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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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KP.4.2.4(S:S256L,S:S31del)+S:R190S(57 seqs,>10 places) #2759

Open xz-keg opened 2 months ago

xz-keg commented 2 months ago

From branch 21 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502 and branch 4 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1771

This used to be a UK cluster but further seqs show it clearly circulating in undersampled regions of eastern Europe and middle east.

KP.4.2+A1989G(Orf1a:Q575R)+C22329T(S:S256L)+C6040T, C28744T,del21653_21655(S:S31-)

GISAID query: del21653,A1989G,C6070T No. of seqs: 19(Sweden 1 France 1 Moldova 1 USA 3(2 from UAE) UK 13)

First: EPI_ISL_19265289, UK, 2024-6-26 Latest: EPI_ISL_19369879, USA from UAE, 2024-8-21

GISAID query for S:R190S branch:A1989G,C6070T, G22132T(16 seqs)

Everything on the C6070T,C28744T branch have S:S31-, while the UK cluster has further S:R190S.

usher image

xz-keg commented 2 months ago

22, Netherlands, Norway

xz-keg commented 2 months ago

24, Croatia

FedeGueli commented 2 months ago

5/25 are very recent (end of August start of September) it should be stay open

xz-keg commented 1 month ago

29, Greece, Canada

DailyCovidCases commented 1 month ago

Tree now: usher Covspectrum: KP.4.2* & A1989G & C6070T & 21653- Screenshot (246) @corneliusroemer Is this branch worth a designation?

FedeGueli commented 1 month ago

Slowing down a lot

xz-keg commented 1 month ago

38, Also from Bahrain and Czech Republic

xz-keg commented 4 weeks ago

a lot of submissions from Russia, making it 49-41

xz-keg commented 3 weeks ago

The S256L+31del branch is designated KP.4.2.3

FedeGueli commented 3 weeks ago

The S256L+31del branch is designated KP.4.2.3

via https://github.com/cov-lineages/pango-designation/commit/e9456680079b8527d68e29009be40db72c1a709f

NkRMnZr commented 3 weeks ago

it's KP.4.2.4 from lineage_notes.txt and lineages.csv, I think the title of the commit cov-lineages/pango-designation@e945668 is mislabeled

xz-keg commented 3 weeks ago

45, Italy, New Zealand

xz-keg commented 1 week ago

some seqs have problem recognizing the 31del(they also don't register all nearby mutations like S:24-26del or S:ins16), edit query, real toll shall be 57.

FedeGueli commented 1 week ago

A1989G,C6070T, G22132T

there are only 4 sequences of KP.4.2.4 without 190S , i suggest to close this and if @corneliusroemer can to add it to defining of KP.4.2.4