From 69be2905de137333e7c5ca7fa0881cee20f6a05d Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Sat, 14 Dec 2024 15:21:30 +0100 Subject: [PATCH 1/2] flu: add new subclade proposals --- data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md | 3 +++ data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json | 2 +- data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md | 3 +++ data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json | 2 +- data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md | 3 +++ data/nextstrain/flu/h3n2/ha/CY163680/tree.json | 2 +- data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md | 3 +++ data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json | 2 +- 8 files changed, 16 insertions(+), 4 deletions(-) diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md index 5d77e3ab..5da5bb92 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md @@ -1,3 +1,6 @@ +## Unreleased + - include subclade proposals for C.1.9.a/b/c + ## 2024-11-27T02:51:00Z - update reference trees diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json index 84007b41..69c25c55 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h1n1pdm segment:ha with root CY121680 built on 2024-11-23", "updated": "2024-11-23", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": [{"name": "GISAID"}], "maintainers": [{"name": "Nextstrain team", "url": "https://nextstrain.org"}], "display_defaults": {"color_by": "subclade", "distance_measure": "div", "branch_label": "subclade"}, "genome_annotations": {"HA1": {"end": 1052, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 72, "strand": "+", "type": "gene"}, "HA2": {"end": 1718, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 71, "seqid": "dataset_config/h1n1pdm/ha/CY121680/annotation.gff", "start": 21, "strand": "+", "type": "gene"}, "nuc": {"end": 1752, "start": 1, "strand": "+", "type": "source"}}, "colorings": [{"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "type": "categorical"}, {"key": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "short-clade", "title": "short-clade", "type": "categorical"}, {"key": "strain", "title": "strain", "type": "categorical"}, {"key": "region", "title": "Region", "type": "categorical", "scale": [["China", "#4042C7"], ["Southeast Asia", "#4274CE"], ["South Asia", "#5199B7"], ["Japan Korea", "#69B091"], ["Oceania", "#88BB6C"], ["West Asia", "#ADBD51"], ["Africa", "#CEB541"], ["Europe", "#E39B39"], ["South America", "#E56C2F"], ["North America", "#DC2F24"]]}, {"key": "country", "title": "Country", "type": "categorical"}, {"key": "date", "title": "Sample Date", "type": "ordinal"}, {"key": "gisaid_epi_isl", "title": "gisaid_epi_isl", "type": "categorical"}, {"key": "accession_ha", "title": "accession_ha", "type": "categorical"}], "filters": ["region", "country", "clade_membership", "subclade"], "panels": ["tree", "entropy"], "extensions": {"nextclade": {"clade_node_attrs": [{"name": "short-clade", "displayName": "short-clade", "description": ""}, {"name": "subclade", "displayName": "Subclade", "description": "Experimental fine-grained subclade annotation."}, {"name": "proposedSubclade", "displayName": "Proposed subclade", "description": "Includes proposals of new subclades. 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{}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md index 2a3eaded..3a4229d6 100644 --- a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md @@ -1,3 +1,6 @@ +## Unreleased + - include subclade proposals for J.2.a/b/c + ## 2024-11-27T02:51:00Z - update reference trees diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json index abfb6592..4b5882c5 100644 --- a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json +++ b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h3n2 segment:ha with root CY163680 built on 2024-11-23", "updated": "2024-11-23", "build_url": "https://github.com/nextstrain/seasonal-flu", "data_provenance": 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{"mutations": {}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md index 46a6e639..d770d075 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md @@ -1,3 +1,6 @@ +## Unreleased + - include subclade proposals for J.2.a/b/c + ## 2024-11-27T02:51:00Z - update reference trees diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json index 9017ed5f..de09d60e 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h3n2 segment:ha with root EPI1857216 built on 2024-11-23", "updated": "2024-11-23", 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{}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file From d4d44612a630731d78816c4872b017d0848ca676 Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Sat, 14 Dec 2024 14:23:24 +0000 Subject: [PATCH 2/2] chore: rebuild [skip ci] --- data_output/index.json | 60 +- .../ha/CY121680/unreleased/CHANGELOG.md | 34 + .../h1n1pdm/ha/CY121680/unreleased/README.md | 40 + .../ha/CY121680/unreleased/dataset.zip | Bin 0 -> 1206083 bytes .../unreleased/genome_annotation.gff3 | 5 + .../ha/CY121680/unreleased/pathogen.json | 126 ++ .../ha/CY121680/unreleased/reference.fasta | 2 + .../ha/CY121680/unreleased/sequences.fasta | 1550 +++++++++++++++++ .../h1n1pdm/ha/CY121680/unreleased/tree.json | 1 + .../ha/MW626062/unreleased/CHANGELOG.md | 36 + .../h1n1pdm/ha/MW626062/unreleased/README.md | 37 + .../ha/MW626062/unreleased/dataset.zip | Bin 0 -> 1188770 bytes .../unreleased/genome_annotation.gff3 | 5 + .../ha/MW626062/unreleased/pathogen.json | 128 ++ .../ha/MW626062/unreleased/reference.fasta | 27 + .../ha/MW626062/unreleased/sequences.fasta | 1550 +++++++++++++++++ .../h1n1pdm/ha/MW626062/unreleased/tree.json | 1 + .../h3n2/ha/CY163680/unreleased/CHANGELOG.md | 46 + .../flu/h3n2/ha/CY163680/unreleased/README.md | 37 + .../h3n2/ha/CY163680/unreleased/dataset.zip | Bin 0 -> 1410314 bytes .../unreleased/genome_annotation.gff3 | 5 + .../h3n2/ha/CY163680/unreleased/pathogen.json | 126 ++ .../ha/CY163680/unreleased/reference.fasta | 26 + .../ha/CY163680/unreleased/sequences.fasta | 1500 ++++++++++++++++ .../flu/h3n2/ha/CY163680/unreleased/tree.json | 1 + .../ha/EPI1857216/unreleased/CHANGELOG.md | 50 + .../h3n2/ha/EPI1857216/unreleased/README.md | 37 + .../h3n2/ha/EPI1857216/unreleased/dataset.zip | Bin 0 -> 1515676 bytes .../unreleased/genome_annotation.gff3 | 5 + .../ha/EPI1857216/unreleased/pathogen.json | 174 ++ .../ha/EPI1857216/unreleased/reference.fasta | 23 + .../ha/EPI1857216/unreleased/sequences.fasta | 1500 ++++++++++++++++ .../h3n2/ha/EPI1857216/unreleased/tree.json | 1 + 33 files changed, 7115 insertions(+), 18 deletions(-) create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3 create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/tree.json create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/genome_annotation.gff3 create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta create mode 100644 data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/genome_annotation.gff3 create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/sequences.fasta create mode 100644 data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/tree.json create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/genome_annotation.gff3 create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta create mode 100644 data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/tree.json diff --git a/data_output/index.json b/data_output/index.json index 3f9082e4..0b0058ec 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -885,7 +885,7 @@ "customClades": { "short-clade": 16, "subclade": 22, - "proposedSubclade": 22 + "proposedSubclade": 25 }, "qc": [ "privateMutations", @@ -898,6 +898,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-27T02:51:00Z", "tag": "2024-11-27--02-51-00Z", @@ -940,8 +947,7 @@ } ], "version": { - "updatedAt": "2024-11-27T02:51:00Z", - "tag": "2024-11-27--02-51-00Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -998,7 +1004,7 @@ "customClades": { "short-clade": 16, "subclade": 22, - "proposedSubclade": 22 + "proposedSubclade": 25 }, "qc": [ "privateMutations", @@ -1011,6 +1017,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-27T02:51:00Z", "tag": "2024-11-27--02-51-00Z", @@ -1053,8 +1066,7 @@ } ], "version": { - "updatedAt": "2024-11-27T02:51:00Z", - "tag": "2024-11-27--02-51-00Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -1207,11 +1219,11 @@ "treeJson": "tree.json" }, "capabilities": { - "clades": 37, + "clades": 36, "customClades": { - "subclade": 45, - "short-clade": 37, - "proposedSubclade": 45 + "subclade": 44, + "short-clade": 36, + "proposedSubclade": 47 }, "qc": [ "privateMutations", @@ -1224,6 +1236,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-27T02:51:00Z", "tag": "2024-11-27--02-51-00Z", @@ -1274,8 +1293,7 @@ } ], "version": { - "updatedAt": "2024-11-27T02:51:00Z", - "tag": "2024-11-27--02-51-00Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -1328,11 +1346,11 @@ "treeJson": "tree.json" }, "capabilities": { - "clades": 37, + "clades": 36, "customClades": { - "subclade": 45, - "short-clade": 37, - "proposedSubclade": 45 + "subclade": 44, + "short-clade": 36, + "proposedSubclade": 47 }, "qc": [ "privateMutations", @@ -1346,6 +1364,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-27T02:51:00Z", "tag": "2024-11-27--02-51-00Z", @@ -1404,8 +1429,7 @@ } ], "version": { - "updatedAt": "2024-11-27T02:51:00Z", - "tag": "2024-11-27--02-51-00Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md new file mode 100644 index 00000000..5da5bb92 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md @@ -0,0 +1,34 @@ +## Unreleased + - include subclade proposals for C.1.9.a/b/c + +## 2024-11-27T02:51:00Z + + - update reference trees + - include subclade D.5 (included as proposed clades on 2024-11-05) + +## 2024-11-05T09:19:52Z + + - update reference trees + - include subclade proposals + +## 2024-07-03T08:29:55Z + + - add representative samples from early pandemic-era clades including 1, 2, 3, 4, 6C, 7, and 8 to improve clade label annotations for older sequences + + - added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. See Nextclade documentation for more details about 'relative mutations' functionality. + +## 2024-04-19T07:50:39Z + + - aliasing of C.1.1.1 as D + - addition of subclades D.1 - D.4: [D.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.1.yml), [D.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.2.yml), [D.3](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.3.yml), [D.4](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.4.yml) + - addition of subclades [C.1.8](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.8.yml) and [C.1.9](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.9.yml) + - addition of subclades [C.1.7.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.1.yml) and [C.1.7.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.2.yml) + + +## 2024-01-16T20:31:02Z + +Initial release for Nextclade v3! + + - addition of subclade [C.1.7](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.yml) + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md new file mode 100644 index 00000000..dff32cdf --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/README.md @@ -0,0 +1,40 @@ +# Influenza A(H1N1pdm) HA based on reference "A/California/07/2009" + +| Key | Value | +| -------------------- | -------------------- | +| authors | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) | +| name | Influenza A(H1N1pdm) HA | +| reference | A/California/07/2009 | +| dataset path | flu/h1n1pdm/ha/CY121680 | +| reference accession | CY121680 | +| clade definitions | [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/) | + + +## Scope of this dataset +This dataset uses an older reference sequence (A/California/07/2009) and recent sequences will differ at a large number of positions from this reference. +For the analysis of currently circulating viruses, the dataset using A/Wisconsin/588/2019 as reference might be more appropriate. + +## Features +This dataset supports + + * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/) + * Identification of glycosilation motifs + * Sequence QC + * Phylogenetic placement + +## Clades of seasonal influenza viruses + +The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses. +Clade demarcation do not always coincide with significantly different antigenic properties of the viruses. +Clade names are structured as _Number-Letter_ binomials separated by periods as in `6B.1A.5a.2a.1`. These sometimes get shortened by omission of leading binomials like `5a.2a.1`. + +In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups. +These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `C.1.2`. +The leading letter is an alias of a previous name. +Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/). + + + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/dataset.zip new file mode 100644 index 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a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json new file mode 100644 index 00000000..3063dca1 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json @@ -0,0 +1,126 @@ +{ + "schemaVersion": "3.0.0", + "alignmentParams": { + "excessBandwidth": 9, + "terminalBandwidth": 100, + "allowedMismatches": 4, + "gapAlignmentSide": "right", + "minSeedCover": 0.1 + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "defaultCds": "HA1", + "files": { + "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "qc": { + "privateMutations": { + "enabled": true, + "typical": 5, + "cutoff": 15, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "missingData": { + "enabled": false, + "missingDataThreshold": 100, + "scoreBias": 10 + }, + "snpClusters": { + "enabled": false, + "windowSize": 100, + "clusterCutOff": 5, + "scoreWeight": 50 + }, + "mixedSites": { + "enabled": true, + "mixedSitesThreshold": 4 + }, + "frameShifts": { + "enabled": true + }, + "stopCodons": { + "enabled": true, + "ignoredStopCodons": [] + } + }, + "cdsOrderPreference": [ + "HA1", + "HA2" + ], + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/seasonal-flu" + ], + "source code": [ + "https://github.com/nextstrain/seasonal_flu" + ], + "issues": [ + "https://github.com/nextstrain/seasonal_flu/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "nucMutLabelMap": {}, + "nucMutLabelMapReverse": {}, + "shortcuts": [ + "flu_h1n1pdm_ha_broad", + "nextstrain/flu/h1n1pdm/ha/california-7-2009" + ], + "aaMotifs": [ + { + "name": "glycosylation", + "nameShort": "Glyc.", + "nameFriendly": "Glycosylation", + "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", + "includeCdses": [ + { + "cds": "HA1", + "ranges": [] + }, + { + "cds": "HA2", + "ranges": [ + { + "begin": 0, + "end": 186 + } + ] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ], + "attributes": { + "name": "Influenza A H1N1pdm HA", + "segment": "ha", + "reference accession": "CY121680", + "reference name": "A/California/7/2009-egg" + }, + "version": { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } +} diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta new file mode 100644 index 00000000..a3b664be --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/reference.fasta @@ -0,0 +1,2 @@ +>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds +GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta new file mode 100644 index 00000000..7e2eb2df --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta @@ -0,0 +1,1550 @@ +>A/Connecticut/54/2022 +ggaaaacaaaagcaacaaaaatgaaggcaatactagtagttatgctgtatacatttacaa +ccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtgg +acacagtactagaaaagaatgtaacagtaacacactctgtcaatcttctagaagacaagc +ataacggaaaactatgcaaactaagaggggtagccccattgcatttgggtcaatgtaaca +ttgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagatcatggt +cctacattgtggaaacatctaattcagacaatggaacgtgttacccaggagatttcatca +attatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgaaatat +tccccaagacaagttcatggcctaatcatgactcggacaatggtgtaacggcagcatgtt +ctcacgctggagcaaggagcttctacaaaaacttgatatggctggttaaaaaaggaaaat +cgtacccaaagattaaccaaacctacattaatgataaagggaaagaagtcctcgtgctgt 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{"value": "Usa"}, "gisaid_epi_isl": {"value": "EPI_ISL_19519515"}, "date": {"value": "2024-10-02"}, "proposedSubclade": {"value": "C.1.9.c"}}, "branch_attrs": {"mutations": {"nuc": ["C1659T"]}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md new file mode 100644 index 00000000..0693cc01 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md @@ -0,0 +1,36 @@ +## Unreleased + - include subclade proposals for C.1.9.a/b/c + +## 2024-11-27T02:51:00Z + + - update reference trees + - include subclade D.5 (included as proposed clades on 2024-11-05) + +## 2024-11-05T09:19:52Z + + - update reference trees + - include subclade proposals + +## 2024-07-03T08:29:55Z + +Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. + +The datasets themselves remain unchanged. + +See Nextclade documentation for more details about 'relative mutations' functionality. + +## 2024-04-19T07:50:39Z + + - aliasing of C.1.1.1 as D + - addition of subclades D.1 - D.4: [D.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.1.yml), [D.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.2.yml), [D.3](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.3.yml), [D.4](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/D.4.yml) + - addition of subclades [C.1.8](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.8.yml) and [C.1.9](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.9.yml) + - addition of subclades [C.1.7.1](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.1.yml) and [C.1.7.2](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.2.yml) + + +## 2024-01-16T20:31:02Z + +Initial release for Nextclade v3! + + - addition of subclade [C.1.7](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/blob/main/subclades/C.1.7.yml) + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md new file mode 100644 index 00000000..9c589a21 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/README.md @@ -0,0 +1,37 @@ +# Influenza A(H1N1pdm) HA based on reference "A/Wisconsin/588/2019" + +| Key | Value | +| -------------------- | -------------------- | +| authors | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) | +| name | Influenza A(H1N1pdm) HA | +| reference | A/Wisconsin/588/2019 | +| dataset path | flu/h1n1pdm/ha/MW626062 | +| reference accession | MW626062 | +| clade definitions | [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/) | + +# Scope of this dataset +This dataset uses a recent reference sequence (A/Wisconsin/588/2019) and is suitable for the analysis of currently circulating viruses. + + +## Features +This dataset supports + + * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/) + * Identification of glycosilation motifs + * Sequence QC + * Phylogenetic placement + +## Clades of seasonal influenza viruses + +The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses. +Clade demarcation do not always coincide with significantly different antigenic properties of the viruses. +Clade names are structured as _Number-Letter_ binomials separated by periods as in `6B.1A.5a.2a.1`. These sometimes get shortened by omission of leading binomials like `5a.2a.1`. + +In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups. +These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `C.1.2`. +The leading letter is an alias of a previous name. +Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H1N1pdm_HA/). + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/dataset.zip new file mode 100644 index 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00000000..825fe437 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/genome_annotation.gff3 @@ -0,0 +1,5 @@ +##gff-version 3 +##sequence-region MW626062.1 1 1752 +MW626062.1 feature gene 21 71 . + . gene_name="SigPep" +MW626062.1 feature gene 72 1052 . + . gene_name="HA1" +MW626062.1 feature gene 1053 1718 . + . gene_name="HA2" diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json new file mode 100644 index 00000000..b8379077 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json @@ -0,0 +1,128 @@ +{ + "schemaVersion": "3.0.0", + "alignmentParams": { + "excessBandwidth": 9, + "terminalBandwidth": 100, + "allowedMismatches": 4, + "gapAlignmentSide": "right", + "minSeedCover": 0.1 + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "defaultCds": "HA1", + "files": { + "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "qc": { + "privateMutations": { + "enabled": true, + "typical": 5, + "cutoff": 15, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "missingData": { + "enabled": false, + "missingDataThreshold": 100, + "scoreBias": 10 + }, + "snpClusters": { + "enabled": false, + "windowSize": 100, + "clusterCutOff": 5, + "scoreWeight": 50 + }, + "mixedSites": { + "enabled": true, + "mixedSitesThreshold": 4 + }, + "frameShifts": { + "enabled": true + }, + "stopCodons": { + "enabled": true, + "ignoredStopCodons": [] + } + }, + "cdsOrderPreference": [ + "HA1", + "HA2" + ], + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/seasonal-flu" + ], + "source code": [ + "https://github.com/nextstrain/seasonal_flu" + ], + "issues": [ + "https://github.com/nextstrain/seasonal_flu/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "nucMutLabelMap": {}, + "nucMutLabelMapReverse": {}, + "shortcuts": [ + "flu_h1n1pdm_ha", + "nextstrain/flu/h1n1pdm", + "nextstrain/flu/h1n1pdm/ha", + "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019" + ], + "aaMotifs": [ + { + "name": "glycosylation", + "nameShort": "Glyc.", + "nameFriendly": "Glycosylation", + "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", + "includeCdses": [ + { + "cds": "HA1", + "ranges": [] + }, + { + "cds": "HA2", + "ranges": [ + { + "begin": 0, + "end": 186 + } + ] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ], + "attributes": { + "name": "Influenza A H1N1pdm HA", + "segment": "ha", + "reference accession": "MW626062", + "reference name": "A/Wisconsin/588/2019" + }, + "version": { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } +} diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta new file mode 100644 index 00000000..546126e1 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/reference.fasta @@ -0,0 +1,27 @@ +>MW626062.1 Influenza A virus (A/Wisconsin/588/2019(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds +GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTATGCTGTATACATTTACAACCGCAAATGC +AGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTGGACACAGTACTAGAAAAGAAT +GTAACAGTAACACACTCTGTCAATCTTCTGGAAGACAAGCATAACGGAAAACTATGCAAACTAAGAGGGG +TAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACT +CTCCACAGCAAGATCATGGTCCTACATTGTGGAAACATCTAATTCAGACAATGGAACGTGTTACCCAGGA 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{"value": "5a.2a"}, "date": {"value": "2024-02-16"}, "region": {"value": "Europe"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "strain": {"value": "A/France/NAQ-RELAB-HCL024031134901/2024"}, "country": {"value": "France"}, "proposedSubclade": {"value": "C.1.9.b"}, "gisaid_epi_isl": {"value": "EPI_ISL_19011509"}, "accession_ha": {"value": "EPI3153278"}, "subclade": {"value": "C.1.9"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/Valencia/VAHNSI-GIHSN-07_5791/2024", "node_attrs": {"div": 0.0577, "short-clade": {"value": "5a.2a"}, "date": {"value": "2024-01-13"}, "region": {"value": "Europe"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "strain": {"value": "A/Valencia/VAHNSI-GIHSN-07_5791/2024"}, "country": {"value": "Spain"}, "proposedSubclade": {"value": "C.1.9.b"}, "gisaid_epi_isl": {"value": "EPI_ISL_19232060"}, "accession_ha": {"value": "EPI3413449"}, "subclade": {"value": "C.1.9"}}, "branch_attrs": {"mutations": {}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md new file mode 100644 index 00000000..3a4229d6 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md @@ -0,0 +1,46 @@ +## Unreleased + - include subclade proposals for J.2.a/b/c + +## 2024-11-27T02:51:00Z + + - update reference trees + - include subclades J.1.1, J.2.1, J.2.2 (included as proposed clades on 2024-11-05) + +## 2024-11-05T09:19:52Z + + - update reference trees + - include subclade proposals + +## 2024-07-03T08:29:55Z + +Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. + +The datasets themselves remain unchanged. + +See Nextclade documentation for more details about 'relative mutations' functionality. + +## 2024-04-19T07:50:39Z + +Update of the datasets with more recent data. No new clades were added on this occasion. + +## 2024-02-22T16:12:03Z + +After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with `H` have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias `J`. + + - `H` --> `J` + - `H.1` --> `J.1` + - `H.2` --> `J.2` + - `H.3` --> `J.3` + - `H.4` --> `J.4` + +The subclades `H` and `H.*` were revoked, and a comment was added to explain the reason. No subclade definitions were changed. + + +## 2024-01-16T20:31:02Z + +Initial release for Nextclade v3! + + - Addition of subclade H.1, H.2, H.3, and H.4 + - Aliasing of G.1.3.1.1 as subclade H + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md new file mode 100644 index 00000000..59c9a903 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/README.md @@ -0,0 +1,37 @@ +# Influenza A(H3N2) HA dataset based on reference "A/Wisconsin/67/2005" + +| Key | Value | +| -------------------- | -------------------- | +| authors | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) | +| name | Influenza A(H3N2) HA | +| reference | A/Wisconsin/67/2005 | +| dataset path | flu/h3n2/ha/CY163680 | +| reference accession | CY163680 | +| clade definitions | [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/) | + +## Scope of this dataset +This dataset uses an older reference sequence (A/Wisconsin/67/2005) and recent sequences will differ at a large number of positions from this reference. +For the analysis of currently circulating viruses, the dataset using A/Darwin/6/2021 as reference might be more appropriate. + +## Features +This dataset supports + + * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/) + * Identification of glycosilation motifs + * Sequence QC + * Phylogenetic placement + +## Clades of seasonal influenza viruses + +The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses. +Clade demarcation do not always coincide with significantly different antigenic properties of the viruses. +Clade names are structured as _Number-Letter_ binomials (with exceptions) separated by periods as in `3C.2a1b.2a.2a.1a`. These sometimes get shortened by omission of leading binomials like `2a.1`. + +In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups. +These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `G.1.3.1`. +The leading letter is an alias of a previous name. +Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/). + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/dataset.zip new file mode 100644 index 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b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json new file mode 100644 index 00000000..a55f3330 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json @@ -0,0 +1,126 @@ +{ + "schemaVersion": "3.0.0", + "alignmentParams": { + "excessBandwidth": 9, + "terminalBandwidth": 100, + "allowedMismatches": 4, + "gapAlignmentSide": "right", + "minSeedCover": 0.1 + }, + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + }, + "defaultCds": "HA1", + "files": { + "changelog": "CHANGELOG.md", + "examples": "sequences.fasta", + "genomeAnnotation": "genome_annotation.gff3", + "pathogenJson": "pathogen.json", + "readme": "README.md", + "reference": "reference.fasta", + "treeJson": "tree.json" + }, + "qc": { + "privateMutations": { + "enabled": true, + "typical": 5, + "cutoff": 15, + "weightLabeledSubstitutions": 2, + "weightReversionSubstitutions": 1, + "weightUnlabeledSubstitutions": 1 + }, + "missingData": { + "enabled": false, + "missingDataThreshold": 100, + "scoreBias": 10 + }, + "snpClusters": { + "enabled": false, + "windowSize": 100, + "clusterCutOff": 5, + "scoreWeight": 50 + }, + "mixedSites": { + "enabled": true, + "mixedSitesThreshold": 4 + }, + "frameShifts": { + "enabled": true + }, + "stopCodons": { + "enabled": true, + "ignoredStopCodons": [] + } + }, + "cdsOrderPreference": [ + "HA1", + "HA2" + ], + "maintenance": { + "website": [ + "https://nextstrain.org", + "https://clades.nextstrain.org" + ], + "documentation": [ + "https://github.com/nextstrain/seasonal-flu" + ], + "source code": [ + "https://github.com/nextstrain/seasonal_flu" + ], + "issues": [ + "https://github.com/nextstrain/seasonal_flu/issues" + ], + "organizations": [ + "Nextstrain" + ], + "authors": [ + "Nextstrain team " + ] + }, + "nucMutLabelMap": {}, + "nucMutLabelMapReverse": {}, + "shortcuts": [ + "flu_h3n2_ha_broad", + "nextstrain/flu/h3n2/ha/wisconsin-67-2005" + ], + "aaMotifs": [ + { + "name": "glycosylation", + "nameShort": "Glyc.", + "nameFriendly": "Glycosylation", + "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", + "includeCdses": [ + { + "cds": "HA1", + "ranges": [] + }, + { + "cds": "HA2", + "ranges": [ + { + "begin": 0, + "end": 186 + } + ] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ], + "attributes": { + "name": "Influenza A H3N2 HA", + "segment": "ha", + "reference accession": "CY163680", + "reference name": "A/Wisconsin/67/2005-egg" + }, + "version": { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } +} diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta new file mode 100644 index 00000000..a4df05fb --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/reference.fasta @@ -0,0 +1,26 @@ +>CY163680.1 Influenza A virus (A/Wisconsin/67/2005(H3N2)) hemagglutinin 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{"mutations": {}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ No newline at end of file diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md new file mode 100644 index 00000000..d770d075 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md @@ -0,0 +1,50 @@ +## Unreleased + - include subclade proposals for J.2.a/b/c + +## 2024-11-27T02:51:00Z + + - update reference trees + - include subclades J.1.1, J.2.1, J.2.2 (included as proposed clades on 2024-11-05) + +## 2024-11-05T09:19:52Z + + - update reference trees + - include subclade proposals + +## 2024-08-08T05:08:21Z + +Fix numbering of RBD sites it the `pathogen.json`. The relevant positions were indexed 1-based, when they should have been indexed 0-based. + +## 2024-07-03T08:29:55Z + +Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. + +The datasets themselves remain unchanged. + +See Nextclade documentation for more details about 'relative mutations' functionality. + +## 2024-04-19T07:50:39Z + +Update of the datasets with more recent data. No new clades were added on this occasion. + +## 2024-02-22T16:12:03Z + +After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with `H` have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias `J`. + + - `H` --> `J` + - `H.1` --> `J.1` + - `H.2` --> `J.2` + - `H.3` --> `J.3` + - `H.4` --> `J.4` + +The subclades `H` and `H.*` were revoked, and a comment was added to explain the reason. No subclade definitions were changed. + + +## 2024-01-16T20:31:02Z + +Initial release for Nextclade v3! + + - Addition of subclade H.1, H.2, H.3, and H.4 + - Aliasing of G.1.3.1.1 as subclade H + +Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md new file mode 100644 index 00000000..af06f06f --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/README.md @@ -0,0 +1,37 @@ +# Influenza A(H3N2) HA dataset based on reference "A/Darwin/6/2021" + +| Key | Value | +| -------------------- | -------------------- | +| authors | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) | +| name | Influenza A H3N2 HA | +| reference | A/Darwin/6/2021 | +| dataset path | flu/h3n2/ha/EPI1857216 | +| reference accession | EPI1857216 | +| clade definitions | [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/) | + +## Scope of this dataset +This dataset uses a recent reference sequence (A/Darwin/6/2021) and is suitable for the analysis of circulating viruses. + +## Features +This dataset supports + + * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/) + * Identification of glycosilation motifs + * Counting of mutations in the RBD + * Sequence QC + * Phylogenetic placement + +## Clades of seasonal influenza viruses + +The WHO Collaborating centers define "clades" as genetic groups of viruses with signature mutations to facilitate discussion of circulating diversity of the viruses. +Clade demarcation do not always coincide with significantly different antigenic properties of the viruses. +Clade names are structured as _Number-Letter_ binomials (with exceptions) separated by periods as in `3C.2a1b.2a.2a.1a`. These sometimes get shortened by omission of leading binomials like `2a.1`. + +In addition to these clades, "subclades" are defined to break down diversity at higher resolution and allow following the spread of different viral groups. +These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `G.1.3.1`. +The leading letter is an alias of a previous name. +Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/). + +## What is Nextclade dataset + +Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/dataset.zip new file mode 100644 index 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(145, 155, 156, 158, 159, 189, and 193 in HA1)", + "cds": "HA1", + "aaRange": { + "begin": 100, + "end": 200 + }, + "ignore": { + "clades": [ + "outgroup" + ] + }, + "data": [ + { + "name": "differences", + "weight": 1, + "locations": { + "144": { + "default": 1 + }, + "154": { + "default": 1 + }, + "155": { + "default": 1 + }, + "157": { + "default": 1 + }, + "158": { + "default": 1 + }, + "188": { + "default": 1 + }, + "192": { + "default": 1 + } + } + } + ] + } + ], + "aaMotifs": [ + { + "name": "glycosylation", + "nameShort": "Glyc.", + "nameFriendly": "Glycosylation", + "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)", + "includeCdses": [ + { + "cds": "HA1", + "ranges": [] + }, + { + "cds": "HA2", + "ranges": [ + { + "begin": 0, + "end": 186 + } + ] + } + ], + "motifs": [ + "N[^P][ST]" + ] + } + ], + "attributes": { + "name": "Influenza A H3N2 HA", + "segment": "ha", + "reference accession": "EPI1857216", + "reference name": "A/Darwin/6/2021" + }, + "version": { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + } +} diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta new file mode 100644 index 00000000..427694bc --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/reference.fasta @@ -0,0 +1,23 @@ +>EPI_ISL_1563628 | A/Darwin/6/2021 | A / H3N2 | | 2021-03-16 +ATGAAGACTATCATTGCTTTGAGCAACATTCTATGTCTTGTTTTCGCTCAAAAAATACCTGGAAATGACAATAGCACGGC +AACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTA +ATGCTACTGAGTTGGTTCAGAATTCATCAATAGGTGAAATATGCGGCAGTCCTCATCAGATCCTTGATGGAGGGAACTGC +ACACTAATAGATGCTCTATTGGGGGACCCTCAGTGTGACGGCTTTCAAAATAAGGAATGGGACCTTTTTGTTGAAAGAAG +CAGAGCCAACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACAC +TGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCAAACAAAACGGAACAAGTTCTGCGTGCATAAGGGGATCTAGT +AGTAGTTTTTTTAGTAGATTAAATTGGTTGACCAGCTTAAACAACATATATCCAGCACAGAACGTGACTATGCCAAACAA +GGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGATACGGACAAGAACCAAATCTCCCTGTTTGCTCAAT +CATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCAAATATCGGATCTAGACCCAGAATAAGG +GATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCT +AATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGTA +AGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCGTTCCAAAATGTAAACAGGATCACATACGGGGCC +TGTCCCAGATATGTTAAGCAAAGCACCCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACCAGAGGCAT +ATTTGGCGCAATAGCGGGTTTCATAGAAAATGGATGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATT +CTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTG +ATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGAAGAGTTCAAGACCTTGAGAA +ATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACGATTG +ACCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGAAAT +GGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATAAGAAATGAAACTTATGACCACAATGTGTA +CAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGA +TTTCCTTTGCCATGTCATGTTTTTTGCTTTGTATTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATT +AGATGCAACATTTGCATTTGAGTGCATTAATTAAAAAC diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta new file mode 100644 index 00000000..dd804496 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/sequences.fasta @@ -0,0 +1,1500 @@ +>A/Ohio/6/2021 +ggataattctatcaaccatgagaaccatcattgttttgagccaaattctatatctgattt +tcgctcaaaaacttcctggtaatgacaacaacatggcaacgctgtgccttggacaccatg +cagtgccaaacggaacgatagtgaaaacaatcacgaatgatcaaattgaagttactaatg +ctaccgagctggttcagagtttctctacaggcgaaatatgcaacagtccttatcagatcc 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