Merge pull request #45 from mpxv-lineages/designations-2024-11

Designation of 11 new B.1 sublineages

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.

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"
 }