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JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (11 seqs in Australia, Japan, Thailand, US) #1015

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HynnSpylor opened this issue Oct 26, 2023 · 5 comments
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JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (11 seqs in Australia, Japan, Thailand, US) #1015

HynnSpylor opened this issue Oct 26, 2023 · 5 comments
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designated FLip = S:L455F / S:F456L S:52 S:356 S:478
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JR.1.1.1

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@HynnSpylor
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Defining mutations:
JR.1.1>A27388C>C9447T (ORF1a:A3061V), A22628C (S:K356Q)
GISAID query: C9447T, A22628C, A27388C
Earliest seq: 2023-09-13 (Japan, detected in US International Airport- EPI_ISL_18295307)
Most recent seq: 2023-10-10 (NSW, Australia- EPI_ISL_18411613)
Countries detected: Australia (4), Japan (2, including 1 detected in US International Airport)

Usher Tree:
QQ截图20231027013540
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21742_a9f310.json?c=gt-S_356

JR.1.1 (EG.5.1.11.1.1) is one of FlippeR (S:L455F+S:F456L+S:K478R) lineages. Now the branch gets S:K356Q, which is different with the popular S:K356T, can slightly increase the escape potential.
Also, the US International Airport seq gets S:Q677H.

Genomes:
EPI_ISL_18295307, EPI_ISL_18410942, EPI_ISL_18411613, EPI_ISL_18411657, EPI_ISL_18435046, EPI_ISL_18435384,
@FedeGueli FedeGueli added S:478 S:356 FLip = S:L455F / S:F456L labels Oct 26, 2023
@NkRMnZr NkRMnZr mentioned this issue Nov 2, 2023
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@xz-keg
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xz-keg commented Nov 5, 2023

+1 Thailand

@FedeGueli FedeGueli changed the title JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (6 seqs in Australia and Japan) JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (7 seqs in Australia,Japan,Thailand) Nov 6, 2023
@FedeGueli FedeGueli changed the title JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (7 seqs in Australia,Japan,Thailand) JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (10 seqs in Australia,Japan,Thailand,US) Nov 13, 2023
@FedeGueli
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+3 CALIFORNIA, THAILAND, AUSTRALIA(QLD)

@FedeGueli
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This is promising.

@FedeGueli FedeGueli added the S:52 label Nov 13, 2023
@HynnSpylor
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11 seqs now

@HynnSpylor HynnSpylor changed the title JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (10 seqs in Australia,Japan,Thailand,US) JR.1.1 (EG.5.1.11.1.1) sublineage with S:K356Q and ORF1a:A3061V (11 seqs in Australia, Japan, Thailand, US) Nov 17, 2023
Over-There-Is referenced this issue in cov-lineages/pango-designation Nov 30, 2023
@corneliusroemer
Designate JR.1.1.1 (S:K356Q, Thailand) with 18 seqs
2c95200
@FedeGueli FedeGueli added this to the JR.1.1.1 milestone Nov 30, 2023
@FedeGueli
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Designated JR.1.1.1 from cov-lineages/pango-designation@2c95200#commitcomment-133911458

@xz-keg xz-keg closed this as completed Dec 1, 2023
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