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KP.4.2.4(S:S256L,S:S31del)+S:R190S(46 seqs,>10 places) #2759

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xz-keg opened this issue Sep 2, 2024 · 12 comments
Open

KP.4.2.4(S:S256L,S:S31del)+S:R190S(46 seqs,>10 places) #2759

xz-keg opened this issue Sep 2, 2024 · 12 comments

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@xz-keg
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xz-keg commented Sep 2, 2024 •
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From branch 21 of sars-cov-2-variants/lineage-proposals#1502
and branch 4 of sars-cov-2-variants/lineage-proposals#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:del21653,A1989G,C6070T, G22132T(16 seqs)

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

usher
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@xz-keg xz-keg mentioned this issue Sep 2, 2024
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@xz-keg
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xz-keg commented Sep 14, 2024

22, Netherlands, Norway

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(19 seqs, 6 countries, 16 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(22 seqs, 8 countries, 18 with S:R190S) Sep 14, 2024
@xz-keg
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xz-keg commented Sep 19, 2024

24, Croatia

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(22 seqs, 8 countries, 18 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(24 seqs, 9 countries, 18 with S:R190S) Sep 19, 2024
@FedeGueli
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5/25 are very recent (end of August start of September) it should be stay open

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(24 seqs, 9 countries, 18 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(29 seqs, 11 countries, 22 with S:R190S) Sep 28, 2024
@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(29 seqs, 11 countries, 22 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(29 seqs,>10 places, 22 with S:R190S) Sep 28, 2024
@xz-keg
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xz-keg commented Sep 28, 2024

29, Greece, Canada

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

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(29 seqs,>10 places, 22 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(30 seqs,>10 places, 23 with S:R190S) Oct 8, 2024
@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(30 seqs,>10 places, 23 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(31 seqs,>10 places, 24 with S:R190S) Oct 11, 2024
@FedeGueli
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Slowing down a lot

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(31 seqs,>10 places, 24 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(38 seqs,>10 places, 30 with S:R190S) Oct 19, 2024
@xz-keg
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xz-keg commented Oct 19, 2024

38, Also from Bahrain and Czech Republic

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(38 seqs,>10 places, 30 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(39 seqs,>10 places, 31 with S:R190S) Oct 23, 2024
@xz-keg
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xz-keg commented Oct 26, 2024

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

@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(39 seqs,>10 places, 31 with S:R190S) KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(49 seqs,>10 places, 41 with S:R190S) Oct 26, 2024
@xz-keg xz-keg changed the title KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(49 seqs,>10 places, 41 with S:R190S) KP.4.2.3(S:S256L,S:S31del)+S:R190S(41 seqs,>10 places) Oct 27, 2024
@xz-keg
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xz-keg commented Oct 27, 2024

The S256L+31del branch is designated KP.4.2.3

@FedeGueli
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The S256L+31del branch is designated KP.4.2.3

via e945668

FedeGueli referenced this issue Oct 27, 2024
@corneliusroemer
Designate KP.4.2.3/4
e945668
@NkRMnZr
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NkRMnZr commented Oct 28, 2024

it's KP.4.2.4 from lineage_notes.txt and lineages.csv, I think the title of the commit e945668 is mislabeled

@xz-keg xz-keg changed the title KP.4.2.3(S:S256L,S:S31del)+S:R190S(41 seqs,>10 places) KP.4.2.4(S:S256L,S:S31del)+S:R190S(41 seqs,>10 places) Oct 28, 2024
@xz-keg
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xz-keg commented Nov 2, 2024

45, Italy, New Zealand

@xz-keg xz-keg changed the title KP.4.2.4(S:S256L,S:S31del)+S:R190S(41 seqs,>10 places) KP.4.2.4(S:S256L,S:S31del)+S:R190S(45 seqs,>10 places) Nov 2, 2024
@xz-keg xz-keg changed the title KP.4.2.4(S:S256L,S:S31del)+S:R190S(45 seqs,>10 places) KP.4.2.4(S:S256L,S:S31del)+S:R190S(46 seqs,>10 places) Nov 12, 2024
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@xz-keg @FedeGueli @DailyCovidCases @NkRMnZr