.1" } @@ -24132,26 +20618,14 @@ "A9488G", "G9533A", "G10085A" - ], - "E": [ - "V482I" - ], - "M": [ - "E85Q" - ], - "NS4B": [ - "M84L" ] - }, - "labels": { - "aa": "E: V482I; M: E85Q; NS4B: M84L" } } }, { - "name": "NODE_0000097", + "name": "NODE_0000112", "node_attrs": { - "div": 0.28990285999999993, + "div": 0.29, "clade_membership": { "value": "4I_A.1.2" } @@ -24198,17 +20672,9 @@ "A9809G", "A9881G", "T10154C" - ], - "NS1": [ - "H293L" - ], - "NS5": [ - "H201Y", - "I409M" ] }, "labels": { - "aa": "NS1: H293L; NS5: H201Y, I409M", "lineage": "4I_A.1.2" } }, @@ -24216,7 +20682,7 @@ { "name": "MN018394.1|2015-10-03", "node_attrs": { - "div": 0.3010547599999999, + "div": 0.301, "country": { "value": "China" }, @@ -24337,73 +20803,14 @@ "C9890G", "T9895G", "A10226G" - ], - "C": [ - "L56P", - "P60A", - "T61I", - "I64S", - "Q70K" - ], - "E": [ - "G159R", - "D375L" - ], - "M": [ - "Y142H" - ], - "NS1": [ - "A121R", - "C280S", - "G282P", - "T283V" - ], - "NS2A": [ - "I177V" - ], - "NS3": [ - "M42T", - "R170K", - "F265I", - "Y509F", - "A510G" - ], - "NS4A": [ - "A63R", - "T65G", - "A66S", - "G67T" - ], - "NS4B": [ - "A18V" - ], - "NS5": [ - "V77A", - "V78M", - "E158V", - "G159W", - "R160S", - "T161P", - "G369R", - "N502T", - "K657V", - "M659K", - "A660V", - "W763X", - "L775F", - "A776T", - "M778R" ] - }, - "labels": { - "aa": "C: L56P, P60A, T61I, I64S, Q70K; E: G159R, D375L; M: Y142H; NS1: A121R, C280S, G282P, T283V; NS2A: I177V; NS3: M42T, R170K, F265I, Y509F, A510G; NS4A: A63R, T65G, A66S, G67T; NS4B: A18V; NS5: V77A, V78M, E158V, G159W, R160S, T161P, G369R, N502T, K657V, M659K, A660V, W763X, L775F, A776T, M778R" } } }, { - "name": "NODE_0000098", + "name": "NODE_0000113", "node_attrs": { - "div": 0.2901036699999999, + "div": 0.29, "clade_membership": { "value": "4I_A.1.2" } @@ -24416,22 +20823,16 @@ "A5957G", "G6377A", "T8231C" - ], - "NS3": [ - "I190V" ] - }, - "labels": { - "aa": "NS3: I190V" } }, "children": [ { "name": "OQ427041.1|2019-01-07", "node_attrs": { - "div": 0.29395418999999995, + "div": 0.294, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.2" @@ -24479,36 +20880,14 @@ "G9788A", "G9827A", "T9899C" - ], - "C": [ - "S38F" - ], - "NS1": [ - "S141P" - ], - "NS2A": [ - "T4A" - ], - "NS3": [ - "L434S" - ], - "NS4B": [ - "L49M" - ], - "NS5": [ - "V66A", - "K389R" ] - }, - "labels": { - "aa": "C: S38F; NS1: S141P; NS2A: T4A; NS3: L434S; NS4B: L49M; NS5: V66A, K389R" } } }, { - "name": "NODE_0000099", + "name": "NODE_0000114", "node_attrs": { - "div": 0.29049880999999994, + "div": 0.29, "clade_membership": { "value": "4I_A.1.2" } @@ -24527,9 +20906,9 @@ { "name": "OQ427062.1|2018-12-25", "node_attrs": { - "div": 0.29375884999999996, + "div": 0.294, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.2" @@ -24571,27 +20950,14 @@ "A9455G", "C9587T", "T10055G" - ], - "M": [ - "A73T" - ], - "NS2A": [ - "I167V", - "A215T" - ], - "NS2B": [ - "M123V" ] - }, - "labels": { - "aa": "M: A73T; NS2A: I167V, A215T; NS2B: M123V" } } }, { - "name": "NODE_0000100", + "name": "NODE_0000115", "node_attrs": { - "div": 0.2933564799999999, + "div": 0.293, "clade_membership": { "value": "4I_A.1.2" } @@ -24628,41 +20994,16 @@ "A9644G", "C10232T", "T10243A" - ], - "C": [ - "M45V" - ], - "E": [ - "V140A" - ], - "M": [ - "I31V" - ], - "NS1": [ - "H84Y" - ], - "NS2A": [ - "A101V" - ], - "NS5": [ - "S19L", - "T98A", - "A440T", - "I530M", - "F894Y" ] - }, - "labels": { - "aa": "C: M45V; E: V140A; M: I31V; NS1: H84Y; NS2A: A101V; NS5: S19L, T98A, A440T, I530M, F894Y" } }, "children": [ { "name": "OQ427047.1|2019-01-15", "node_attrs": { - "div": 0.2933574799999999, + "div": 0.293, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.2" @@ -24675,9 +21016,9 @@ { "name": "OQ427046.1|2019-01-15", "node_attrs": { - "div": 0.2933574799999999, + "div": 0.293, "country": { - "value": "Vietnam" + "value": "Viet Nam" }, "clade_membership": { "value": "4I_A.1.2" @@ -24721,4 +21062,4 @@ } ] } -} +} \ No newline at end of file