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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Proposal for South African Delta sub-lineage (~50%, 15k seq) #246

Closed corneliusroemer closed 3 years ago

corneliusroemer commented 3 years ago

New lineage proposal by @CorneliusRoemer

Description Sub-lineage of: B.1.617.2 Earliest sequence: May 2021 (South Africa) Most recent sequence: Current Countries circulating: Mostly South Africa where it makes up ~50 of all sequences

Defining: nuc:25413T then ORF1b:115I There is another smaller lineage, also mostly South Africa with nuc:25413T + ORF1a:536L + ORF8:115C that may be designated as well.

One could always choose nuc:25413T by itself as common ancestor of both because that lineage is present in many more countries. Narrowing to ORF1b:115I makes it more focused on South Africa.

I'd designate the parent of both that has nuc:25413T, since that's the epidemiologically significant (it seems, single introduction to SA)

https://nextstrain.org/groups/neherlab/ncov/global?branchLabel=aa&c=gt-nuc_25413 image

Genomes nuc:25413T.txt ORF1b:115I.txt

Proposed lineage name AY.x

chrisruis commented 3 years ago

Thanks @corneliusroemer It looks like these sequences have been split in the latest UShER tree so they are now in several clades that branch off a large polytomy. There is a clear South Africa clade that contains a lot of the sequences and we've designated this clade as AY.45 in v1.2.87. AY.45 starts on a branch with G13812T (Orf1ab:M4516I) and has 3669 sequence designations. It looks like the other sequences are in small clades without clear geographical clustering so we haven't designated these for now.

FedeGueli commented 3 years ago

cc @chrisruis @corneliusroemer The previously undesignated subclade proposed here starting with ORF8:R115C has now been designated as AY.91

commits: https://github.com/cov-lineages/pango-designation/commit/d11d64b93df7a664779b5c38c3cdc8347ad4585e

and

https://github.com/cov-lineages/pango-designation/commit/086bbc11a7c6f1cf7ac4caeeb85dc3dea780b0e4