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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.4.2+S:S60P+Orf1b:P2313S,S:I212T (13 seqs, 5 countries) #1667

Open aviczhl2 opened 2 weeks ago

aviczhl2 commented 2 weeks ago

KP.4.2+A15171G+T21740C, A29700G(S:S60P)+A17637G,T22197C(Orf1b:P2313S,S:I212T)

This branch suddenly emerges in multiple countries, deserve watching.

Note that the S:I212T is read as S:N211T+S:L212del to replace the S: N211del+S:L212I in JN.1 on GISAID. It is read as S:L212S in usher. However, both reads are incorrect. As S:L212I being default in BA.2.86, this shall be S:I212T. @AngieHinrichs, why is it read as S:L212S instead of S:I212T?

GISAID query: A15171G,A17637G, T22197C No. of seqs: 6(UK 1 France 2 Canada 1 USA 2( 1 from Iceland))

First: EPI_ISL_19194097, USA, 2024-5-21 Latest: EPI_ISL_19221275, USA from Iceland, 2024-6-16

usher image

FedeGueli commented 2 weeks ago

Usher doesnt read deletion so: wrongly it is TCA for it so >> S. But the correct way is shown by CovSpectrum:

Screenshot 2024-07-02 alle 15 41 39
AngieHinrichs commented 2 weeks ago

@AngieHinrichs, why is it read as S:L212S instead of S:I212T?

Probably a difference in left/right alignment between mafft (with NC_045512 reference) and whatever tool CoVSpectrum is using to align sequences.

FedeGueli commented 1 week ago

+2 GBW from France