rsv: update rsv-b only

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

@@ -1,3 +1,11 @@
+## Unreleased
+
+ - designate new lineage B.D.4.1.2 and B.D.4.1.3. The former is an older group that doesn't seem to circulating at the moment, but is added for consistency
+ - designate lineages B.D.E.1.2-6: these are several recent groups defined to break up the dominant B.D.E.1 lineage
+ - designate lineage B.D.E.5: this is a small group with several substitutions in the F-protein.
+ - update with new sequence data
+ - remove deprecated G-clades
+
 ## 2024-11-27T02:51:00Z
 
  - update reference tree with more recent data.

data_output/index.json

@@ -2074,10 +2074,7 @@
             "treeJson": "tree.json"
           },
           "capabilities": {
-            "clades": 18,
-            "customClades": {
-              "G_clade": 10
-            },
+            "clades": 26,
             "qc": [
               "privateMutations",
               "mixedSites",
@@ -2086,6 +2083,13 @@
             ]
           },
           "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",
@@ -2120,8 +2124,7 @@
             }
           ],
           "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"

data_output/nextstrain/rsv/b/EPI_ISL_1653999/unreleased/CHANGELOG.md

@@ -0,0 +1,27 @@
+## Unreleased
+
+ - designate new lineage B.D.4.1.2 and B.D.4.1.3. The former is an older group that doesn't seem to circulating at the moment, but is added for consistency
+ - designate lineages B.D.E.1.2-6: these are several recent groups defined to break up the dominant B.D.E.1 lineage
+ - designate lineage B.D.E.5: this is a small group with several substitutions in the F-protein.
+ - update with new sequence data
+ - remove deprecated G-clades
+
+## 2024-11-27T02:51:00Z
+
+ - 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.
+
+
+## 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/b/EPI_ISL_1653999/unreleased/README.md

@@ -0,0 +1,20 @@
+# RSV-B dataset with reference genome B/Australia/VIC-RCH056/2019
+
+| 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/b/EPI_ISL_1653999                                                                                    |
+| reference              | [OP975389](https://www.ncbi.nlm.nih.gov/nuccore/OP975389.1)                                                         |
+| clade definitions      | [github.com/rsv-lineages/lineage-designation-B](https://github.com/rsv-lineages/lineage-designation-B)              |
+
+## Scope of this dataset
+This dataset for RSV-B uses reference sequence B/Australia/VIC-RCH056/2019 with is available at [OP975389](https://www.ncbi.nlm.nih.gov/nuccore/OP975389.1) and also deposited under accession number EPI_ISL_1653999 in GISAID. This sequence has the duplication in the G-protein shared by all currently circulating variants.
+The reference tree covers the diversity of RSV-B 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-B](https://github.com/rsv-lineages/lineage-designation-B).
+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/b/EPI_ISL_1653999/unreleased/genome_annotation.gff3

@@ -0,0 +1,14 @@
+##gff-version 3
+##sequence-region EPI_ISL_1653999 1 15222
+EPI_ISL_1653999	feature	source	1	15222	.	.	.	mol_type=viral cRNA;organism=Human respiratory syncytial virus B
+EPI_ISL_1653999	feature	CDS	57	476	.	.	0	codon_start=1;locus_tag=NS1;Name=NS1;product=nonstructural protein 1;protein_id=QPB74302.1
+EPI_ISL_1653999	feature	CDS	584	958	.	.	0	codon_start=1;locus_tag=NS2;Name=NS2;product=nonstructural protein 2;protein_id=QPB74303.1
+EPI_ISL_1653999	feature	CDS	1097	2272	.	.	0	codon_start=1;locus_tag=N;Name=N;product=nucleocapsid protein;protein_id=QPB74304.1
+EPI_ISL_1653999	feature	CDS	2305	3030	.	.	0	codon_start=1;locus_tag=P;Name=P;product=phosphoprotein;protein_id=QPB74305.1
+EPI_ISL_1653999	feature	CDS	3220	3990	.	.	0	codon_start=1;locus_tag=M;Name=M;product=matrix protein;protein_id=QPB74306.1
+EPI_ISL_1653999	feature	CDS	4259	4456	.	.	0	codon_start=1;locus_tag=SH;Name=SH;product=small hydrophobic protein;protein_id=QPB74307.1
+EPI_ISL_1653999	feature	CDS	4646	5578	.	.	0	codon_start=1;locus_tag=G;Name=G;product=attachment glycoprotein;protein_id=QPB74308.1
+EPI_ISL_1653999	feature	CDS	5676	7400	.	.	0	codon_start=1;locus_tag=F;Name=F;product=fusion glycoprotein;protein_id=QPB74309.1
+EPI_ISL_1653999	feature	CDS	7627	8214	.	.	0	codon_start=1;locus_tag=M2-1;Name=M2-1;product=transcription elongation factor M2-1;protein_id=QPB74310.1
+EPI_ISL_1653999	feature	CDS	8180	8452	.	.	0	codon_start=1;locus_tag=M2-2;Name=M2-2;product=transcription elongation factor M2-2;protein_id=QPB74311.1
+EPI_ISL_1653999	feature	CDS	8518	15018	.	.	0	codon_start=1;locus_tag=L;Name=L;product=RNA-directed RNA polymerase L;protein_id=QPB74312.1

data_output/nextstrain/rsv/b/EPI_ISL_1653999/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_b",
+    "nextstrain/rsv/b",
+    "nextstrain/rsv/b/hRSV-B-Australia-VIC-RCH056-2019"
+  ],
+  "attributes": {
+    "name": "RSV-B",
+    "reference accession": "EPI_ISL_1653999",
+    "reference name": "hRSV/B/Australia/VIC-RCH056/2019"
+  },
+  "geneOrderPreference": [
+    "F",
+    "G",
+    "L"
+  ],
+  "version": {
+    "tag": "unreleased",
+    "compatibility": {
+      "cli": "3.0.0-alpha.0",
+      "web": "3.0.0-alpha.0"
+    }
+  }
+}