From ee00f8c9058dc256620cd57db061116394d88a4e Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 5 Nov 2024 18:59:53 +0100 Subject: [PATCH 1/7] Newly designated lineages --- lineages/B.1.20.yml | 1 + lineages/B.1.23.yml | 19 +++++++++++++++++++ lineages/B.1.6.yml | 1 + lineages/C.1.1.yml | 1 + lineages/D.1.yml | 18 ++++++++++++++++++ lineages/E.1.yml | 16 ++++++++++++++++ lineages/E.2.yml | 16 ++++++++++++++++ lineages/E.3.yml | 12 ++++++++++++ lineages/F.1.yml | 20 ++++++++++++++++++++ lineages/F.2.yml | 14 ++++++++++++++ lineages/F.3.yml | 14 ++++++++++++++ lineages/F.4.yml | 20 ++++++++++++++++++++ lineages/F.5.yml | 17 +++++++++++++++++ lineages/F.6.yml | 17 +++++++++++++++++ 14 files changed, 186 insertions(+) create mode 100644 lineages/B.1.23.yml create mode 100644 lineages/D.1.yml create mode 100644 lineages/E.1.yml create mode 100644 lineages/E.2.yml create mode 100644 lineages/E.3.yml create mode 100644 lineages/F.1.yml create mode 100644 lineages/F.2.yml create mode 100644 lineages/F.3.yml create mode 100644 lineages/F.4.yml create mode 100644 lineages/F.5.yml create mode 100644 lineages/F.6.yml 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 From b2a4d9aca18749d100c2dab79cf5b119328447cf Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 5 Nov 2024 19:23:47 +0100 Subject: [PATCH 2/7] Add designation records --- .../B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md diff --git a/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md b/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md new file mode 100644 index 0000000..af0598a --- /dev/null +++ b/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md @@ -0,0 +1,83 @@ +# Designation of multiple B.1 sublineages, including deep aliases + +Transmission of descendants of the 2022 outbreak lineage B.1 is ongoing in 2024. The new lineage designations aim to capture current circulation (since July 2024), most of which has been concentrated into B.1.20 and C.1.1 - at least based on publicly available genomes which are predominantly from the US, Germany, Portugal, and Australia. + +The newly designated lineages are B.1.23; D.1 (B.1.6.1); E.1, E.2, E.3 (all children of C.1.1); and F.1, F.2, F.3, F.4, F.5, and F.6 (children of B.1.20). With these designations, the B.1 descendants are more clearly distinguished from each other. + +All of the 11 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.1.23 + +This lineage is a close sibling of B.1.20 and has been first sequenced in 2024, in Germany, Portugal and the US. + +The yaml file can be found [here](../lineages/B.1.23.yml). + +#### D.1 (alias of B.1.6.1) + +This is a predominantly South American lineage with public samples being available from Europe and North America. It was proposed for designation by the Peruvian Genomic Surveillance team of the Instituto Nacional de Salud in . + +The yaml file can be found [here](../lineages/D.1.yml). + +#### E.1 (alias of C.1.1.1) + +This descendant of C.1.1 has been sequenced in Portugal, Germany, and the US. + +The yaml file can be found [here](../lineages/E.1.yml). + +#### E.2 (alias of C.1.1.2) + +This descendant of C.1.1 has been sequenced in Portugal, Germany, Ireland, and the US. + +The yaml file can be found [here](../lineages/E.2.yml). + +#### E.3 (alias of C.1.1.3) + +This descendant of C.1.1 has been sequenced in Portugal, Germany, Australia, and the US. + +The yaml file can be found [here](../lineages/E.3.yml). + +#### F.1 (alias of B.1.20.1) + +Like most of B.1.20 and its descendants, this lineage is predominantly found in the US, but has also been sequenced in Germany and Australia. + +This lineage was proposed by Ammar Aziz of the Doherty Institute for Infection and Immunity in . + +The yaml file can be found [here](../lineages/F.1.yml). + +#### F.2 (alias of B.1.20.2) + +This B.1.20 sublineage is particularly common in the US and Australia, but was also sequenced in Germany. + +This lineage was proposed by Ammar Aziz of the Doherty Institute for Infection and Immunity in . + +The yaml file can be found [here](../lineages/F.2.yml). + +#### F.3 (alias of B.1.20.3) + +This B.1.20 sublineage is predominantly found in the US, but has also been sequenced in Germany. + +The yaml file can be found [here](../lineages/F.3.yml). + +#### F.4 (alias of B.1.20.4) + +This B.1.20 sublineage has been sequenced in the US, Germany and Portugal. + +The yaml file can be found [here](../lineages/F.4.yml). + +#### F.5 (alias of B.1.20.5) + +This B.1.20 sublineage has been sequenced in the US, Germany and Portugal. + +The yaml file can be found [here](../lineages/F.5.yml). + +#### F.6 (alias of B.1.20.6) + +This B.1.20 sublineage has been sequenced in the US and Germany. + +The yaml file can be found [here](../lineages/F.6.yml). From 998118bb266861d7e8100153a3b93e2c443fe6cd Mon Sep 17 00:00:00 2001 From: corneliusroemer Date: Tue, 5 Nov 2024 18:24:31 +0000 Subject: [PATCH 3/7] Update auto-generated files --- auto-generated/alias_key.json | 5 +- auto-generated/lineages.json | 312 +++++++++++++++++++++++++++++++++- auto-generated/lineages.md | 59 +++++++ 3 files changed, 374 insertions(+), 2 deletions(-) diff --git a/auto-generated/alias_key.json b/auto-generated/alias_key.json index d7750c6..eb9965c 100644 --- a/auto-generated/alias_key.json +++ b/auto-generated/alias_key.json @@ -1,5 +1,8 @@ { "A": "", "B": "A.1.1", - "C": "A.1.1.1.3" + "C": "A.1.1.1.3", + "D": "A.1.1.1.6", + "E": "A.1.1.1.3.1.1", + "F": "A.1.1.1.20" } diff --git a/auto-generated/lineages.json b/auto-generated/lineages.json index 9551fa2..823aad9 100644 --- a/auto-generated/lineages.json +++ b/auto-generated/lineages.json @@ -508,6 +508,7 @@ "unaliased_name": "A.1.1.1.2" }, { + "alias": "F", "defining_snps": [ { "nucleotide": "A", @@ -585,6 +586,38 @@ ], "unaliased_name": "A.1.1.1.22" }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 27935 + }, + { + "nucleotide": "G", + "pos": 64171 + }, + { + "nucleotide": "T", + "pos": 73235 + } + ], + "designation_date": "2024-11-05", + "name": "B.1.23", + "parent": "B.1", + "reference_sequences": [ + { + "accession": "PP754993", + "isolate": "WA-UW-288850", + "source": "genbank" + }, + { + "accession": "PQ036000", + "isolate": "MPXV/PT0823/2024", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.23" + }, { "alias": "C", "defining_snps": [ @@ -654,6 +687,7 @@ "unaliased_name": "A.1.1.1.5" }, { + "alias": "D", "defining_snps": [ { "nucleotide": "A", @@ -753,6 +787,7 @@ "unaliased_name": "A.1.1.1" }, { + "alias": "E", "defining_snps": [ { "nucleotide": "T", @@ -806,8 +841,283 @@ } ], "unaliased_name": "A.1.1.1.3.1" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 10945 + }, + { + "nucleotide": "A", + "pos": 39515 + }, + { + "nucleotide": "T", + "pos": 44627 + }, + { + "nucleotide": "A", + "pos": 56276 + } + ], + "designation_date": "2024-11-05", + "name": "D.1", + "parent": "B.1.6", + "reference_sequences": [ + { + "accession": "OQ503831", + "isolate": "MPXV/Human/USA/CA-LACPHL-MA00408/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.6.1" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 13563 + }, + { + "nucleotide": "T", + "pos": 121394 + }, + { + "nucleotide": "A", + "pos": 162280 + } + ], + "designation_date": "2024-11-05", + "name": "E.1", + "parent": "C.1.1", + "reference_sequences": [ + { + "accession": "OR804499", + "isolate": "MPV/PT0732/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.3.1.1.1" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 13563 + }, + { + "nucleotide": "A", + "pos": 151847 + }, + { + "nucleotide": "T", + "pos": 37738 + } + ], + "designation_date": "2024-11-05", + "name": "E.2", + "parent": "C.1.1", + "reference_sequences": [ + { + "accession": "OR487983", + "isolate": "MPXV/PT0661/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.3.1.1.2" + }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 142797 + } + ], + "designation_date": "2024-11-05", + "name": "E.3", + "parent": "C.1.1", + "reference_sequences": [ + { + "accession": "OR326991", + "isolate": "MPXV/PT0627/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.3.1.1.3" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 11668 + }, + { + "nucleotide": "A", + "pos": 35132 + }, + { + "nucleotide": "T", + "pos": 70414 + }, + { + "nucleotide": "T", + "pos": 70666 + }, + { + "nucleotide": "T", + "pos": 96938 + } + ], + "designation_date": "2024-11-05", + "name": "F.1", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "PP533295", + "isolate": "NY-NYCPHL-001231", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.1" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 161629 + }, + { + "nucleotide": "T", + "pos": 22167 + } + ], + "designation_date": "2024-11-05", + "name": "F.2", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "PQ160003", + "isolate": "hMpxV/USA/CA-CDPH-1M1000491/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.2" + }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 174050 + }, + { + "nucleotide": "T", + "pos": 180618 + } + ], + "designation_date": "2024-11-05", + "name": "F.3", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "OR473623", + "isolate": "hMpxV/USA/IL-RIPHL-MPXV-050-0081/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.3" + }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 34277 + }, + { + "nucleotide": "T", + "pos": 92382 + }, + { + "nucleotide": "T", + "pos": 122551 + }, + { + "nucleotide": "A", + "pos": 126919 + }, + { + "nucleotide": "A", + "pos": 176643 + } + ], + "designation_date": "2024-11-05", + "name": "F.4", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "PP556326", + "isolate": "hMpxV/USA/IL-RIPHL-050-0153/2024", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.4" + }, + { + "defining_snps": [ + { + "nucleotide": "T", + "pos": 150831 + }, + { + "nucleotide": "A", + "pos": 126169 + } + ], + "designation_date": "2024-11-05", + "name": "F.5", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "PQ160004", + "isolate": "hMpxV/USA/CA-CDPH-1M1000492/2023", + "source": "genbank" + }, + { + "accession": "PP533312", + "isolate": "NY-NYCPHL-001278", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.5" + }, + { + "defining_snps": [ + { + "nucleotide": "A", + "pos": 146690 + }, + { + "nucleotide": "T", + "pos": 159608 + }, + { + "nucleotide": "A", + "pos": 168964 + } + ], + "designation_date": "2024-11-05", + "name": "F.6", + "parent": "B.1.20", + "reference_sequences": [ + { + "accession": "OR665162", + "isolate": "MpxV/human/USA/WA-UW-097833/2023", + "source": "genbank" + } + ], + "unaliased_name": "A.1.1.1.20.6" } ], "schemaVersion": "1.0.0", - "timestamp": "2024-04-17T15:08:38" + "timestamp": "2024-11-05T18:24:30" } diff --git a/auto-generated/lineages.md b/auto-generated/lineages.md index 573bbc2..a582566 100644 --- a/auto-generated/lineages.md +++ b/auto-generated/lineages.md @@ -144,6 +144,13 @@ - [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.1.23 + * parent: [B.1](#B1) + * defining SNPs: 27935A,64171G,73235T + * reference sequences: + - [WA-UW-288850](https://www.ncbi.nlm.nih.gov/nuccore/PP754993) + - [MPXV/PT0823/2024](https://www.ncbi.nlm.nih.gov/nuccore/PQ036000) + ## B.1.3 * parent: [B.1](#B1) * defining SNPs: 190660A @@ -194,3 +201,55 @@ - [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) +## D.1 + * parent: [B.1.6](#B16) + * defining SNPs: 10945A,39515A,44627T,56276A + * reference sequence: [MPXV/Human/USA/CA-LACPHL-MA00408/2023](https://www.ncbi.nlm.nih.gov/nuccore/OQ503831) + +## E.1 + * parent: [C.1.1](#C11) + * defining SNPs: 13563A,121394T,162280A + * reference sequence: [MPV/PT0732/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR804499) + +## E.2 + * parent: [C.1.1](#C11) + * defining SNPs: 13563A,151847A,37738T + * reference sequence: [MPXV/PT0661/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR487983) + +## E.3 + * parent: [C.1.1](#C11) + * defining SNPs: 142797T + * reference sequence: [MPXV/PT0627/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR326991) + +## F.1 + * parent: [B.1.20](#B120) + * defining SNPs: 11668A,35132A,70414T,70666T,96938T + * reference sequence: [NY-NYCPHL-001231](https://www.ncbi.nlm.nih.gov/nuccore/PP533295) + +## F.2 + * parent: [B.1.20](#B120) + * defining SNPs: 161629A,22167T + * reference sequence: [hMpxV/USA/CA-CDPH-1M1000491/2023](https://www.ncbi.nlm.nih.gov/nuccore/PQ160003) + +## F.3 + * parent: [B.1.20](#B120) + * defining SNPs: 174050T,180618T + * reference sequence: [hMpxV/USA/IL-RIPHL-MPXV-050-0081/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR473623) + +## F.4 + * parent: [B.1.20](#B120) + * defining SNPs: 34277T,92382T,122551T,126919A,176643A + * reference sequence: [hMpxV/USA/IL-RIPHL-050-0153/2024](https://www.ncbi.nlm.nih.gov/nuccore/PP556326) + +## F.5 + * parent: [B.1.20](#B120) + * defining SNPs: 150831T,126169A + * reference sequences: + - [hMpxV/USA/CA-CDPH-1M1000492/2023](https://www.ncbi.nlm.nih.gov/nuccore/PQ160004) + - [NY-NYCPHL-001278](https://www.ncbi.nlm.nih.gov/nuccore/PP533312) + +## F.6 + * parent: [B.1.20](#B120) + * defining SNPs: 146690A,159608T,168964A + * reference sequence: [MpxV/human/USA/WA-UW-097833/2023](https://www.ncbi.nlm.nih.gov/nuccore/OR665162) + From e8da626094b266e53089005c5646baeb9d09bd95 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 5 Nov 2024 19:27:12 +0100 Subject: [PATCH 4/7] Add a few more issues --- designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md b/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md index af0598a..f9bedc9 100644 --- a/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md +++ b/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md @@ -16,6 +16,8 @@ All of the 11 lineages satisfy the criteria for lineage designation last updated This lineage is a close sibling of B.1.20 and has been first sequenced in 2024, in Germany, Portugal and the US. +The associated Github issue is . + The yaml file can be found [here](../lineages/B.1.23.yml). #### D.1 (alias of B.1.6.1) @@ -28,18 +30,24 @@ The yaml file can be found [here](../lineages/D.1.yml). This descendant of C.1.1 has been sequenced in Portugal, Germany, and the US. +The associated Github issue is . + The yaml file can be found [here](../lineages/E.1.yml). #### E.2 (alias of C.1.1.2) This descendant of C.1.1 has been sequenced in Portugal, Germany, Ireland, and the US. +The associated Github issue is . + The yaml file can be found [here](../lineages/E.2.yml). #### E.3 (alias of C.1.1.3) This descendant of C.1.1 has been sequenced in Portugal, Germany, Australia, and the US. +The associated Github issue is . + The yaml file can be found [here](../lineages/E.3.yml). #### F.1 (alias of B.1.20.1) From 9a501684245a0544f5d57602a80140f7df9b9b60 Mon Sep 17 00:00:00 2001 From: corneliusroemer Date: Tue, 5 Nov 2024 18:27:30 +0000 Subject: [PATCH 5/7] Update auto-generated files --- auto-generated/lineages.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/auto-generated/lineages.json b/auto-generated/lineages.json index 823aad9..6f76631 100644 --- a/auto-generated/lineages.json +++ b/auto-generated/lineages.json @@ -1119,5 +1119,5 @@ } ], "schemaVersion": "1.0.0", - "timestamp": "2024-11-05T18:24:30" + "timestamp": "2024-11-05T18:27:29" } From e9e4fcb0b8d04ebe334e2022f78e9a0c85f16c72 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 5 Nov 2024 19:36:19 +0100 Subject: [PATCH 6/7] Update Readme, fix filename of C.1.1 designation record --- README.md | 31 ++++++++++++------- ...5.md => B.1.21-B.1.22-C.1.1_2024-04-15.md} | 0 2 files changed, 19 insertions(+), 12 deletions(-) rename designation_records/{B.1.21-B.1.22-C.1_2024-04-15.md => B.1.21-B.1.22-C.1.1_2024-04-15.md} (100%) diff --git a/README.md b/README.md index ce8c33e..3b3fa20 100644 --- a/README.md +++ b/README.md @@ -9,19 +9,21 @@ The recent outbreak among humans originated from clade IIb. ## [Lineage summary](auto-generated/lineages.md) ## Designation of lineages + New lineages are designated as more cases are sequenced and the outbreak gets more diverse. The criteria for lineage designation will evolve as the outbreak continues. Currently, we aim to designate a new lineage if it - - has spread internationally - - has at least 1 mutation above its parent - - contains at least 15 sequences or plausibly represents undersampled diversity - - has a 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 (high quality meaning that it doesn't show unusually large numbers of frame shifts and/or stop codons) +- has spread internationally +- has at least 1 mutation above its parent +- contains at least 15 sequences or plausibly represents undersampled diversity +- has a 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 (high quality meaning that it doesn't show unusually large numbers of frame shifts and/or stop codons) Each new lineage is defined by a `yaml` file according the [schema](schemas/single_lineage/lineage_schema_1-0-0.yml). For lineage [B.1](lineages/B.1.yml), for example, this looks like this -``` + +```yaml # yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml name: B.1 unaliased_name: A.1.1.1 @@ -41,11 +43,16 @@ A human readable summary of all designated lineages can be found [here](auto-gen You can find markdown documents describing the rationale of lineage designation (including which lineages and why) in the "designation_records" folder. - - [2022-08-08: B.1.1-B.1.5](designation_records/B.1.1-B.1.5_2022-08-08.md) - - [2022-08-25: B.1.6-B.1.8](designation_records/B.1.6-B.1.8_2022-08-25.md) - - [2022-09-13: B.1.9-A.2.1](designation_records/B.1.9-A.2.1_2022-09-13.md) - - [2022-09-26: B.1.10-A.2.2](designation_records/B.1.10-A.2.2_2022-09-26.md) +- [2022-08-08: B.1.1-B.1.5](designation_records/B.1.1-B.1.5_2022-08-08.md) +- [2022-08-25: B.1.6-B.1.8](designation_records/B.1.6-B.1.8_2022-08-25.md) +- [2022-09-13: B.1.9-A.2.1](designation_records/B.1.9-A.2.1_2022-09-13.md) +- [2022-09-26: B.1.10-A.2.2](designation_records/B.1.10-A.2.2_2022-09-26.md) +- [2022-10-31: B.1.13-B.1.14-A.2.3-A.3](designation_records/B.1.13-B.1.14-A.2.3-A.3_2022-10-31.md) +- [2023-01-11: B.1.15-B.1.16-B.1.17](designation_records/B.1.15-B.1.16-B.1.17_2023-01-11.md) +- [2023-08-01: B.1.18-B.1.19-B.1.20-C.1](designation_records/B.1.18-B.1.19-B.1.20-C.1_2023-08-01.md) +- [2024-04-15: B.1.21-B.1.22-C.1.1](designation_records/B.1.21-B.1.22-C.1.1_2024-04-15.md) +- [2024-11-05: B.1.23-D.1-E.1-3-F.1-6](designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md) -### Lineage proposals -To propose additional lineages, open a github issue in this repository. +## Lineage proposals +To propose additional lineages, open a github issue in this repository. 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.1.1_2024-04-15.md similarity index 100% rename from designation_records/B.1.21-B.1.22-C.1_2024-04-15.md rename to designation_records/B.1.21-B.1.22-C.1.1_2024-04-15.md From 3bb84415a687bea2ca7e3101b60e926735211b13 Mon Sep 17 00:00:00 2001 From: corneliusroemer Date: Tue, 5 Nov 2024 18:37:06 +0000 Subject: [PATCH 7/7] Update auto-generated files --- auto-generated/lineages.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/auto-generated/lineages.json b/auto-generated/lineages.json index 72ee821..e9980ed 100644 --- a/auto-generated/lineages.json +++ b/auto-generated/lineages.json @@ -1112,5 +1112,5 @@ } ], "schemaVersion": "1.0.0", - "timestamp": "2024-11-05T18:31:03" + "timestamp": "2024-11-05T18:37:05" }