From a6b7af9ebc83e93035cceb758640ade4c8f75695 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Tue, 12 Nov 2024 10:45:27 +0100 Subject: [PATCH 1/2] flu: update IAV HA datasets after promotion of subclades --- data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md | 5 +++++ data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json | 2 +- data/nextstrain/flu/h1n1pdm/ha/MW626062/CHANGELOG.md | 7 ++++++- data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json | 2 +- data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md | 4 +++- data/nextstrain/flu/h3n2/ha/CY163680/tree.json | 2 +- data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md | 5 ++++- data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json | 2 +- 8 files changed, 22 insertions(+), 7 deletions(-) diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md index 076306db..89db5f98 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/CHANGELOG.md @@ -1,8 +1,13 @@ +## Unreleased + +This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. + ## 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 diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json index 71066a2c..25dbd8ae 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 2024-11-03", "updated": "2024-11-03", "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": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "short-clade", "title": "short-clade", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "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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"short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-13"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A864G"], "HA1": ["I265V"]}, "labels": {"aa": "HA1: I265V"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ 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 d31d4875..89969ecd 100644 --- a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md @@ -1,5 +1,7 @@ -## 2024-11-05T09:19:52Z +## Unreleased +This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. +## 2024-11-05T09:19:52Z - update reference trees - include subclade proposals diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json index 2ccba6a8..cd5f27c4 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 2024-11-03", "updated": "2024-11-03", "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/h3n2/ha/CY163680/annotation.gff", "start": 66, "strand": "+", "type": "gene"}, "HA2": {"end": 1715, "seqid": "dataset_config/h3n2/ha/CY163680/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 65, "seqid": "dataset_config/h3n2/ha/CY163680/annotation.gff", 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{"value": "J.2"}}, "branch_attrs": {"mutations": {"nuc": ["T602C", "G1247A"]}}, "children": [{"name": "A/StPetersburg/RII-MH151514S/2023", "node_attrs": {"div": 0.0779, "accession_ha": {"value": "EPI2867784"}, "country": {"value": "Russia"}, "strain": {"value": "A/StPetersburg/RII-MH151514S/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18685279"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-11-17"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["T617C"]}}}, {"name": "A/StPetersburg/RII-6787S/2023", "node_attrs": {"div": 0.0773, "accession_ha": {"value": "EPI2870837"}, "country": {"value": "Russia"}, "strain": {"value": "A/StPetersburg/RII-6787S/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18698244"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-09"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {}}}, {"name": "A/Victoria/53/2024", "node_attrs": {"div": 0.0791, "accession_ha": {"value": "EPI3006736"}, "country": {"value": "Australia"}, "strain": {"value": "A/Victoria/53/2024"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18876507"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2024-01-20"}, "subclade": {"value": "J.2"}, "region": {"value": "Oceania"}}, "branch_attrs": {"mutations": {"nuc": ["G163A", "C259A", "C1220T"], "HA1": ["R33Q", "T65K"]}, "labels": {"aa": "HA1: R33Q, T65K"}}}, {"name": "A/Saratov/RII-10/2023", "node_attrs": {"div": 0.0785, "accession_ha": {"value": "EPI2970695"}, "country": {"value": "Russia"}, "strain": {"value": "A/Saratov/RII-10/2023"}, "proposedSubclade": {"value": "J.2"}, "gisaid_epi_isl": {"value": "EPI_ISL_18846030"}, "clade_membership": {"value": "3C.2a1b.2a.2a.3a.1"}, "short-clade": {"value": "2a.3a.1"}, "date": {"value": "2023-12-22"}, "subclade": {"value": "J.2"}, "region": {"value": "West Asia"}}, "branch_attrs": {"mutations": {"nuc": ["G688A", "A1170G"], "HA1": ["R208K"], "HA2": ["S40G"]}, "labels": {"aa": "HA1: R208K; HA2: S40G"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ 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 25d41ee8..4afc72cb 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md @@ -1,8 +1,11 @@ -## 2024-11-05T09:19:52Z +## Unreleased +This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. +## 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. diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json index 7658bf51..a8a1e540 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 2024-11-03", "updated": "2024-11-03", "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": 1035, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 49, "strand": "+", "type": "gene"}, "HA2": {"end": 1698, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 1036, "strand": "+", "type": "gene"}, "SigPep": {"end": 48, "seqid": "dataset_config/h3n2/ha/EPI1857216/annotation.gff", "start": 1, "strand": "+", "type": "gene"}, "nuc": {"end": 1718, "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": "subclade", "displayName": "Subclade", "description": "Experimental fine-grained subclade annotation."}, {"name": "short-clade", "displayName": "short-clade", "description": ""}, {"name": "proposedSubclade", "displayName": "Proposed subclade", "description": "Includes proposals of new subclades. 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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 c0831cf9..9880cbb3 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -804,7 +804,7 @@ "clades": 25, "customClades": { "short-clade": 16, - "subclade": 21, + "subclade": 22, "proposedSubclade": 22 }, "qc": [ @@ -818,6 +818,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-05T09:19:52Z", "tag": "2024-11-05--09-19-52Z", @@ -852,8 +859,7 @@ } ], "version": { - "updatedAt": "2024-11-05T09:19:52Z", - "tag": "2024-11-05--09-19-52Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -909,7 +915,7 @@ "clades": 25, "customClades": { "short-clade": 16, - "subclade": 21, + "subclade": 22, "proposedSubclade": 22 }, "qc": [ @@ -923,6 +929,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-05T09:19:52Z", "tag": "2024-11-05--09-19-52Z", @@ -957,8 +970,7 @@ } ], "version": { - "updatedAt": "2024-11-05T09:19:52Z", - "tag": "2024-11-05--09-19-52Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -1113,7 +1125,7 @@ "capabilities": { "clades": 37, "customClades": { - "subclade": 42, + "subclade": 45, "short-clade": 37, "proposedSubclade": 45 }, @@ -1128,6 +1140,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-05T09:19:52Z", "tag": "2024-11-05--09-19-52Z", @@ -1170,8 +1189,7 @@ } ], "version": { - "updatedAt": "2024-11-05T09:19:52Z", - "tag": "2024-11-05--09-19-52Z", + "tag": "unreleased", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -1226,7 +1244,7 @@ "capabilities": { "clades": 34, "customClades": { - "subclade": 39, + "subclade": 42, "short-clade": 34, "proposedSubclade": 42 }, @@ -1242,6 +1260,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-11-05T09:19:52Z", "tag": "2024-11-05--09-19-52Z", @@ -1292,8 +1317,7 @@ } ], "version": { - "updatedAt": "2024-11-05T09:19:52Z", - "tag": "2024-11-05--09-19-52Z", + "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..89db5f98 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/CHANGELOG.md @@ -0,0 +1,31 @@ +## Unreleased + +This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. + +## 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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zU)KNNKl&g3?MIK)KmV@zuKL%%{Db=c)91yj+0lz{W>2o(wO{$uU;oAb{D1ttM~~D$ z_;3Ax|MCz28{X^esCf4B$nvs(@!$V z>Yv>gfA^m~dUU<`r?=|0*Y+3xfB)6=>VNug{{2VlpWXBNum8(GJi6H|7UmEBxBia$ UyZ$cz^WQ=U|NKA2u{`?!0e74C*8l(j literal 0 HcmV?d00001 diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3 b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3 new file mode 100644 index 00000000..a3952a1f --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/genome_annotation.gff3 @@ -0,0 +1,5 @@ +##gff-version 3 +##sequence-region CY121680.1 1 1752 +CY121680.1 feature gene 21 71 . + . gene_name="SigPep" +CY121680.1 feature gene 72 1052 . + . gene_name="HA1" +CY121680.1 feature gene 1053 1718 . + . gene_name="HA2" diff --git 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..6c731514 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/sequences.fasta @@ -0,0 +1,1549 @@ +>A/Connecticut/39/2022 +ggaaaacaaaagcaacaaaaatgaaggcaatactagtagttatgctgtatacatttacaa +ccgcaaatgcagacacattatgtataggttatcatgcgaacaattcaacagacactgtgg +acacagtactagaaaagaatgtaacagtaacacactctgtcaatcttctagaagacaagc +ataacggaaaactatgcaaactaagaggggtagccccattgcatttgggtcaatgtaaca +ttgctggctggatcctgggaaatccagagtgtgaatcactctccacagcaagatcatggt +cctacattgtggaaacatctaattcagacaatggaacgtgttacccaggagatttcatca +attatgaggagctaagagagcaattgagctcagtgtcatcatttgaaaggtttgaaatat +tccccaagacaagttcatggcctaatcatgactcggacaatggtgtaacggcagcatgtt +ctcacgctggagcaaggagcttctacaaaaacttgatatggctggttaaaaaaggaaaat +cgtacccaaagattaaccaaacctacattaatgataaagggaaagaagtcctcgtgctgt 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"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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"A1491G"], "HA2": ["T147A"]}, "labels": {"aa": "HA2: T147A"}}}, {"name": "A/Canberra/158/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_19234700"}, "accession_ha": {"value": "EPI3415473"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "Oceania"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Australia"}, "date": {"value": "2024-05-22"}, "strain": {"value": "A/Canberra/158/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["G1286A", "A1668G"], "HA2": ["I206V"]}, "labels": {"aa": "HA2: I206V"}}}, {"name": "NODE_0000667", "node_attrs": {"div": 0.0609, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "proposedSubclade": {"value": "C.1.9"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A1058G"]}}, "children": [{"name": "A/India/883/2024", "node_attrs": {"div": 0.0615, "gisaid_epi_isl": {"value": "EPI_ISL_19355178"}, "accession_ha": {"value": "EPI3518924"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "South Asia"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "India"}, "date": {"value": "2024-02-06"}, "strain": {"value": "A/India/883/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["A839C"]}}}, {"name": "A/Manitoba/RV03655/2024", "node_attrs": {"div": 0.0643, "gisaid_epi_isl": {"value": "EPI_ISL_19254984"}, "accession_ha": {"value": "EPI3426913"}, "clade_membership": {"value": "6B.1A.5a.2a"}, "subclade": {"value": "C.1.9"}, "region": {"value": "North America"}, "proposedSubclade": {"value": "C.1.9"}, "country": {"value": "Canada"}, "date": {"value": "2024-05-28"}, "strain": {"value": "A/Manitoba/RV03655/2024"}, "short-clade": {"value": "5a.2a"}}, "branch_attrs": {"mutations": {"nuc": ["G515A", "G771A", "G843A", "C1316T", "C1673T", "A1739C"], "HA1": ["V234I", "E258K"]}, "labels": {"aa": "HA1: V234I, E258K"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ 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..da7157e2 --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/CHANGELOG.md @@ -0,0 +1,33 @@ +## Unreleased + +This release adds the subclade D.5 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. + +## 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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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 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+CCAAAGTATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTA +GAGGCCTATTCGGGGCCATTGCTGGCTTCATCGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGG +TTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGATCTGAAGAGCACACAAAATGCCATTGAT +AAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTTGGTAAAGAGT +TCAACCACCTTGAAAAAAGAATAGAGAATCTAAATAAAAAGGTTGATGATGGTTTCCTGGACATTTGGAC +TTACAATGCCGAACTGTTGGTTCTACTGGAAAACGAAAGAACTTTGGACTATCACGATTCAAATGTGAAG +AACTTGTATGAAAAAGTAAGAAACCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAAT +TTTACCACAAATGCGACAACACATGCATGGAAAGTGTCAAGAATGGGACTTATGACTACCCAAAATACTC +AGAGGAAGCAAAATTAAACAGAGAAAAAATAGATGGAGTAAAGCTGGACTCAACAAGGATCTACCAGATT +TTGGCGATCTATTCAACTGTTGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGCTTCTGGA +TGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAATCATGAGAAAAAC +AC diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/sequences.fasta new file mode 100644 index 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b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json new file mode 100644 index 00000000..48a52ecd --- /dev/null +++ b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/tree.json @@ -0,0 +1 @@ +{"version": "v2", "meta": {"title": "Nextclade reference tree for Influenza type:h1n1pdm segment:ha with root MW626062 built on 2024-11-12", "updated": "2024-11-12", "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/MW626062/annotation.gff", "start": 72, "strand": "+", "type": "gene"}, "HA2": {"end": 1718, "seqid": "dataset_config/h1n1pdm/ha/MW626062/annotation.gff", "start": 1053, "strand": "+", "type": "gene"}, "SigPep": {"end": 71, "seqid": "dataset_config/h1n1pdm/ha/MW626062/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": "proposedSubclade", "title": "Subclade proposals", "type": "categorical"}, {"key": "subclade", "title": "Subclade", "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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"short-clade": {"value": "5a.2a"}, "date": {"value": "2024-02-13"}, "region": {"value": "Europe"}}, "branch_attrs": {"mutations": {"nuc": ["A864G"], "HA1": ["I265V"]}, "labels": {"aa": "HA1: I265V"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}} \ 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..89969ecd --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/CHANGELOG.md @@ -0,0 +1,40 @@ +## Unreleased +This release adds the subclades J.1.1, J.2.1, and J.2.2 as specified in the (influenza-clade-nomenclature repository)[https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/blob/main/CHANGELOG.md#2024-11-12]. + +## 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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