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Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 11 seqs in NY, US) #823

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HynnSpylor opened this issue Sep 16, 2023 · 3 comments
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Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 11 seqs in NY, US) #823

HynnSpylor opened this issue Sep 16, 2023 · 3 comments
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designated FLip = S:L455F / S:F456L S:356
Milestone
GK.2.4

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@HynnSpylor
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Defining mutations:
GK.2>T10204C>C21781T>A22629C (S:K356T)
GISAID query: C21781T, A22629C, G23093A
Earliest seq: 2023-09-03 (NY, US- EPI_ISL_18269252)
Most recent seq: 2023-09-09 (NY, US- EPI_ISL_18269255)
Countries detected: US (3)
Usher Tree:
QQ截图20230916173417
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_30986_55c500.json?c=gt-S_356

Another convergent branch of GK.2+S:K356T (the first one on G16236A branch is proposed in #813). S:K356T is a popular mutation with increased escape effect.

Genomes:
EPI_ISL_18265096, EPI_ISL_18269252, EPI_ISL_18269255
@HynnSpylor HynnSpylor changed the title Another GK.2 (XBB.1.5.70) sublineage with S:K356T (on T10204C branch, 3 seqs in NY, US) Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 3 seqs in NY, US) Sep 16, 2023
@FedeGueli FedeGueli added FLip = S:L455F / S:F456L S:356 labels Sep 16, 2023
@NkRMnZr
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NkRMnZr commented Sep 18, 2023

T10204C looks suspicious, potentially recombinant with another XBB.1.5+T10204C?

@FedeGueli FedeGueli changed the title Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 3 seqs in NY, US) Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 4 seqs in NY, US) Sep 24, 2023
@FedeGueli
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+1 NY

@FedeGueli FedeGueli changed the title Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 4 seqs in NY, US) Another GK.2 (XBB.1.5.70.2) sublineage with S:K356T (on T10204C branch, 11 seqs in NY, US) Oct 7, 2023
@FedeGueli
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11 now

Over-There-Is referenced this issue in cov-lineages/pango-designation Oct 13, 2023
@corneliusroemer
Designate GK.2.4 (S:K356T, USA-NY) with 15 seqs
b14b69a
@FedeGueli FedeGueli added this to the GK.2.4 milestone Oct 13, 2023
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@FedeGueli @HynnSpylor @NkRMnZr