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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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JN.2+S:V193L(92 seqs, 16 countries) #2442

Closed aviczhl2 closed 6 months ago

aviczhl2 commented 6 months ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1181

JN.2+G22139T(S:V193L)

GISAID query: G22139T,A2127G,-19325 No. of seqs: 92(Austria 1 Belgium 1 Denmark 30 UK 8 France 8 Germany 3 Ireland 1 Luxembourg 1 Netherlands 9 Norway 2 Poland 3 Slovakia 2 Spain 1 Sweden 20 Switzerland 1 USA 1)

First: EPI_ISL_18387106,France, 2023-10-1 Latest: EPI_ISL_18724511, Netherlands, 2023-12-28

usher

image

corneliusroemer commented 6 months ago

IIRC, this one could as well be a JN.6 with ORf1a:Y621C homoplasically acquired?

corneliusroemer commented 6 months ago

OK, A->G (ORF1a:Y621C) has a much lower rate (right panel) than S:V193L:

image

https://pubmed.ncbi.nlm.nih.gov/37039557/

So let's go with JN.2 sublineage

aviczhl2 commented 6 months ago

IIRC, this one could as well be a JN.6 with ORf1a:Y621C homoplasically acquired?

Yeah. Also possible for JN.2/JN.6 recombinant.