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XBB.1.9.1 with S:F456L starting in Vietnam(66 seqs, 11 countries) #1994

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xz-keg opened this issue May 13, 2023 · 6 comments
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XBB.1.9.1 with S:F456L starting in Vietnam(66 seqs, 11 countries) #1994

xz-keg opened this issue May 13, 2023 · 6 comments
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@xz-keg
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xz-keg commented May 13, 2023

This is the 1st XBB.1.9.1 sub-lineage with the convergent S:F456L.
From sars-cov-2-variants/lineage-proposals#27

Sub-lineage of: XBB.1.9.1
Mutations on top of XBB.1.9.1: C28846T, G2174A(orf1a:E637K), T22928C(S:456L)
GISAID query: C28846T, G2174A, T22928C

No. of seqs: 27(3 USA 4 China 7 Vietnam 1 Singapore(from Vietnam) 2 France 2 Canada 3 South Korea(1 from Vietnam) 5 Japan)

Note that all 3 green Vietnamese seqs have S:456 dropout, they're likely to also have 456L.
GISAID query for the green Vietnamese seqs: C28846T, G2174A, G1464T,-T22928C,C12890T

First seq: 17481621, 2023-3-9, Vietnam
Latest seq: 17641519, 2023-5-1 ,Canada

usher
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@xz-keg
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xz-keg commented May 23, 2023

53 seqs now, new country of Australia and Spain(exported to South Korea).

@xz-keg xz-keg changed the title XBB.1.9.1 with S:F456L starting in Vietnam(27 seqs, 9 countries) XBB.1.9.1 with S:F456L starting in Vietnam(53 seqs, 11 countries) May 23, 2023
@xz-keg xz-keg changed the title XBB.1.9.1 with S:F456L starting in Vietnam(53 seqs, 11 countries) XBB.1.9.1 with S:F456L starting in Vietnam(56 seqs, 11 countries) May 24, 2023
@xz-keg xz-keg changed the title XBB.1.9.1 with S:F456L starting in Vietnam(56 seqs, 11 countries) XBB.1.9.1 with S:F456L starting in Vietnam(66 seqs, 11 countries) May 27, 2023
@JosetteSchoenma
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This seems to grow quickly. Lots of new samples on the ORF1ab:G400V branch from Australia/NSW.
Screenshot_20230528_082905_Twitter.jpg

Screenshot_20230528_082832_Twitter.jpg

@FedeGueli
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ping @corneliusroemer @InfrPopGen
reason to fast designate this one

  1. growing fast outside the area where emerged from
  2. 456L convergent evo able to increase fitness(escape)

@InfrPopGen InfrPopGen self-assigned this May 29, 2023
InfrPopGen pushed a commit to InfrPopGen/pango-designation that referenced this issue May 29, 2023
…esignations, and 0 updated designations
InfrPopGen added a commit that referenced this issue May 29, 2023
Added new lineage FL.15 from #1994 with 53 new sequence designations, and 0 updated designations
@InfrPopGen InfrPopGen added this to the FL.15 milestone May 29, 2023
@InfrPopGen
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Thanks for submitting. We've added lineage FL.15 with 53 newly designated sequences, and 0 updated designations. Defining mutation T22928C (S:F456L). There's currently two adjacent clades with S:F456L on the usher tree, but as it is likely that these are really one clade, they have been designated as if monophyletic.

@AngieHinrichs
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Good catch @InfrPopGen, I'll try to fix that soon.

@FedeGueli
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One sequence got S:L455F check via G15649A, G22927T,G1464T
ID:EPI_ISL_17836859

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