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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.2.3(no 31del)+S:T572I(96 seqs, 5 countries) #1735

Closed aviczhl2 closed 2 weeks ago

aviczhl2 commented 1 month ago

Most KP.2.3 has S:31del, however the 31del is after the KP.2.3 defining mutations of S:H146Q, Orf3a:K67N I find a KP.2.3 sub-branch with S:T572I that emerges from a KP.2.3 branch before the S:31del.

KP.2.3(no 31del)+C23277T(S:T572I)+C7420T

GISAID query for C7420T branch only : C7420T,C22000A, C23277T, G25593T GISAID query for general no-31del S:T572I branch: C22000A, C23277T, G25593T, -del21653, -28714 No. of seqs: 32(Israel 5 USA 27(2 from France))

First: EPI_ISL_19233571, 2024-4-16, USA Latest: EPI_ISL_19256471, 2024-7-3, Israel

Usher cannot handle deletions so put this branch together with other KP.2.3+S:T572I branches with S:S31del.

usher image

FedeGueli commented 1 month ago

I was thinking it could have been recombination with a KP.3.3.1 Canadian branch but being there G15543T it would mean multiple breakpoints so it is likely just homoplasy

aviczhl2 commented 1 month ago

38, Canada

aviczhl2 commented 2 weeks ago

80, Spain

FedeGueli commented 2 weeks ago

pls propose it

FedeGueli commented 2 weeks ago

96 now with a big batch from. texas uploaded after your last update