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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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JN.1.11+S:F59L,R346T,F456L+Orf3a:K16N+S:K478T(rev)( 6 seqs, 4 countries) #2068

Open aviczhl2 opened 1 week ago

aviczhl2 commented 1 week ago

Most seqs on this JN.1.11+S:R346T branch are dropouts from KP.2*. However, there seems to be a real branch hiding inside.

JN.1.11+C7979T, A12463G,T21737C,G22599C, T22928C(S:F59L,R346T,F456L)+G25440T(Orf3a:K16N)+C20436T, C21381T,A22995C(S:K478T rev)

All seqs have C7979T,A12463G have G17334T but not C7113T, this means it shall be a descendant directly from JN.1.11. And these two mutations do not appear in other lineages so small chance of recombinant.

And the S:K478T rev sub-branch is particularly interesting as it harbors recent GBW seqs from both China and India as well as USA local seq.

GISAID query: C7979T, A12463G,C20436T No. of seqs: 6(Canada 1 USA 5(1 from China, 2 from India))

First: EPI_ISL_19264665, 2024-7-9,Canada Latest: EPI_ISL_19427404, 2024-9-9, USA from China

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FedeGueli commented 1 week ago

this is a sublineage of branch 61 of #1089 ! then proposed in Pango https://github.com/cov-lineages/pango-designation/issues/2542 , but better to trrack the 478T sublineage here, not worth reopening the old things. thx for spotting it.

FedeGueli commented 5 days ago

i was tracking this too with C7979T, A12463G,C21381T but your query catches one more.