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KS.1.1/JN.1* recombinant (154 seqs, 18 countries, 9% South Korea) #2751

Open aviczhl2 opened 3 weeks ago

aviczhl2 commented 3 weeks ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1806

KS.1.1--JN.1

Breakpoint between 22929 and 24820

Additional mutations: C6701T, C19716T, T25510C, C29311T

Orf1a:L2146F, Orf3a:S40P

C6701T, C19716T from a KS.1.1 branch, One of T25510C, C29311T from a JN.1* branch, the other is private.

GISAID query: T25510C, C29311T,C19716T,T3565C No. of seqs: 56(Canada 1 Japan 2 Russia 1 China 1 USA 7(2 from South Korea 1 from France) Netherlands 1 South Korea 41 Ireland 1 Israel 1)

First: EPI_ISL_19257990, South Korea, 2024-6-17 Latest: EPI_ISL_19352398, South Korea, 2024-8-3

30/556 of South Korean seqs after 7/20. usher image

FedeGueli commented 2 weeks ago

61 now, to be noticed that the last two GBW samples from Korea both carry S:K458N . Query for them: C1960T, T25510C, G22936T

Screenshot 2024-08-28 alle 23 18 29
aviczhl2 commented 2 weeks ago

86, Singapore,

aviczhl2 commented 2 weeks ago

South Korea prevalence climbs from 5% to 24/262=9% in seqs sampled after 8-1

FedeGueli commented 2 weeks ago

87 Finland

aviczhl2 commented 2 weeks ago

@corneliusroemer @AngieHinrichs This recomb is now placed under JN.1.18.6, but due to C6701T, C19716T and S:T22N,F59S it is still better explained as KS.1.1/JN.1* recombinant. When designation please be careful and not designate it as JN.1.18.6 descendant.

aviczhl2 commented 1 week ago

96, Denmark, Australia

FedeGueli commented 1 week ago

123 now , Denmark

aviczhl2 commented 1 week ago

Also in Germany

aviczhl2 commented 2 days ago

133, Bangladesh, Indonesia, Italy

Over-There-Is commented 2 days ago

KP.3.2.3+C29311T?

Over-There-Is commented 2 days ago

-C6701, -G25352T, C8293T, T25510C, C29311T=8 1 is Serbian old sequence, 3 are dropout of this sequences, and the rest 4 are KP.3.2.3

Over-There-Is commented 2 days ago

153 now

FedeGueli commented 2 days ago

ping @corneliusroemer this should get designated.

aviczhl2 commented 2 days ago

-C6701, -G25352T, C8293T, T25510C, C29311T=8 1 is Serbian old sequence, 3 are dropout of this sequences, and the rest 4 are KP.3.2.3

Shouldn't be. It lacks S:V1104L and its breakpoint is before S:1087, so cannot recomb with any KP*.