From 3354843a8242680c84ba4089149bca0bcfbbd045 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Thu, 8 Aug 2024 06:43:21 +0200 Subject: [PATCH 1/2] fix: RBD position numbering --- .../nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md | 6 +++++- .../flu/h3n2/ha/EPI1857216/pathogen.json | 14 +++++++------- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md index e31de8b0..0572a0d2 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md @@ -1,3 +1,7 @@ +## Unreleased + +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. @@ -20,7 +24,7 @@ After discussion with various members of the seasonal influenza virus surveillan - `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. +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 diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json index db723a65..09065585 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json @@ -106,25 +106,25 @@ "name": "differences", "weight": 1, "locations": { - "145": { + "144": { "default": 1 }, - "155": { + "154": { "default": 1 }, - "156": { + "155": { "default": 1 }, - "158": { + "157": { "default": 1 }, - "159": { + "158": { "default": 1 }, - "189": { + "188": { "default": 1 }, - "193": { + "192": { "default": 1 } } From 707b8cbdbffdaff371b78318ec35efa35ae34e32 Mon Sep 17 00:00:00 2001 From: nextstrain-bot Date: Thu, 8 Aug 2024 04:45:07 +0000 Subject: [PATCH 2/2] chore: rebuild [skip ci] --- data_output/index.json | 10 +- .../ha/EPI1857216/unreleased/CHANGELOG.md | 37 + .../h3n2/ha/EPI1857216/unreleased/README.md | 37 + .../h3n2/ha/EPI1857216/unreleased/dataset.zip | Bin 0 -> 11268257 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 | 106695 +++++++++++++++ 9 files changed, 108479 insertions(+), 2 deletions(-) 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 1164227b..c62e2dfb 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -1123,6 +1123,13 @@ ] }, "versions": [ + { + "tag": "unreleased", + "compatibility": { + "cli": "3.0.0-alpha.0", + "web": "3.0.0-alpha.0" + } + }, { "updatedAt": "2024-07-03T08:29:55Z", "tag": "2024-07-03--08-29-55Z", @@ -1157,8 +1164,7 @@ } ], "version": { - "updatedAt": "2024-07-03T08:29:55Z", - "tag": "2024-07-03--08-29-55Z", + "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/CHANGELOG.md b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md new file mode 100644 index 00000000..0572a0d2 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/CHANGELOG.md @@ -0,0 +1,37 @@ +## Unreleased + +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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gene 49 1035 . + . gene_name="HA1" +EPI1857216 feature gene 1036 1698 . + . gene_name="HA2" diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json new file mode 100644 index 00000000..6a442760 --- /dev/null +++ b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json @@ -0,0 +1,174 @@ +{ + "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", + "nextstrain/flu/h3n2", + "nextstrain/flu/h3n2/ha", + "nextstrain/flu/h3n2/ha/darwin-6-2021" + ], + "phenotypeData": [ + { + "name": "RBD", + "nameFriendly": "RBD mutations", + "description": "This column displays the number of differences between the sequence and the reference at positions identified by Koel et al. (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 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