diff --git a/lineages/B.1.20.yml b/lineages/B.1.20.yml index 4b38481..e713985 100644 --- a/lineages/B.1.20.yml +++ b/lineages/B.1.20.yml @@ -2,6 +2,7 @@ name: B.1.20 unaliased_name: A.1.1.1.20 parent: B.1 +alias: F designation_date: "2023-08-01" defining_snps: - pos: 53326 diff --git a/lineages/B.1.23.yml b/lineages/B.1.23.yml new file mode 100644 index 0000000..3a335d6 --- /dev/null +++ b/lineages/B.1.23.yml @@ -0,0 +1,19 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: B.1.23 +unaliased_name: A.1.1.1.23 +parent: B.1 +designation_date: "2024-11-05" +defining_snps: + - pos: 27935 + nucleotide: A + - pos: 64171 + nucleotide: G + - pos: 73235 + nucleotide: T +reference_sequences: + - source: genbank + accession: PP754993 + isolate: WA-UW-288850 + - source: genbank + accession: PQ036000 + isolate: MPXV/PT0823/2024 diff --git a/lineages/B.1.6.yml b/lineages/B.1.6.yml index 9d08499..36ec6e2 100644 --- a/lineages/B.1.6.yml +++ b/lineages/B.1.6.yml @@ -2,6 +2,7 @@ name: B.1.6 unaliased_name: A.1.1.1.6 parent: B.1 +alias: D designation_date: "2022-08-25" defining_snps: - pos: 111029 diff --git a/lineages/C.1.1.yml b/lineages/C.1.1.yml index b3867be..392af11 100644 --- a/lineages/C.1.1.yml +++ b/lineages/C.1.1.yml @@ -2,6 +2,7 @@ name: C.1.1 unaliased_name: A.1.1.1.3.1.1 parent: C.1 +alias: E designation_date: "2024-04-15" defining_snps: - pos: 21062 diff --git a/lineages/D.1.yml b/lineages/D.1.yml new file mode 100644 index 0000000..cd999d0 --- /dev/null +++ b/lineages/D.1.yml @@ -0,0 +1,18 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: D.1 +unaliased_name: A.1.1.1.6.1 +parent: B.1.6 +designation_date: "2024-11-05" +defining_snps: + - pos: 10945 + nucleotide: A + - pos: 39515 + nucleotide: A + - pos: 44627 + nucleotide: T + - pos: 56276 + nucleotide: A +reference_sequences: + - source: genbank + accession: OQ503831 + isolate: MPXV/Human/USA/CA-LACPHL-MA00408/2023 diff --git a/lineages/E.1.yml b/lineages/E.1.yml new file mode 100644 index 0000000..73fc179 --- /dev/null +++ b/lineages/E.1.yml @@ -0,0 +1,16 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: E.1 +unaliased_name: A.1.1.1.3.1.1.1 +parent: C.1.1 +designation_date: "2024-11-05" +defining_snps: + - pos: 13563 + nucleotide: A + - pos: 121394 + nucleotide: T + - pos: 162280 + nucleotide: A +reference_sequences: + - source: genbank + accession: OR804499 + isolate: MPV/PT0732/2023 diff --git a/lineages/E.2.yml b/lineages/E.2.yml new file mode 100644 index 0000000..2beef08 --- /dev/null +++ b/lineages/E.2.yml @@ -0,0 +1,16 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: E.2 +unaliased_name: A.1.1.1.3.1.1.2 +parent: C.1.1 +designation_date: "2024-11-05" +defining_snps: + - pos: 13563 + nucleotide: A + - pos: 151847 + nucleotide: A + - pos: 37738 + nucleotide: T +reference_sequences: + - source: genbank + accession: OR487983 + isolate: MPXV/PT0661/2023 diff --git a/lineages/E.3.yml b/lineages/E.3.yml new file mode 100644 index 0000000..7f34796 --- /dev/null +++ b/lineages/E.3.yml @@ -0,0 +1,12 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: E.3 +unaliased_name: A.1.1.1.3.1.1.3 +parent: C.1.1 +designation_date: "2024-11-05" +defining_snps: + - pos: 142797 + nucleotide: T +reference_sequences: + - source: genbank + accession: OR326991 + isolate: MPXV/PT0627/2023 diff --git a/lineages/F.1.yml b/lineages/F.1.yml new file mode 100644 index 0000000..37711ed --- /dev/null +++ b/lineages/F.1.yml @@ -0,0 +1,20 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.1 +unaliased_name: A.1.1.1.20.1 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: + - pos: 11668 + nucleotide: A + - pos: 35132 + nucleotide: A + - pos: 70414 + nucleotide: T + - pos: 70666 + nucleotide: T + - pos: 96938 + nucleotide: T +reference_sequences: + - source: genbank + accession: PP533295 + isolate: NY-NYCPHL-001231 diff --git a/lineages/F.2.yml b/lineages/F.2.yml new file mode 100644 index 0000000..0776a3e --- /dev/null +++ b/lineages/F.2.yml @@ -0,0 +1,14 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.2 +unaliased_name: A.1.1.1.20.2 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: + - pos: 161629 + nucleotide: A + - pos: 22167 + nucleotide: T +reference_sequences: + - source: genbank + accession: PQ160003 + isolate: hMpxV/USA/CA-CDPH-1M1000491/2023 diff --git a/lineages/F.3.yml b/lineages/F.3.yml new file mode 100644 index 0000000..d176b06 --- /dev/null +++ b/lineages/F.3.yml @@ -0,0 +1,14 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.3 +unaliased_name: A.1.1.1.20.3 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: + - pos: 174050 + nucleotide: T + - pos: 180618 + nucleotide: T +reference_sequences: + - source: genbank + accession: OR473623 + isolate: hMpxV/USA/IL-RIPHL-MPXV-050-0081/2023 diff --git a/lineages/F.4.yml b/lineages/F.4.yml new file mode 100644 index 0000000..62eddcd --- /dev/null +++ b/lineages/F.4.yml @@ -0,0 +1,20 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.4 +unaliased_name: A.1.1.1.20.4 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: + - pos: 34277 + nucleotide: T + - pos: 92382 + nucleotide: T + - pos: 122551 + nucleotide: T + - pos: 126919 + nucleotide: A + - pos: 176643 + nucleotide: A +reference_sequences: + - source: genbank + accession: PP556326 + isolate: hMpxV/USA/IL-RIPHL-050-0153/2024 diff --git a/lineages/F.5.yml b/lineages/F.5.yml new file mode 100644 index 0000000..91ebcc9 --- /dev/null +++ b/lineages/F.5.yml @@ -0,0 +1,17 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.5 +unaliased_name: A.1.1.1.20.5 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: + - pos: 150831 + nucleotide: T + - pos: 126169 + nucleotide: A +reference_sequences: + - source: genbank + accession: PQ160004 + isolate: hMpxV/USA/CA-CDPH-1M1000492/2023 + - source: genbank + accession: PP533312 + isolate: NY-NYCPHL-001278 diff --git a/lineages/F.6.yml b/lineages/F.6.yml new file mode 100644 index 0000000..402b5d3 --- /dev/null +++ b/lineages/F.6.yml @@ -0,0 +1,17 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: F.6 +unaliased_name: A.1.1.1.20.6 +parent: B.1.20 +designation_date: "2024-11-05" +defining_snps: +# G146690A, C159608T, G168964A + - pos: 146690 + nucleotide: A + - pos: 159608 + nucleotide: T + - pos: 168964 + nucleotide: A +reference_sequences: + - source: genbank + accession: OR665162 + isolate: MpxV/human/USA/WA-UW-097833/2023