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xz-keg opened this issue Mar 28, 2025 · 11 comments
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PC.2.2+S:S680P(46 seqs) #2922

xz-keg opened this issue Mar 28, 2025 · 11 comments

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@xz-keg
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xz-keg commented Mar 28, 2025 •
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From sars-cov-2-variants/lineage-proposals#2456

There seems to be an interesting branch with double Orf3a mutations that has advantage over other LF.7+S:A475Vs and is now the dominate branch of Singapore.

LF.7.2.1+T111C,G25429C(Orf3a:V13L)+C25624T(Orf3a:H78Y)

GISAID query: T20799C,G25429C,C25624T
GISAID query for the general Orf3a:V13L branch: T20799C,G25429C,C8818T
GISAID query for S:S680P branch: T20799C,G25429C,C25624T,T23600C
No. of seqs: 187(Denmark 1 UK 1 Germany 1 China 1(Hong Kong) Italy 1 Japan 2(from Malaysia and Singapore) South Korea 1 USA 4(GBW from Saudi Arabia) Singapore 175)

First: EPI_ISL_19467915, Singapore, 2024-10-1
Latest: EPI_ISL_19794266, Singapore, 2025-3-18

usher

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There is a large T111C sub-branch on the Orf3a:V13L branch, however after further investigation it seems that T111C is on all seqs with Orf3a:V13L branch. Just some Singapore seqs have 111 missing coverage disturbs the branch. @AngieHinrichs
@FedeGueli
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Ah good catch! silly me that i didn't check that.

@xz-keg xz-keg mentioned this issue Mar 30, 2025
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@FedeGueli
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+2 GBW from Hk

@AngieHinrichs
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AngieHinrichs commented Apr 2, 2025 •
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There is a large T111C sub-branch on the Orf3a:V13L branch, however after further investigation it seems that T111C is on all seqs with Orf3a:V13L branch. Just some Singapore seqs have 111 missing coverage disturbs the branch. @AngieHinrichs

I see, thanks, should be fixed in 2025-04-02 build.

@xz-keg
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xz-keg commented Apr 8, 2025 •
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286/236, also in Canada-ON

@xz-keg xz-keg changed the title LF.7.2.1+T111C,Orf3a:V13L(228 seqs)+Orf3a:H78Y( 187 seqs, 9 places) LF.7.2.1+T111C,Orf3a:V13L(286 seqs)+Orf3a:H78Y( 236 seqs, 10 places) Apr 8, 2025
@xz-keg
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xz-keg commented Apr 11, 2025

designated PC.2 starting from Orf3a:V13L

@xz-keg xz-keg closed this as completed Apr 11, 2025
@FedeGueli
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designated PC.2 starting from Orf3a:V13L

via 864eea0

FedeGueli referenced this issue Apr 11, 2025
@corneliusroemer
Designate a bunch of lineages
864eea0
@xz-keg
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xz-keg commented Apr 20, 2025 •
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It seems there is a large S:S680P branch under PC.2 in Singapore and Japan-EIS from Malaysia, re-open to track it.

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@xz-keg xz-keg reopened this Apr 20, 2025
@xz-keg xz-keg changed the title LF.7.2.1+T111C,Orf3a:V13L(286 seqs)+Orf3a:H78Y( 236 seqs, 10 places) PC.2+Orf3a:H78Y( 281 seqs, >10 places, 26 with S:S680P) Apr 20, 2025
@xz-keg xz-keg changed the title PC.2+Orf3a:H78Y( 281 seqs, >10 places, 26 with S:S680P) PC.2+Orf3a:H78Y( 347 seqs, >10 places, 35 with S:S680P) Apr 26, 2025
@FedeGueli
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FedeGueli commented Apr 28, 2025 •
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46 for 680P ( 16 of them with S:G75V)

@FedeGueli FedeGueli mentioned this issue Apr 29, 2025
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@Walde1nsamkeit
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46 for 680P ( 16 of them with S:G75V)

44(all 3 Japanese sequences are from the same sample)

@FedeGueli
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46 for 680P ( 16 of them with S:G75V)

44(all 3 Japanese sequences are from the same sample)

thx good to know, but lets keep the gisaid count as usual.

@xz-keg xz-keg changed the title PC.2+Orf3a:H78Y( 347 seqs, >10 places, 35 with S:S680P) PC.2+Orf3a:H78Y( 397 seqs, >10 places, 46 with S:S680P) May 6, 2025
@xz-keg xz-keg changed the title PC.2+Orf3a:H78Y( 397 seqs, >10 places, 46 with S:S680P) PC.2+Orf3a:H78Y( 400 seqs, >10 places, 46 with S:S680P) May 14, 2025
@xz-keg xz-keg changed the title PC.2+Orf3a:H78Y( 400 seqs, >10 places, 46 with S:S680P) PC.2.2+S:S680P(46 seqs) May 14, 2025
@xz-keg
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xz-keg commented May 14, 2025

Sub-lineages of the Orf3a:H78Y are designated PC.2.1 and PC.2.2, while S:S680P becomes sub-branch of PC.2.2

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@AngieHinrichs @xz-keg @Walde1nsamkeit @FedeGueli