Designate B.1.21, B.1.22 and C.1.1

designation_records/B.1.21-B.1.22-C.1_2024-04-15.md

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+# 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).

lineages/B.1.21.yml

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+# 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

lineages/B.1.22.yml

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+# 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

lineages/C.1.1.yml

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+# 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