diff --git a/auto-generated/lineages.json b/auto-generated/lineages.json index 5a6bf5c..fbf22a0 100644 --- a/auto-generated/lineages.json +++ b/auto-generated/lineages.json @@ -534,6 +534,57 @@ ], "unaliased_name": "A.1.1.1.20" }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 22415 + }, + { + "nucleotide": "T", + "pos": 132698 + } + ], + "designation_date": "2023-04-15", + "name": "B.1.21", + "parent": "B.1", + "reference_sequences": [ + { + "accession": "OP539939", + "isolate": "MPX/Human/USA/CA-LACPHL-MA00153/2022", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.21" + }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 34784 + }, + { + "nucleotide": "T", + "pos": 101418 + } + ], + "designation_date": "2023-04-15", + "name": "B.1.22", + "parent": "B.1", + "reference_sequences": [ + { + "accession": "OQ773522", + "isolate": "MPXV/Germany/2022/ON/RKI903", + "source": "genbank" + }, + { + "accession": "OR095023", + "isolate": "MPXV/UZ_REGA_205/Belgium/2022", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.22" + }, { "alias": "C", "defining_snps": [ @@ -701,6 +752,34 @@ ], "unaliased_name": "A.1.1.1" }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 21062 + }, + { + "nucleotide": "T", + "pos": 149963 + } + ], + "designation_date": "2024-04-15", + "name": "C.1.1", + "parent": "C.1", + "reference_sequences": [ + { + "accession": "OR643705", + "isolate": "MPV/Human/USA/CA-LACPHL-MA00563/2023", + "source": "genbank" + }, + { + "accession": "OR804476", + "isolate": "MPV/PT0706/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.3.1.1" + }, { "defining_snps": [ { @@ -730,5 +809,5 @@ } ], "schemaVersion": "1.0.0", - "timestamp": "2023-07-31T09:17:14" + "timestamp": "2024-04-15T18:13:21" } diff --git a/auto-generated/lineages.md b/auto-generated/lineages.md index 6925957..573bbc2 100644 --- a/auto-generated/lineages.md +++ b/auto-generated/lineages.md @@ -132,6 +132,18 @@ * defining SNPs: 53326A,164385T,187620T * reference sequence: [MPXV_USA_2022_TX0040](https://www.ncbi.nlm.nih.gov/nuccore/OQ320441) +## B.1.21 + * parent: [B.1](#B1) + * defining SNPs: 22415A,132698T + * reference sequence: [MPX/Human/USA/CA-LACPHL-MA00153/2022](https://www.ncbi.nlm.nih.gov/nuccore/OP539939) + +## B.1.22 + * parent: [B.1](#B1) + * defining SNPs: 34784T,101418T + * reference sequences: + - [MPXV/Germany/2022/ON/RKI903](https://www.ncbi.nlm.nih.gov/nuccore/OQ773522) + - [MPXV/UZ_REGA_205/Belgium/2022](https://www.ncbi.nlm.nih.gov/nuccore/OR095023) + ## B.1.3 * parent: [B.1](#B1) * defining SNPs: 190660A @@ -175,3 +187,10 @@ * defining SNPs: 105923A,64426T,55133A * reference sequence: [MPXV/human/Japan/Tokyo/2022/TKY220165](https://www.ncbi.nlm.nih.gov/nuccore/LC753968) +## C.1.1 + * parent: [C.1](#C1) + * defining SNPs: 21062T,149963T + * reference sequences: + - [MPV/Human/USA/CA-LACPHL-MA00563/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR643705) + - [MPV/PT0706/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR804476) + diff --git a/designation_records/B.1.21-B.1.22-C.1_2024-04-15.md b/designation_records/B.1.21-B.1.22-C.1_2024-04-15.md new file mode 100644 index 0000000..2e04b86 --- /dev/null +++ b/designation_records/B.1.21-B.1.22-C.1_2024-04-15.md @@ -0,0 +1,32 @@ +# Designation of two B.1 sublineages and one C.1 sublineage + +Transmission of descendants of the 2022 outbreak lineage B.1 is ongoing in 2023 and 2024. Most of the sequenced genomes fall within one of 4 lineages, 3 of which are newly designated here: B.1.21, B.1.22, C.1.1, while B.1.20 is a previously designated lineage. With these designations. + +All of the 3 lineages satisfy the criteria for lineage designation last updated in October 2023: + +- International spread +- Having at least 2 mutation above the parent lineage (increased from 1) +- Containing at least 15 sequences or plausibly represents undersampled diversity +- Clear common phylogenetic structure (no uncertainty about possibly being designated as 2 lineages instead of 1) +- Has at least one freely available high quality reference sequence + +#### B.1.21 + +This is a mostly cross-US lineage with the most recent sequence collected in February 2024. + +It is defined by `G22415A` and `C132698T`. +The yaml file can be found [here](../lineages/B.1.21.yml). + +#### B.1.22 + +This is a mostly German lineage with the most recent sequence collected in March 2024. + +It is defined by `C34784T` and `C101418T`. +The yaml file can be found [here](../lineages/B.1.22.yml). + +#### C.1.1 (alias of B.1.3.1.1) + +This is a global lineage with the most recent sequence collected in March 2024. It was sequenced particularly frequently in Portugal, but also in Germany and the US - which are the major sequencing countries that submit to the INSDC. GISAID-only sequences indicate this lineage was common in China. + +It is defined by `C21062T` and `C149963T`. +The `yaml` file can be found [here](../lineages/C.1.1.yml). diff --git a/lineages/B.1.21.yml b/lineages/B.1.21.yml new file mode 100644 index 0000000..ca527b0 --- /dev/null +++ b/lineages/B.1.21.yml @@ -0,0 +1,14 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: B.1.21 +unaliased_name: A.1.1.1.21 +parent: B.1 +designation_date: "2023-04-15" +defining_snps: + - pos: 22415 + nucleotide: A + - pos: 132698 + nucleotide: T +reference_sequences: + - source: genbank + accession: OP539939 + isolate: MPX/Human/USA/CA-LACPHL-MA00153/2022 \ No newline at end of file diff --git a/lineages/B.1.22.yml b/lineages/B.1.22.yml new file mode 100644 index 0000000..633c0d3 --- /dev/null +++ b/lineages/B.1.22.yml @@ -0,0 +1,17 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: B.1.22 +unaliased_name: A.1.1.1.22 +parent: B.1 +designation_date: "2023-04-15" +defining_snps: + - pos: 34784 + nucleotide: T + - pos: 101418 + nucleotide: T +reference_sequences: + - source: genbank + accession: OQ773522 + isolate: MPXV/Germany/2022/ON/RKI903 + - source: genbank + accession: OR095023 + isolate: MPXV/UZ_REGA_205/Belgium/2022 \ No newline at end of file diff --git a/lineages/C.1.1.yml b/lineages/C.1.1.yml new file mode 100644 index 0000000..b3867be --- /dev/null +++ b/lineages/C.1.1.yml @@ -0,0 +1,17 @@ +# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml +name: C.1.1 +unaliased_name: A.1.1.1.3.1.1 +parent: C.1 +designation_date: "2024-04-15" +defining_snps: + - pos: 21062 + nucleotide: T + - pos: 149963 + nucleotide: T +reference_sequences: + - source: genbank + accession: OR643705 + isolate: MPV/Human/USA/CA-LACPHL-MA00563/2023 + - source: genbank + accession: OR804476 + isolate: MPV/PT0706/2023