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LB.1+S:V83F,445P(26 seqs, >10 places) #2123

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xz-keg opened this issue Oct 6, 2024 · 7 comments
Closed

LB.1+S:V83F,445P(26 seqs, >10 places) #2123

xz-keg opened this issue Oct 6, 2024 · 7 comments
Labels
DeFLiRT S:S31/F32-+S:R346T+S:F456L designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest LB.1 S:83 S:183 S:445
Milestone
LB.1.10

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@xz-keg
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xz-keg commented Oct 6, 2024

This seems prevalent in Kosovo.

LB.1+G21809T, A29700G,A22896C(S:V83F,H445P)

GISAID query: G21809T,A29700G,G22111T
No. of seqs: 18(Serbia-Kosovo 5 Sweden 2 USA 9(NY,CA,NJ,PA) Denmark 1 Israel 1)

First: EPI_ISL_19203579, Israel, 2024-6-2
Latest: EPI_ISL_19447137, USA-NY, 2024-9-16

Some seqs have S:445 no coverage, I check and there seems no 445H seq. Everything on the V83F branch shall have S:H445P.
usher
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@xz-keg xz-keg changed the title LB.1+S:V83,445P(18 seqs, 8 places) LB.1+S:V83,445P(18 seqs, 8 places, 7% Kosovo) Oct 6, 2024
@xz-keg xz-keg changed the title LB.1+S:V83,445P(18 seqs, 8 places, 7% Kosovo) LB.1+S:V83F,445P(18 seqs, 8 places, 7% Kosovo) Oct 6, 2024
@Over-There-Is
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Over-There-Is commented Oct 6, 2024 •
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I've just seen this one too.

@FedeGueli FedeGueli added S:445 S:183 S:83 DeFLiRT S:S31/F32-+S:R346T+S:F456L LB.1 labels Oct 6, 2024
@FedeGueli
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I've just seen this one too.

always good when more than one sees things

@FedeGueli
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It seems that also KP.3.1.1 got V83F. i m analyzing it.

@xz-keg
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xz-keg commented Oct 24, 2024

no new seqs

@xz-keg xz-keg closed this as not planned Won't fix, can't repro, duplicate, stale Oct 24, 2024
@FedeGueli FedeGueli changed the title LB.1+S:V83F,445P(18 seqs, 8 places, 7% Kosovo) LB.1+S:V83F,445P(21 seqs, 8 places, 7% Kosovo) Oct 27, 2024
@FedeGueli FedeGueli changed the title LB.1+S:V83F,445P(21 seqs, 8 places, 7% Kosovo) LB.1+S:V83F,445P(21 seqs, 9 places, 7% Kosovo) Oct 27, 2024
@FedeGueli
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  • 3 very old samples from Mauritius!

@xz-keg xz-keg added the Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest label Oct 28, 2024
@FedeGueli FedeGueli changed the title LB.1+S:V83F,445P(21 seqs, 9 places, 7% Kosovo) LB.1+S:V83F,445P(26 seqs, >10 places) Nov 10, 2024
@FedeGueli
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+5 Bayern Germany reopening for a while

@FedeGueli FedeGueli reopened this Nov 10, 2024
@FedeGueli FedeGueli added this to the LB.1.10 milestone Nov 12, 2024
@FedeGueli
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Designated LB.1.10 via cov-lineages/pango-designation@ad2242f

FedeGueli referenced this issue in cov-lineages/pango-designation Nov 12, 2024
@corneliusroemer
Designating NP.1/2 and XEP
ad2242f
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DeFLiRT S:S31/F32-+S:R346T+S:F456L designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest LB.1 S:83 S:183 S:445
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@xz-keg @Over-There-Is @FedeGueli