Merge pull request #245 from nextstrain/2024-11-23_rsv_update

rsv: update rsv datasets with more recent data and the B.D.E.1.1 clad…

data/nextstrain/rsv/a/EPI_ISL_412866/CHANGELOG.md

@@ -1,3 +1,8 @@
+## Unreleased
+
+ - update reference tree with more recent data
+
+
 ## 2024-08-01T22:31:31Z
 
  - add subclades A.D.1.4-8

data/nextstrain/rsv/a/EPI_ISL_412866/README.md

@@ -10,7 +10,7 @@
 | clade definitions      | [github.com/rsv-lineages/lineage-designation-A](https://github.com/rsv-lineages/lineage-designation-A)              |
 
 ## Scope of this dataset
-This dataset for RSV-B uses reference sequence A/England/397/2017 with is available at under accession number EPI_ISL_412866 in GISAID. An almost identical sequence (slightly longer, 12 mutations, no gaps or indels) is available in NCBI as [LR699737](https://www.ncbi.nlm.nih.gov/nuccore/LR699737).
+This dataset for RSV-A uses reference sequence A/England/397/2017 with is available at under accession number EPI_ISL_412866 in GISAID. An almost identical sequence (slightly longer, 12 mutations, no gaps or indels) is available in NCBI as [LR699737](https://www.ncbi.nlm.nih.gov/nuccore/LR699737).
 This sequence has the duplication in the G-protein shared by all currently circulating variants.
 The reference tree covers the diversity of RSV-A since the first sequenced samples.
 

data/nextstrain/rsv/b/EPI_ISL_1653999/CHANGELOG.md

@@ -1,3 +1,8 @@
+## Unreleased
+
+ - update reference tree with more recent data.
+ - include designation of B.D.E.1.1
+
 ## 2024-08-01T22:31:31Z
 
  - update of reference tree with additional data. No new clades.

data_output/index.json

@@ -1836,6 +1836,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-08-01T22:31:31Z",
               "tag": "2024-08-01--22-31-31Z",
@@ -1862,8 +1869,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-08-01T22:31:31Z",
-            "tag": "2024-08-01--22-31-31Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"
@@ -1914,9 +1920,9 @@
             "treeJson": "tree.json"
           },
           "capabilities": {
-            "clades": 17,
+            "clades": 18,
             "customClades": {
-              "G_clade": 9
+              "G_clade": 10
             },
             "qc": [
               "privateMutations",
@@ -1926,6 +1932,13 @@
             ]
           },
           "versions": [
+            {
+              "tag": "unreleased",
+              "compatibility": {
+                "cli": "3.0.0-alpha.0",
+                "web": "3.0.0-alpha.0"
+              }
+            },
             {
               "updatedAt": "2024-08-01T22:31:31Z",
               "tag": "2024-08-01--22-31-31Z",
@@ -1952,8 +1965,7 @@
             }
           ],
           "version": {
-            "updatedAt": "2024-08-01T22:31:31Z",
-            "tag": "2024-08-01--22-31-31Z",
+            "tag": "unreleased",
             "compatibility": {
               "cli": "3.0.0-alpha.0",
               "web": "3.0.0-alpha.0"

data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/CHANGELOG.md

@@ -0,0 +1,22 @@
+## Unreleased
+
+ - update reference tree with more recent data
+
+
+## 2024-08-01T22:31:31Z
+
+ - add subclades A.D.1.4-8
+ - add subclades A.D.3.2-6, add representatives to A.D.3.1
+ - add subclade A.D.5.4, adjust definition of A.D.5.3 to make it a clear sibling
+
+
+## 2024-01-29T10:29:43Z
+
+ - fix definitions of G_clades (legacy) for RSV-A and RSV-B
+
+
+## 2024-01-16T20:31:02Z
+
+**first release of v3 dataset.**
+
+Updated consortium nomenclature.

data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/README.md

@@ -0,0 +1,21 @@
+# RSV-A dataset with reference genome A/England/397/2017
+
+| Key                    | Value                                                                                                               |
+| ---------------------- | --------------------------------------------------------------------------------------------------------------------|
+| authors                | [Richard Neher](https://neherlab.org), Laura Urbanska, [Nextstrain](https://nextstrain.org)                         |
+| data source            | Genbank + authorized other sequences                                                                                |
+| workflow               | [github.com/nextstrain/rsv](https://github.com/nextstrain/rsv)                                                      |
+| nextclade dataset path | nextstrain/rsv/a/EPI_ISL_412866                                                                                     |
+| reference              | EPI_ISL_412866                                                                                                      |
+| clade definitions      | [github.com/rsv-lineages/lineage-designation-A](https://github.com/rsv-lineages/lineage-designation-A)              |
+
+## Scope of this dataset
+This dataset for RSV-A uses reference sequence A/England/397/2017 with is available at under accession number EPI_ISL_412866 in GISAID. An almost identical sequence (slightly longer, 12 mutations, no gaps or indels) is available in NCBI as [LR699737](https://www.ncbi.nlm.nih.gov/nuccore/LR699737).
+This sequence has the duplication in the G-protein shared by all currently circulating variants.
+The reference tree covers the diversity of RSV-A since the first sequenced samples.
+
+
+## Nomenclature
+The dataset follows the consortium nomenclature established in 2023 that uses a combination of letters and numbers to designate lineages in a hierarchical fashion.
+Definitions of individuals lineages are available on github in the repository [rsv-lineages/lineage-designation-A](https://github.com/rsv-lineages/lineage-designation-A).
+Legacy clade definitions for the nomenclature defined by Goya et al (`G_clade`) are included for orientation. These clade definitions will not be updated and are incomplete. We encourage users to use the new consortium nomenclature.

data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/genome_annotation.gff3

@@ -0,0 +1,16 @@
+##gff-version 3
+##sequence-region EPI_ISL_412866 1 15225
+EPI_ISL_412866	annotation	remark	1	15225	.	.	.	molecule_type=cRNA;organism=Human orthopneumovirus;taxonomy=Viruses,Riboviria,Orthornavirae,Negarnaviricota,Haploviricotina,Monjiviricetes,Mononegavirales,Pneumoviridae,Orthopneumovirus,Orthopneumovirus hominis
+EPI_ISL_412866	feature	source	1	15225	.	.	.	mol_type=viral cRNA;organism=Human orthopneumovirus
+EPI_ISL_412866	feature	5'UTR	1	15	.	.	.	citation=%5B1%5D;function=Leader region 5%27UTR
+EPI_ISL_412866	feature	CDS	70	489	.	.	0	codon_start=1;db_xref=GeneID:37607636;gene=NS1;gene_name=NS1;Name=NS1;product=nonstructural protein 1;protein_id=YP_009518850.1;translation=MGSNSLSMIKVRLQNLFDNDEVALLKITCYTDKLIQLTNALAKAVIHTIKLNGIVFVHVITSSDICPNNNIVVKSNFTTMPVLQNGGYIWEMMELTHCSQPNGLIDDNCEIKFSKKLSDSTMTNYMNQLSELLGFDLNP%2A
+EPI_ISL_412866	feature	CDS	599	973	.	.	0	codon_start=1;db_xref=GeneID:37607637;gene=NS2;gene_name=NS2;Name=NS2;product=nonstructural protein 2;protein_id=YP_009518851.1;translation=MDTTHNDTTPQRLMITDMRPLSLETIITSLTRDIITHKFIYLINHECIVRKLDERQATFTFLVNYEMKLLHKVGSTKYKKYTEYNTKYGTFPMPIFINHDGFLECIGIKPTKHTPIIYKYDLNP%2A
+EPI_ISL_412866	feature	CDS	1111	2286	.	.	0	codon_start=1;db_xref=GeneID:37607638;gene=N;gene_name=N;Name=N;product=nucleoprotein;protein_id=YP_009518852.1;translation=MALSKVKLNDTLNKDQLLSSSKYTIQRSTGDSIDTPNYDVQKHINKLCGMLLITEDANHKFTGLIGMLYAMSRLGREDTIKILKDAGYHVKANGVDVTTHRQDINGKEMKFEVLTLASLTTEIQINIEIESRKSYKKMLKEMGEVAPEYRHDSPDCGMIILCIAALVITKLAAGDRSGLTAVIRRANNVLKNEMKRYKGLLPKDIANSFYEVFEKYPHFIDVFVHFGIAQSSTRGGSRVEGIFAGLFMNAYGAGQVMLRWGVLAKSVKNIMLGHASVQAEMEQVVEVYEYAQKLGGEAGFYHILNNPKASLLSLTQFPHFSSVVLGNAAGLGIMGEYRGTPRNQDLYDAAKVYAEQLKENGVINYSVLDLTAEELEAIKHQLNPKDNDVEL%2A
+EPI_ISL_412866	feature	CDS	2318	3043	.	.	0	codon_start=1;db_xref=GeneID:37607639;gene=P;gene_name=P;Name=P;product=phosphoprotein;protein_id=YP_009518853.1;translation=MEKFAPEFHGEDANNRATKFLESIKGKFTSPKDPKKKDSIISVNSIDIEVTKESLITSNSTIINPINETDDTVGNKPNYQRKPLVSFKEDPTPSDNPFSKLYKETIETFDNNEEESSYSYEEINDQTNDNITARLDRIDEKLSEILGMLHTLVVASAGPTSARDGIRDAMVGLREEMIEKIRTEALMTNDRLEAMARLRNEESEKMAKDTSDEVSLNPTSEKLNNLLEGNDSDNDLSLEDF%2A
+EPI_ISL_412866	feature	CDS	3226	3996	.	.	0	codon_start=1;db_xref=GeneID:37607640;gene=M;gene_name=M;Name=M;product=matrix protein;protein_id=YP_009518854.1;translation=METYVNKLHEGSTYTAAVQYNVLEKDDDPASLTIWVPMFQSSMPADLLIKELANVNILVKQISTPKGPSLRVMINSRSAVLAQMPSKFTICANVSLDERSKLAYDVTTPCEIKACSLTCLKSKNMLTTVKDLTMKTLNPTHDIIALCEFENIVTSKKVIIPTYLRSISVRNKDLNTLENITTTEFKNAITNAKIIPYSGLLLVITVTDNKGAFKYIKPQSQFIVDLGAYLEKESIYYVTTNWKHTATRFAIKPMED%2A
+EPI_ISL_412866	feature	CDS	4266	4460	.	.	0	codon_start=1;db_xref=GeneID:37607641;gene=SH;gene_name=SH;Name=SH;product=small hydrophobic protein;protein_id=YP_009518855.1;translation=MENTSITIEFSSKFWPYFTLIHMITTIISLIIIISIMIAILNKLCEYNVFHNKTFELPRARVNT%2A
+EPI_ISL_412866	feature	CDS	4652	5617	.	.	0	codon_start=1;db_xref=GeneID:37607642;gene=G;gene_name=G;Name=G;product=attachment glycoprotein;protein_id=YP_009518856.1;translation=MSKTKDQRTAKTLERTWDTLNHLLFISSCLYKLNLKSIAQITLSILAMIISTSLIIAAIIFIASANHKVTPTTAIIQDATNQIKNTTPTHLTQNPQLGISLSNLSGTTSQSTTILASTTPSAESTPQSTTVKIINTTTTQILPSKPTTKQRQNKPQNKPNNDFHFEVFNFVPCSICSNNPTCWAICKRIPNKKPGKKTTTKPTKKPTLKTTKKDPKPQTTKPKGVLTTKPTGKPTINTTKTNSRTTLLTSNTKGNPEHTSQKETIHSTTSEGYPSPSQVYTTSDQEETLHSTTSEGYPSPSQVYTTSEYLSQSLSSSNTTK%2A
+EPI_ISL_412866	feature	CDS	5697	7421	.	.	0	codon_start=1;db_xref=GeneID:37607643;gene=F;gene_name=F;Name=F;product=fusion glycoprotein;protein_id=YP_009518857.1;translation=MELPILKTNAITTILAAVTLCFASSQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPAANSRARRELPRFMNYTLNNTKNTNVTLSKKRKRRFLGFLLGVGSAIASGIAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSSNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNIDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVNAGKSTTNIMITTIIIVIIVILLALIAVGLLLYCKARSTPVTLSKDQLSGINNIAFSN%2A
+EPI_ISL_412866	feature	CDS	7640	8224	.	.	0	codon_start=1;db_xref=GeneID:37607644;gene=M2;gene_name=M2-1;Name=M2-1;note=ORF 1%2C matrix protein 2;product=M2-1 protein;protein_id=YP_009518858.1;translation=MSRRNPCKFEIRGHCLNGKRCHFSHNYFEWPPHALLVRQNFMLNRILKSMDKSIDTLSEISGAAELDRTEEYALGVVGVLESYIGSINNITKQSACVAMSKLLTELNSDDIKKLRDNEEPNSPKVRVYNTVISYIESNRKNNKQTIHLLKRLPADVLKKTIKNTLDIHKSITINNSKESTVSDTNDHAKNNDTT%2A
+EPI_ISL_412866	feature	CDS	8193	8465	.	.	0	codon_start=1;db_xref=GeneID:37607644;gene=M2;gene_name=M2-2;Name=M2-2;note=ORF 2%2C RNA processivity factor;product=M2-2 protein;protein_id=YP_009518859.1;translation=TTMPKIMILPDKYPCSINSILITSNYRVTMYNQKNTLYINQNNQNSHIYPPDQPFNEIHWTSQDLIDATQNFLQHLGITDDIYTIYILVS%2A
+EPI_ISL_412866	feature	CDS	8532	15029	.	.	0	codon_start=1;db_xref=GeneID:37607645;gene=L;gene_name=L;Name=L;note=RNA dependant RNA polymerase%3B RdRp;product=polymerase protein;protein_id=YP_009518860.1;translation=MDPIISGNSANVYLTDSYLKGVISFSECNALGSYIFNGPYLKNDYTNLISRQNPLIEHINLKKLNITQSLISKYHKGEIKIEEPTYFQSLLMTYKSMTSSEQTTTTNLLKKIIRRAIEISDVKVYAILNKLGLKEKDKIKSNNGQDEDNSVITTIIKDDILLAVKDNQSHPKADKNQSTKQKDTIKTTLLKKLMCSMQHPPSWLIHWFNLYTKLNSILTQYRSSEVKNHGFILIDNHTLSGFQFILNQYGCIVYHRELKRITVTTYNQFLTWKDISLSRLNVCLITWISNCLNTLNKSLGLRCGFNNVILTQLFLYGDCILKLFHNEGFYIIKEVEGFIMSLILNITEEDQFRKRFYNSMLNNITDAANKAQKNLLSRVCHTLLDKTISDNIINGRWIILLSKFLKLIKLAGDNNLNNLSELYFLFRIFGHPMVDERQAMDAVKVNCNETKFYLLSSLSMLRGAFIYRIIKGFVNNYNRWPTLRNAIVLPLRWLTYYKLNTYPSLLELTERDLIVLSGLRFYREFRLPKKVDLEMIINDKAISPPKNLIWTSFPRNYMPSHIQNYIEHEKLKFSDSDKSRRVLEYYLRDNKFNECDLYNCVVNQSYLNNPNHVVSLTGKERELSVGRMFAMQPGMFRQVQILAEKMIAENILQFFPESLTRYGDLELQKILELKAGISNKSNRYNDNYNNYISKCSIITDLSKFNQAFRYETSCICSDVLDELHGVQSLFSWLHLTIPHVTIICTYRHAPPYIKDHIVDLNNVDEQSGLYRYHMGGIEGWCQKLWTIEAISLLDLISLKGKFSITALINGDNQSIDISKPVRLMEGQTHAQADYLLALNSLKLLYKEYAGIGHKLKGTETYISRDMQFMSKTIQHNGVYYPASIKKVLRVGPWINTILDDFKVSLESIGSLTQELEYRGESLLCSLIFRNVWLYNQIALQLKNHALCNNKLYLDILKVLKHLKTFFNLDNIDTALTLYMNLPMLFGGGDPNLLYRSFYRRTPDFLTEAIVHSVFILSYYTNHDLKDKLQDLSDDRLNKFLTCIITFDKNPNAEFVTLMRDPQALGSERQAKITSEINRLAVTEVLSTAPNKIFSKSAQHYTTTEIDLNDIMQNIEPTYPHGLRVVYESLPFYKAEKIVNLISGTKSITNILEKTSAIDLTDIDRATEMMRKNITLLIRILPLDCNRDKREILSMENLSITELSKYVRERSWSLSNIVGVTSPSIMYTMDIKYTTSTIASGIIIEKYNVNSLTRGERGPTKPWVGSSTQEKKTMPVYNRQVLTKKQRDQIDLLAKLDWVYASIDNKDEFMEELSIGTLGLTYEKAKKLFPQYLSVNYLHRLTVSSRPCEFPASIPAYRTTNYHFDTSPINRILTEKYGDEDIDIVFQNCISFGLSLMSVVEQFTNVCPNRIILIPKLNEIHLMKPPIFTGDVDIHKLKLVIQKQHMFLPDKISLTQYVELFLSNKTLKSGSNVNSNLILAHKISDYFHNTYILSTNLAGHWILIIQLMKDSKGIFEKDWGEGYITDHMFINLKVFFNAYKTYLLCFHKGYGRAKLECDMNTSDLLCVLELIDSSYWKSMSKVFLEQKVIKYILSQDASLHRVKGCHSFKLWFLKRLNVAEFTVCPWVVNIDYHPTHMKAILTYIDLVRMGLINIDRIYIKNKHKFNDEFYTSNLFYINYNFSDNTHLLTKHIRIANSELESNYNKLYHPTPETLENILTNPVKNNEKKTLSGYCIGKNVDSIMLPSLSNKKLIKSSTMIRTNYSRQDLYNLFPTVVIDKIIDHSGNTAKSNQLYTTTSHQISLVHNSTSLYCMLPWHHINRFNFVFSSTGCKISIEYILKDLKIKDPNCIAFIGEGAGNLLLRTVVELHPDIRYIYRSLKDCNDHSLPIEFLRLYNGHINIDYGENLTIPATDATNNIHWSYLHIKFAEPISLFVCDAELPVTVNWSKIIIEWSKHVRKCKYCSSVNKCTLIVKYHAQDDIDFKLDNITILKTYVCLGSKLKGSEVYLVLTIGPANVFPVFNVVQNAKLILSRTKNFIMPKKADKESIDANIKSLIPFLCYPITKKGINTALSKLKSVVSGDILSYSIAGRNEVFSNKLINHKHMNILKWFNHVLNFRSTELNYNHLYMVESTYPHLSELLNSLTTNELKKLIKITGSLLYNFYNE%2A

data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/pathogen.json

@@ -0,0 +1,109 @@
+{
+  "schemaVersion": "3.0.0",
+  "alignmentParams": {
+    "excessBandwidth": 9,
+    "terminalBandwidth": 100,
+    "allowedMismatches": 4,
+    "gapAlignmentSide": "left",
+    "minSeedCover": 0.1
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "defaultCds": "F",
+  "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": 50,
+      "cutoff": 150,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "missingData": {
+      "enabled": false,
+      "missingDataThreshold": 2000,
+      "scoreBias": 500
+    },
+    "snpClusters": {
+      "enabled": false,
+      "windowSize": 100,
+      "clusterCutOff": 10,
+      "scoreWeight": 50
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 8
+    },
+    "frameShifts": {
+      "enabled": true
+    },
+    "stopCodons": {
+      "enabled": true,
+      "ignoredStopCodons": [
+        {
+          "codon": 320,
+          "cdsName": "G"
+        }
+      ]
+    }
+  },
+  "cdsOrderPreference": [
+    "F",
+    "G",
+    "L"
+  ],
+  "maintenance": {
+    "website": [
+      "https://nextstrain.org",
+      "https://clades.nextstrain.org"
+    ],
+    "documentation": [
+      "https://github.com/nextstrain/rsv"
+    ],
+    "source code": [
+      "https://github.com/nextstrain/rsv"
+    ],
+    "issues": [
+      "https://github.com/nextstrain/rsv/issues"
+    ],
+    "organizations": [
+      "Nextstrain"
+    ],
+    "authors": [
+      "Nextstrain team <https://nextstrain.org>"
+    ]
+  },
+  "shortcuts": [
+    "rsv_a",
+    "nextstrain/rsv/a",
+    "nextstrain/rsv/a/hRSV-A-England-397-2017"
+  ],
+  "attributes": {
+    "name": "RSV-A",
+    "reference accession": "EPI_ISL_412866",
+    "reference name": "hRSV/A/England/397/2017"
+  },
+  "geneOrderPreference": [
+    "F",
+    "G",
+    "L"
+  ],
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}