Merge pull request #289 from nextstrain/new-clades

Add new clades to phylogenetic
nextstrain · Nov 14, 2024 · 2f88ddb · 2f88ddb
2 parents 64a7476 + 28cbe69
commit 2f88ddb
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Showing 14 changed files with 301 additions and 8 deletions.
diff --git a/nextclade/resources/all-clades/clades.tsv b/nextclade/resources/all-clades/clades.tsv
@@ -73,6 +73,19 @@ C.1.1	clade	C.1
 C.1.1	nuc	21062	T
 C.1.1	nuc	149963	T
 
+E.1	clade	C.1.1
+E.1	nuc	13563	A
+E.1	nuc	121394	T
+E.1	nuc	162280	A
+
+E.2	clade	C.1.1
+E.2	nuc	13563	A
+E.2	nuc	151847	A
+E.2	nuc	37738	T
+
+E.3	clade	C.1.1
+E.3	nuc	142797	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -82,6 +95,12 @@ B.1.5	nuc	70780	T
 B.1.6	clade	B.1
 B.1.6	nuc	111029	A
 
+D.1	clade	B.1.6
+D.1	nuc	10945	A
+D.1	nuc	39515	A
+D.1	nuc	44627	T
+D.1	nuc	56276	A
+
 B.1.7	clade	B.1
 B.1.7	nuc	25644	T
 
@@ -136,10 +155,46 @@ B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
 B.1.20	nuc	187620	T
 
+F.1	clade	B.1.20
+F.1	nuc	11668	A
+F.1	nuc	35132	A
+F.1	nuc	70414	T
+F.1	nuc	70666	T
+F.1	nuc	96938	T
+
+F.2	clade	B.1.20
+F.2	nuc	161629	A
+F.2	nuc	22167	T
+
+F.3	clade	B.1.20
+F.3	nuc	174050	T
+F.3	nuc	180618	T
+
+F.4	clade	B.1.20
+F.4	nuc	34277	T
+F.4	nuc	92382	T
+F.4	nuc	122551	T
+F.4	nuc	126919	A
+F.4	nuc	176643	A
+
+F.5	clade	B.1.20
+F.5	nuc	150831	T
+F.5	nuc	126169	A
+
+F.6	clade	B.1.20
+F.6	nuc	146690	A
+F.6	nuc	159608	T
+F.6	nuc	168964	A
+
 B.1.21	clade	B.1
 B.1.21	nuc	22415	A
 B.1.21	nuc	132698	T
 
 B.1.22	clade	B.1
 B.1.22	nuc	34784	T
 B.1.22	nuc	101418	T
+
+B.1.23	clade	B.1
+B.1.23	nuc	27935	A
+B.1.23	nuc	64171	G
+B.1.23	nuc	73235	T
diff --git a/nextclade/resources/all-clades/include_accessions.txt b/nextclade/resources/all-clades/include_accessions.txt
@@ -7,6 +7,7 @@ MK783033    #reference for A.3
 ON674051    #reference for A.2
 ON676707    #reference for A.2
 ON675438    #reference for A.2
+OP612690    #reference for A.2
 ON676707    #reference for A.2.3
 OP555515    #reference for A.2.3
 OP450997    #reference for A.2.2

diff --git a/nextclade/resources/clade-iib/clades.tsv b/nextclade/resources/clade-iib/clades.tsv
@@ -56,6 +56,19 @@ C.1.1	clade	C.1
 C.1.1	nuc	21062	T
 C.1.1	nuc	149963	T
 
+E.1	clade	C.1.1
+E.1	nuc	13563	A
+E.1	nuc	121394	T
+E.1	nuc	162280	A
+
+E.2	clade	C.1.1
+E.2	nuc	13563	A
+E.2	nuc	151847	A
+E.2	nuc	37738	T
+
+E.3	clade	C.1.1
+E.3	nuc	142797	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -65,6 +78,12 @@ B.1.5	nuc	70780	T
 B.1.6	clade	B.1
 B.1.6	nuc	111029	A
 
+D.1	clade	B.1.6
+D.1	nuc	10945	A
+D.1	nuc	39515	A
+D.1	nuc	44627	T
+D.1	nuc	56276	A
+
 B.1.7	clade	B.1
 B.1.7	nuc	25644	T
 
@@ -119,10 +138,46 @@ B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
 B.1.20	nuc	187620	T
 
+F.1	clade	B.1.20
+F.1	nuc	11668	A
+F.1	nuc	35132	A
+F.1	nuc	70414	T
+F.1	nuc	70666	T
+F.1	nuc	96938	T
+
+F.2	clade	B.1.20
+F.2	nuc	161629	A
+F.2	nuc	22167	T
+
+F.3	clade	B.1.20
+F.3	nuc	174050	T
+F.3	nuc	180618	T
+
+F.4	clade	B.1.20
+F.4	nuc	34277	T
+F.4	nuc	92382	T
+F.4	nuc	122551	T
+F.4	nuc	126919	A
+F.4	nuc	176643	A
+
+F.5	clade	B.1.20
+F.5	nuc	150831	T
+F.5	nuc	126169	A
+
+F.6	clade	B.1.20
+F.6	nuc	146690	A
+F.6	nuc	159608	T
+F.6	nuc	168964	A
+
 B.1.21	clade	B.1
 B.1.21	nuc	22415	A
 B.1.21	nuc	132698	T
 
 B.1.22	clade	B.1
 B.1.22	nuc	34784	T
 B.1.22	nuc	101418	T
+
+B.1.23	clade	B.1
+B.1.23	nuc	27935	A
+B.1.23	nuc	64171	G
+B.1.23	nuc	73235	T
diff --git a/nextclade/resources/clade-iib/include_accessions.txt b/nextclade/resources/clade-iib/include_accessions.txt
@@ -8,6 +8,7 @@ MK783033    #reference for A.3
 ON674051    #reference for A.2
 ON676707    #reference for A.2
 ON675438    #reference for A.2
+OP612690    #reference for A.2
 ON676707    #reference for A.2.3
 OP555515    #reference for A.2.3
 OP450997    #reference for A.2.2

diff --git a/nextclade/resources/color_ordering.tsv b/nextclade/resources/color_ordering.tsv
@@ -239,9 +239,13 @@ lineage	B.1.2
 lineage	B.1.3
 lineage	C.1
 lineage	C.1.1
+lineage	E.1
+lineage	E.2
+lineage	E.3
 lineage	B.1.4
 lineage	B.1.5
 lineage	B.1.6
+lineage	D.1
 lineage	B.1.7
 lineage	B.1.8
 lineage	B.1.9
@@ -256,8 +260,15 @@ lineage	B.1.17
 lineage	B.1.18
 lineage	B.1.19
 lineage	B.1.20
+lineage	F.1
+lineage	F.2
+lineage	F.3
+lineage	F.4
+lineage	F.5
+lineage	F.6
 lineage	B.1.21
 lineage	B.1.22
+lineage	B.1.23
 lineage	A.2
 lineage	A.2.1
 lineage	A.2.2

diff --git a/nextclade/resources/include_accessions.txt b/nextclade/resources/include_accessions.txt
@@ -28,6 +28,20 @@ OQ320441    #reference for B.1.20
 OP539939    #reference for B.1.21
 OQ773522    #reference for B.1.22
 OR095023    #reference for B.1.22
+PP754993    #reference for B.1.23
+PQ036000    #reference for B.1.23
 LC753968    #reference for C.1
 LC753968    #reference for C.1.1
 OR643705    #reference for C.1.1
+OR804476    #reference for C.1.1
+OQ503831    #reference for D.1
+OR804499    #reference for E.1
+OR487983    #reference for E.2
+OR326991    #reference for E.3
+PP533295    #reference for F.1
+PQ160003    #reference for F.2
+OR473623    #reference for F.3
+PP556326    #reference for F.4
+PQ160004    #reference for F.5
+PP533312    #reference for F.5
+OR665162    #reference for F.6
diff --git a/nextclade/resources/lineage-b.1/clades.tsv b/nextclade/resources/lineage-b.1/clades.tsv
@@ -28,6 +28,19 @@ C.1.1	clade	C.1
 C.1.1	nuc	21062	T
 C.1.1	nuc	149963	T
 
+E.1	clade	C.1.1
+E.1	nuc	13563	A
+E.1	nuc	121394	T
+E.1	nuc	162280	A
+
+E.2	clade	C.1.1
+E.2	nuc	13563	A
+E.2	nuc	151847	A
+E.2	nuc	37738	T
+
+E.3	clade	C.1.1
+E.3	nuc	142797	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -37,6 +50,12 @@ B.1.5	nuc	70780	T
 B.1.6	clade	B.1
 B.1.6	nuc	111029	A
 
+D.1	clade	B.1.6
+D.1	nuc	10945	A
+D.1	nuc	39515	A
+D.1	nuc	44627	T
+D.1	nuc	56276	A
+
 B.1.7	clade	B.1
 B.1.7	nuc	25644	T
 
@@ -91,10 +110,46 @@ B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
 B.1.20	nuc	187620	T
 
+F.1	clade	B.1.20
+F.1	nuc	11668	A
+F.1	nuc	35132	A
+F.1	nuc	70414	T
+F.1	nuc	70666	T
+F.1	nuc	96938	T
+
+F.2	clade	B.1.20
+F.2	nuc	161629	A
+F.2	nuc	22167	T
+
+F.3	clade	B.1.20
+F.3	nuc	174050	T
+F.3	nuc	180618	T
+
+F.4	clade	B.1.20
+F.4	nuc	34277	T
+F.4	nuc	92382	T
+F.4	nuc	122551	T
+F.4	nuc	126919	A
+F.4	nuc	176643	A
+
+F.5	clade	B.1.20
+F.5	nuc	150831	T
+F.5	nuc	126169	A
+
+F.6	clade	B.1.20
+F.6	nuc	146690	A
+F.6	nuc	159608	T
+F.6	nuc	168964	A
+
 B.1.21	clade	B.1
 B.1.21	nuc	22415	A
 B.1.21	nuc	132698	T
 
 B.1.22	clade	B.1
 B.1.22	nuc	34784	T
 B.1.22	nuc	101418	T
+
+B.1.23	clade	B.1
+B.1.23	nuc	27935	A
+B.1.23	nuc	64171	G
+B.1.23	nuc	73235	T
diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml
@@ -36,9 +36,15 @@ subsample:
       - B.1.1
       - B.1.2
       - B.1.3
+      - C.1
+      - C.1.1
+      - E.1
+      - E.2
+      - E.3
       - B.1.4
       - B.1.5
       - B.1.6
+      - D.1
       - B.1.7
       - B.1.8
       - B.1.9
@@ -53,10 +59,15 @@ subsample:
       - B.1.18
       - B.1.19
       - B.1.20
+      - F.1
+      - F.2
+      - F.3
+      - F.4
+      - F.5
+      - F.6
       - B.1.21
       - B.1.22
-      - C.1
-      - C.1.1
+      - B.1.23
   b1:
     group_by: "--group-by country year"
     sequences_per_group: "--subsample-max-sequences 100"
-Original file line number
+Diff line change
@@ Expand Up / @@ -36,9 +36,15 @@ subsample: @@
           - B.1.1
           - B.1.2
           - B.1.3
+          - C.1
+          - C.1.1
+          - E.1
+          - E.2
+          - E.3
           - B.1.4
           - B.1.5
           - B.1.6
+          - D.1
           - B.1.7
           - B.1.8
           - B.1.9
@@ Expand All / @@ -53,10 +59,15 @@ subsample: @@
           - B.1.18
           - B.1.19
           - B.1.20
+          - F.1
+          - F.2
+          - F.3
+          - F.4
+          - F.5
+          - F.6
           - B.1.21
           - B.1.22
-          - C.1
-          - C.1.1
+          - B.1.23
       b1:
         group_by: "--group-by country year"
         sequences_per_group: "--subsample-max-sequences 100"
@@ Expand Down @@