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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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XBB.1.16.6+Orf1a:H417Y, D4165G,S:Q14H,L455F,S810L(37 seqs, 8 countries) #2386

Closed xz-keg closed 10 months ago

xz-keg commented 11 months ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/976

I used to think this is sub-branch of JF.1 as it shares C23986T with JF.1 but as usher fixed the misplacement issue it is still not placed under JF.1 so may be independent branch.

XBB.1.16.6+C23986T+C28657T+C1514T, A12759G, G21604T,G22927T,C23991T(Orf1a:H417Y, D4165G, S:Q14H,L455F,S810L)

GISAID query: A12759G,G21604T,G22927T No. of seqs: 27(Australia 6 Canada 5 New Zealand 1 UK 3 Sweden 1 USA 11(1 from France))

25 on GISAID, 2 UK-Climb not on GISAID

First: EPI_ISL_18307795, USA, 2023-9-5 Latest: EPI_ISL_18536616,Australia 2023-11-14

Usher tree shows 26/27 of the seqs has additional S:S810L. For the 25 GISAID seqs, 22 have C23991T and the remaining 3 all have 23991 masked.

So the whole branch shall all have S:S810L.

usher

image

xz-keg commented 11 months ago

+1 Spain

xz-keg commented 10 months ago

Designated JF.3