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KS.1.1/JN.1* recombinant (170 seqs, 19 countries, 9% South Korea) #2751

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aviczhl2 opened this issue Aug 25, 2024 · 17 comments
Open

KS.1.1/JN.1* recombinant (170 seqs, 19 countries, 9% South Korea) #2751

aviczhl2 opened this issue Aug 25, 2024 · 17 comments

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@aviczhl2
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aviczhl2 commented Aug 25, 2024 •
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From sars-cov-2-variants/lineage-proposals#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
@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (56 seqs, 10 countries, >5% South Korea) KS.1.1/JN.1* recombinant (60 seqs, 10 countries, >5% South Korea) Aug 27, 2024
@FedeGueli
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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
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86, Singapore,

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (60 seqs, 10 countries, >5% South Korea) KS.1.1/JN.1* recombinant (86 seqs, 11 countries, >5% South Korea) Aug 30, 2024
@aviczhl2
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South Korea prevalence climbs from 5% to 24/262=9% in seqs sampled after 8-1

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (86 seqs, 11 countries, >5% South Korea) KS.1.1/JN.1* recombinant (86 seqs, 11 countries, 9% South Korea) Aug 30, 2024
@FedeGueli
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87 Finland

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (86 seqs, 11 countries, 9% South Korea) KS.1.1/JN.1* recombinant (87 seqs, 12 countries, 9% South Korea) Aug 30, 2024
@aviczhl2
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@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 aviczhl2 changed the title KS.1.1/JN.1* recombinant (87 seqs, 12 countries, 9% South Korea) KS.1.1/JN.1* recombinant (90 seqs, 12 countries, 9% South Korea) Aug 31, 2024
@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (90 seqs, 12 countries, 9% South Korea) KS.1.1/JN.1* recombinant (92 seqs, 12 countries, 9% South Korea) Sep 3, 2024
@aviczhl2
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aviczhl2 commented Sep 5, 2024

96, Denmark, Australia

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (92 seqs, 12 countries, 9% South Korea) KS.1.1/JN.1* recombinant (96 seqs, 14 countries, 9% South Korea) Sep 5, 2024
@FedeGueli
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123 now , Denmark

@aviczhl2
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aviczhl2 commented Sep 7, 2024

Also in Germany

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (96 seqs, 14 countries, 9% South Korea) KS.1.1/JN.1* recombinant (123 seqs, 15 countries, 9% South Korea) Sep 7, 2024
@aviczhl2
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133, Bangladesh, Indonesia, Italy

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (123 seqs, 15 countries, 9% South Korea) KS.1.1/JN.1* recombinant (133 seqs, 18 countries, 9% South Korea) Sep 13, 2024
@Over-There-Is
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KP.3.2.3+C29311T?

@Over-There-Is
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-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
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153 now

@FedeGueli
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ping @corneliusroemer this should get designated.

@aviczhl2
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-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*.

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (133 seqs, 18 countries, 9% South Korea) KS.1.1/JN.1* recombinant (153 seqs, 18 countries, 9% South Korea) Sep 13, 2024
@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (153 seqs, 18 countries, 9% South Korea) KS.1.1/JN.1* recombinant (154 seqs, 18 countries, 9% South Korea) Sep 14, 2024
@aviczhl2
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164, Sweden

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (154 seqs, 18 countries, 9% South Korea) KS.1.1/JN.1* recombinant (164 seqs, 19 countries, 9% South Korea) Sep 20, 2024
@DailyCovidCases
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Tree now: (150/164 seqs)
usher
Screenshot (221)
i agree @corneliusroemer this branch is worth designation.

@Mydtlwn
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Mydtlwn commented Sep 23, 2024

@corneliusroemer

@aviczhl2 aviczhl2 changed the title KS.1.1/JN.1* recombinant (164 seqs, 19 countries, 9% South Korea) KS.1.1/JN.1* recombinant (170 seqs, 19 countries, 9% South Korea) Sep 23, 2024
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@aviczhl2 @Over-There-Is @Mydtlwn @FedeGueli @DailyCovidCases