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KS.1.1/JN.1* recombinant (337 seqs, >10 places, 16% South Korea 8% Hong Kong) #2751

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xz-keg opened this issue Aug 25, 2024 · 36 comments
Closed

KS.1.1/JN.1* recombinant (337 seqs, >10 places, 16% South Korea 8% Hong Kong) #2751

xz-keg opened this issue Aug 25, 2024 · 36 comments

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@xz-keg
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xz-keg 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
@xz-keg xz-keg 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

@xz-keg
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xz-keg commented Aug 30, 2024

86, Singapore,

@xz-keg xz-keg 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
@xz-keg
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xz-keg commented Aug 30, 2024

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

@xz-keg xz-keg 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

@xz-keg xz-keg 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
@xz-keg
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xz-keg commented Aug 31, 2024

@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.

@xz-keg xz-keg 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
@xz-keg xz-keg 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
@xz-keg
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xz-keg commented Sep 5, 2024

96, Denmark, Australia

@xz-keg xz-keg 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

@xz-keg
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xz-keg commented Sep 7, 2024

Also in Germany

@xz-keg xz-keg 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
@xz-keg
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xz-keg commented Sep 13, 2024

133, Bangladesh, Indonesia, Italy

@xz-keg xz-keg 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.

@xz-keg
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xz-keg commented Sep 13, 2024

-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*.

@xz-keg xz-keg 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
@xz-keg xz-keg 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
@xz-keg
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xz-keg commented Sep 20, 2024

164, Sweden

@xz-keg xz-keg 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

@xz-keg xz-keg 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
@Over-There-Is
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a branch gets Orf8:L60*.

@FedeGueli
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C6701T, C19716T, T25510C, C29311T

yeah from South Korea, some Seqs from South Korea have some movement at the end of Orf6 but apparently it is not related to large deletions of Orf7ab/Orf8 as i was thinking.

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (247 seqs, >10 places, 16% South Korea in Sep) KS.1.1/JN.1* recombinant (254 seqs, >10 places, 16% South Korea in Sep) Oct 1, 2024
@xz-keg
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xz-keg commented Oct 1, 2024

@corneliusroemer this recombinant is huge now.

@FedeGueli
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@corneliusroemer this recombinant is huge now.

Cornelius it is KS.1.1 spike without 1087S , so it belongs to the 22N+59S group with some tuning coming from outside the spike likely

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (254 seqs, >10 places, 16% South Korea in Sep) KS.1.1/JN.1* recombinant (277 seqs, >10 places, 16% South Korea in Sep) Oct 8, 2024
@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (277 seqs, >10 places, 16% South Korea in Sep) KS.1.1/JN.1* recombinant (280 seqs, >10 places, 16% South Korea in Sep) Oct 8, 2024
@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (280 seqs, >10 places, 16% South Korea in Sep) KS.1.1/JN.1* recombinant (280 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 8, 2024
@xz-keg
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xz-keg commented Oct 8, 2024

3/40 in the most recent Hong Kong batch

@FedeGueli
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@corneliusroemer ping

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (280 seqs, >10 places, 16% South Korea 8% Hong Kong) KS.1.1/JN.1* recombinant (288 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 10, 2024
@xz-keg xz-keg mentioned this issue Oct 10, 2024
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@xz-keg
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xz-keg commented Oct 10, 2024

There is a new stepwise S680F-R190S-K478I branch emerging from this.

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (288 seqs, >10 places, 16% South Korea 8% Hong Kong) KS.1.1/JN.1* recombinant (297 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 11, 2024
@xz-keg
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xz-keg commented Oct 13, 2024

329 seqs now.

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (297 seqs, >10 places, 16% South Korea 8% Hong Kong) KS.1.1/JN.1* recombinant (329 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 13, 2024
@FedeGueli
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334 , to me it is slowing down a lot

@xz-keg
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xz-keg commented Oct 15, 2024

334 , to me it is slowing down a lot

image

Looks like it is still growing

@FedeGueli
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334 , to me it is slowing down a lot

image

Looks like it is still growing

Yeah but less than before lets wait S.Korea samples

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (329 seqs, >10 places, 16% South Korea 8% Hong Kong) KS.1.1/JN.1* recombinant (334 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 15, 2024
@Over-There-Is
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kuwait

@xz-keg xz-keg changed the title KS.1.1/JN.1* recombinant (334 seqs, >10 places, 16% South Korea 8% Hong Kong) KS.1.1/JN.1* recombinant (337 seqs, >10 places, 16% South Korea 8% Hong Kong) Oct 15, 2024
@FedeGueli
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Donor designated KS.1.1.2 via KS.1.1 donor now designated KS.1.1.2 via. c542eb9#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1277

This recombinant designated XEL via d247018

@Over-There-Is
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Hubei/HCDC-WH6856/2024|EPI_ISL_19384912|2024-08-14 from malaysia

@FedeGueli
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FedeGueli commented Oct 23, 2024 •
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There is a new stepwise S680F-R190S-K478I branch emerging from this.

Screenshot 2024-10-23 alle 14 45 59

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5a608_8edb70.json?c=userOrOld&label=id:node_7364125

with a new sample from UAE collected in october via GBW
Query for this 190S branch : C1426T, G22132T,C23601T
Samples: 4
Places: 4

@FedeGueli
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There is a new stepwise S680F-R190S-K478I branch emerging from this.

this went up to 5 now found in NY

@FedeGueli
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There is a new stepwise S680F-R190S-K478I branch emerging from this.

this went up to 5 now found in NY

Now 8 cc @xz-keg maybe worth proposing it??

@FedeGueli
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There is a new stepwise S680F-R190S-K478I branch emerging from this.

this went up to 5 now found in NY

Now 8 cc @xz-keg maybe worth proposing it??

scratch that already proposed in sars-cov-2-variants/lineage-proposals#2138

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@xz-keg @Over-There-Is @Mydtlwn @FedeGueli @DailyCovidCases