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/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 6aa945f..e9980ed 100644 --- a/auto-generated/lineages.json +++ b/auto-generated/lineages.json @@ -501,6 +501,7 @@ "unaliased_name": "A.1.1.1.2" }, { + "alias": "F", "defining_snps": [ { "nucleotide": "A", @@ -578,6 +579,38 @@ ], "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": [ @@ -647,6 +680,7 @@ "unaliased_name": "A.1.1.1.5" }, { + "alias": "D", "defining_snps": [ { "nucleotide": "A", @@ -746,6 +780,7 @@ "unaliased_name": "A.1.1.1" }, { + "alias": "E", "defining_snps": [ { "nucleotide": "T", @@ -799,8 +834,283 @@ } ], "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": "2024-11-05T18:31:03" + "timestamp": "2024-11-05T18:37:05" } diff --git a/auto-generated/lineages.md b/auto-generated/lineages.md index e0633b7..64c358e 100644 --- a/auto-generated/lineages.md +++ b/auto-generated/lineages.md @@ -141,6 +141,13 @@ - [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 @@ -191,3 +198,55 @@ - [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) + 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 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..f9bedc9 --- /dev/null +++ b/designation_records/B.1.23-D.1-E.1-3-F.1-6_2024-11-05.md @@ -0,0 +1,91 @@ +# 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 associated Github issue is . + +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 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) + +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). 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