Merge pull request #81 from nextstrain/ba-2-86

Ba 2 86

CHANGELOG.md

@@ -1,5 +1,13 @@
 # CHANGELOG
 
+
+## 2023-08-09
+
+### New SARS-CoV-2 dataset version (tag `2023-08-17T12:00:00Z`)
+Ad-hoc update to include the [saltation variant BA.2.86](https://github.com/cov-lineages/pango-designation/issues/2183).
+Note that this is not a regular data set update, but an update outside of the usual cycle specifically to enable detection of the BA.2.86.
+
+
 ## 2023-08-09
 
 ### New SARS-CoV-2 dataset version (tag `2023-08-09T12:00:00Z`)

data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-08-17T12:00:00Z/files/genemap.gff

@@ -0,0 +1,18 @@
+##gff-version 3
+##sequence-region MN908947 1 29903
+# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
+# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
+# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
+# seqname	source	feature	start	end	score	strand	frame	attribute
+MN908947	GenBank	gene	266	13468	.	+	.	gene_name=ORF1a
+MN908947	GenBank	gene	13468	21555	.	+	.	gene_name=ORF1b
+MN908947	GenBank	gene	25393	26220	.	+	.	gene_name=ORF3a
+MN908947	GenBank	gene	21563	25384	.	+	.	gene_name=S
+MN908947	GenBank	gene	26245	26472	.	+	.	gene_name=E
+MN908947	GenBank	gene	26523	27191	.	+	.	gene_name=M
+MN908947	GenBank	gene	27202	27387	.	+	.	gene_name=ORF6
+MN908947	GenBank	gene	27394	27759	.	+	.	gene_name=ORF7a
+MN908947	GenBank	gene	27756	27887	.	+	.	gene_name=ORF7b
+MN908947	GenBank	gene	27894	28259	.	+	.	gene_name=ORF8
+MN908947	GenBank	gene	28274	29533	.	+	.	gene_name=N
+MN908947	GenBank	gene	28284	28577	.	+	.	gene_name=ORF9b

data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-08-17T12:00:00Z/files/primers.csv

@@ -0,0 +1 @@
+Country (Institute),Target,Oligonucleotide,Sequence

data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-08-17T12:00:00Z/files/tag.json

@@ -0,0 +1,25 @@
+{
+  "tag": "2023-08-17T12:00:00Z",
+  "comment": "Update to include lineage BA.2.86",
+  "compatibility": {
+    "nextcladeCli": {
+      "min": "1.10.0",
+      "max": null
+    },
+    "nextcladeWeb": {
+      "min": "1.13.0",
+      "max": null
+    }
+  },
+  "enabled": true,
+  "files": {
+    "geneMap": "genemap.gff",
+    "primers": "primers.csv",
+    "qc": "qc.json",
+    "reference": "reference.fasta",
+    "sequences": "sequences.fasta",
+    "tree": "tree.json",
+    "virusPropertiesJson": "virus_properties.json"
+  },
+  "metadata": {}
+}

data/datasets/sars-cov-2/references/MN908947/versions/2023-08-17T12:00:00Z/files/genemap.gff

@@ -0,0 +1,18 @@
+##gff-version 3
+##sequence-region MN908947 1 29903
+# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
+# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
+# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
+# seqname	source	feature	start	end	score	strand	frame	attribute
+MN908947	GenBank	gene	266	13468	.	+	.	gene_name=ORF1a
+MN908947	GenBank	gene	13468	21555	.	+	.	gene_name=ORF1b
+MN908947	GenBank	gene	25393	26220	.	+	.	gene_name=ORF3a
+MN908947	GenBank	gene	21563	25384	.	+	.	gene_name=S
+MN908947	GenBank	gene	26245	26472	.	+	.	gene_name=E
+MN908947	GenBank	gene	26523	27191	.	+	.	gene_name=M
+MN908947	GenBank	gene	27202	27387	.	+	.	gene_name=ORF6
+MN908947	GenBank	gene	27394	27759	.	+	.	gene_name=ORF7a
+MN908947	GenBank	gene	27756	27887	.	+	.	gene_name=ORF7b
+MN908947	GenBank	gene	27894	28259	.	+	.	gene_name=ORF8
+MN908947	GenBank	gene	28274	29533	.	+	.	gene_name=N
+MN908947	GenBank	gene	28284	28577	.	+	.	gene_name=ORF9b

data/datasets/sars-cov-2/references/MN908947/versions/2023-08-17T12:00:00Z/files/primers.csv

@@ -0,0 +1,37 @@
+Country (Institute),Target,Oligonucleotide,Sequence
+Charité (Germany),RdRp,Charité_RdRp_F,GTGARATGGTCATGTGTGGCGG
+Charité (Germany),RdRp,Charité_S_RdRp_P,CAGGTGGAACCTCATCAGGAGATGC
+Charité (Germany),RdRp,Charité_RdRp_R,CARATGTTAAASACACTATTAGCATA
+Charité (Germany),E,Charité_E_F,ACAGGTACGTTAATAGTTAATAGCGT
+Charité (Germany),E,Charité_E_P,ACACTAGCCATCCTTACTGCGCTTCG
+Charité (Germany),E,Charité_E_R,ATATTGCAGCAGTACGCACACA
+Charité (Germany),N,Charité_N_F,CACATTGGCACCCGCAATC
+Charité (Germany),N,Charité_N_P,ACTTCCTCAAGGAACAACATTGCCA
+Charité (Germany),N,Charité_N_R,GAGGAACGAGAAGAGGCTTG
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_F,TGGGGYTTTACRGGTAACCT
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_P,TAGTTGTGATGCWATCATGACTAG
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_R,AACRCGCTTAACAAAGCACTC
+HKU (Hong Kong),N,HKU_N_F,TAATCAGACAAGGAACTGATTA
+HKU (Hong Kong),N,HKU_N_P,GCAAATTGTGCAATTTGCGG
+HKU (Hong Kong),N,HKU_N_R,CGAAGGTGTGACTTCCATG
+China CDC (China),N,ChinaCDC_N_F,GGGGAACTTCTCCTGCTAGAAT
+China CDC (China),N,ChinaCDC_N_P,TTGCTGCTGCTTGACAGATT
+China CDC (China),N,ChinaCDC_N_R,CAGACATTTTGCTCTCAAGCTG
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_F,CCCTGTGGGTTTTACACTTAA
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_P,CCGTCTGCGGTATGTGGAAAGGTTATGG
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_R,ACGATTGTGCATCAGCTGA
+US CDC (United States),N1,USCDC_N1_F,GACCCCAAAATCAGCGAAAT
+US CDC (United States),N1,USCDC_N1_P,ACCCCGCATTACGTTTGGTGGACC
+US CDC (United States),N1,USCDC_N1_R,TCTGGTTACTGCCAGTTGAATCTG
+US CDC (United States),N2,USCDC_N2_F,TTACAAACATTGGCCGCAAA
+US CDC (United States),N2,USCDC_N2_P,ACAATTTGCCCCCAGCGCTTCAG
+US CDC (United States),N2,USCDC_N2_R,GCGCGACATTCCGAAGAA
+US CDC (United States),N3,USCDC_N3_F,GGGAGCCTTGAATACACCAAAA
+US CDC (United States),N3,USCDC_N3_P,AYCACATTGGCACCCGCAATCCTG
+US CDC (United States),N3,USCDC_N3_R,TGTAGCACGATTGCAGCATTG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_F,ATGAGCTTAGTCCTGTTG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_P,AGATGTCTTGTGCTGCCGGTA
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_R,CTCCCTTTGTTGTGTTGT
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_F,GGTAACTGGTATGATTTCG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_P,TCATACAAACCACGCCAGG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_R,CTGGTCAAGGTTAATATAGG