JN.1+M:L46F+S:F456L(1356 seqs, 25 countries, 28% China, 8 with S:R346T)

[aviczhl2]

From branch 26 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C)

GISAID query:G26660T, G4162A ,T22928C,T3565C (26 seqs) GISAID supplementary query: G4162A,-22928,G1126A,T3565C (2 seqs, for seqs with no coverage at S:F456 but share mutation) No. of seqs: 28(USA 4(2 from Singapore, 2 from South Korea) China 24(Hubei, Shanxi, Heilongjiang, Gansu, Henan, Hong Kong, Fujian from Taiwan, 1 from Malaysia 1 from Australia 1 from Thailand))

GISAID query for S:R346T branch: G26660T, G4162A ,T22928C,T3565C,G22599C (1 seq)

First: EPI_ISL_18872894, Hong Kong, 2024-1-27 Latest: EPI_ISL_18999287, USA from South Korea, 2024-3-12

Seems widely distributed in China and SE Asian countries. Usher splits into two branches but the G1126A is separated by 2 Hong Kong seqs with no coverage on S:456, they shall have S:F456L too. usher

[FedeGueli]

Thank you great work

[aviczhl2]

+1 Japan

[aviczhl2]

+1 UK

[aviczhl2]

+1 Taiwan

[aviczhl2]

+8 from Fujian, Anhui, Hubei and Taiwan.

[FedeGueli]

To me it seems really a fastg lineage, likely less than FLiRT tough. @corneliusroemer

[aviczhl2]

14/81=17% in the 4-1 Shanxi batch.

[FedeGueli]

ping @corneliusroemer this is fast

[aviczhl2]

+22.

16/207=8% in Hubei seqs from 2024.3.20.

@corneliusroemer

[aviczhl2]

+1 South Korea with the same situation of Hong Kong seqs(share mut+ no coverage at 456)

[FedeGueli]

fast growing and prevalent, ping @corneliusroemer

[aviczhl2]

90, Canada

[FedeGueli]

It got FLiRT! : EPI_ISL_19045970 @corneliusroemer this one is to watch

2531 > ORF1a:S558F (C1938T),S:R346T (G22599C)

Query: C1938T, G22599C,G1126A

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34b0_97b270.json?f_userOrOld=uploaded%20sample

[aviczhl2]

153, New Zeland, France,

[aviczhl2]

19/189=10% in Hubei seqs after 4-1 10/98=10% in Henan seqs after 3-20.

[FedeGueli]

This likely the fastest non Flirt behind KP.3 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=G26660T%2CG4162A%2CT22928C%2CT3565C&analysisMode=CompareToBaseline&

[aviczhl2]

189, Qatar,

[aviczhl2]

251 seqs now

[aviczhl2]

17/153=11% in Heilongjiang seqs after 2024-4 19/111=17% in Hubei seqs after 2024-4-15, growing fast (from 10%)

[FedeGueli]

17/153=11% in Heilongjiang seqs after 2024-4 19/111=17% in Hubei seqs after 2024-4-15, growing fast (from 10%)

@corneliusroemer this is faster than many Flirt lineages , already big enough to exclude founder or cluster effect, i suggest strongly an urgent designation

[aviczhl2]

17/153=11% in Heilongjiang seqs after 2024-4 19/111=17% in Hubei seqs after 2024-4-15, growing fast (from 10%)

@corneliusroemer this is faster than many Flirt lineages , already big enough to exclude founder or cluster effect, i suggest strongly an urgent designation

Maybe like EG.5.1 being faster than many early Flips.

[FedeGueli]

17/153=11% in Heilongjiang seqs after 2024-4 19/111=17% in Hubei seqs after 2024-4-15, growing fast (from 10%)

@corneliusroemer this is faster than many Flirt lineages , already big enough to exclude founder or cluster effect, i suggest strongly an urgent designation

Maybe like EG.5.1 being faster than many early Flips.

Yeah one thing to notice is that in China FLiRT are still very low numbers so baseline is lower there allowing maybe a easier spread than , to say India or other places with higher FLiRT prevalence

[FedeGueli]

+3 South Korea, it starts expanding outside China

[Over-There-Is]

Hong_Kong/HKU-240503-042/2023|EPI_ISL_19093478|2023-12-17 JN.1> G26660T> G4162A> A10066G The earliest sequence with or without T22928C are both from Hong Kong.(Exactly EPI_ISL_18872894 and EPI_ISL_18872895 have no coverage on 22928, but the existence of T22928C could be inferenced by the following G1126A.) I think this branch could originate in some undersampled southern provinces(e. g. Guangdong). Or it could be from Hong Kong too, the only sequence without T22928C in Mainland is collected from Shanghai. Rather than interior provinces which interact frequently with Guangdong, Hong Kong is more closely connected to Shanghai.

[FedeGueli]

Hong_Kong/HKU-240503-042/2023|EPI_ISL_19093478|2023-12-17 JN.1> G26660T> G4162A> A10066G The earliest sequence with or without T22928C are both from Hong Kong.(Exactly EPI_ISL_18872894 and EPI_ISL_18872895 have no coverage on 22928, but the existence of T22928C could be inferenced by the following G1126A.) I think this branch could originates in some undersampled southern provinces(e. g. Guangdong). Or it could be from Hong Kong too, the only sequence without T22928C in Mainland is collected from Shanghai. Rather than interior provinces which interact frequently with Guangdong, Hong Kong is more closely connected to Shanghai.

thx for the analysis

[aviczhl2]

274, Netherlands, Ireland (both via GBW)

[FedeGueli]

imopressive fast , @corneliusroemer when you will be back this is one of the first to need a designation

[Over-There-Is]

Some sequences from Liaoning and Shanxi got 4162 reverted, but I don't think they're true

[Over-There-Is]

Multiple cities, Liaoning 05-10 13/101 Jincheng, Shanxi 05-07 6/51

[Over-There-Is]

*Some sequences have neither G1126A nor G4162A. They should be investigated further.

[FedeGueli]

*Some sequences have neither G1126A nor G4162A. They should be investigated further.

new query G26660T,T22928C,T3565C should catch all of them , count 343

G1162A is not defining of this:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_334cb_f77170.json?c=gt-nuc_1126&f_userOrOld=uploaded%20sample&gmax=2126&gmin=126&label=id:node_6996795

[FedeGueli]

349

[Over-There-Is]

*Some sequences have neither G1126A nor G4162A. They should be investigated further.

new query G26660T,T22928C,T3565C should catch all of them , count 343

G1162A is not defining of this: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_334cb_f77170.json?c=gt-nuc_1126&f_userOrOld=uploaded%20sample&gmax=2126&gmin=126&label=id:node_6996795

But some sequences have reversions on 4162 and 3565, and they could still be identified by G1126A.

[aviczhl2]

377, Germany

[aviczhl2]

18/154=12% in Sichuan seqs after 2024-4-1

[aviczhl2]

401,Swden, New Zealand

[aviczhl2]

@corneliusroemer please designate this one.

[Over-There-Is]

Sichuan (from several cities) 29/182 Hubei (from several cities) 51/240 Henan(Hebi) 5/13

[Over-There-Is]

covSPECTRUM query: nextcladePangoLineage:JN.1* & T22928C & (C7113C | C7113N) & [1-of: G4162A, G26660T] (422 adopted)

GISAID query: -C7113T, C8293T, T22928C, G26660T (519) + G4162A, C8293T, T22928C, -G26660T(32) + T3565C, G4162A, -C8293T, T22928C, G26660T(1)=552

[Over-There-Is]

9% slower than KP globally, and samples of KP from China is too few to be compared. But it's still growing much faster than other JN.1*, both in China or aboard.

[Over-There-Is]

Rather than 3565, 6183 or 8393, C8293T is much more stable in sequences (harder to be dropped out).

[Over-There-Is]

covSPECTRUM query: nextcladePangoLineage:JN.1* & T22928C & (C7113C | C7113N) & [1-of: G4162A, G26660T] (422 adopted)

GISAID query: -C7113T, C8293T, T22928C, G26660T (519) + G4162A, C8293T, T22928C, -G26660T(32) + T3565C, G4162A, -C8293T, T22928C, G26660T(1)=552

Additional GISAID queries: G1126A, G4162A, C8293T, -T22928C=10 (including the earliest 2 Hongkongese sequences) G1126A, -G4162A, C8293T, -T22928C, G26660T=1

-C7113T, C8293T, T22928C, G26660T=577 G4162A, C8293T, T22928C, -G26660T=35 T3565C, G4162A, -C8293T, T22928C, G26660T=2

There are no evidence to prove the existence of 22928 dropped-out sequences from non-G1126A branches. 577+35+2+10+1=625

Updated covSPECTRUM query: NextcladePangoLineage:JN.1* & (C7113C | C7113N) & [1-of: G1126A,T22928C] & [1-of: G4162A,G26660T] =563

[HynnSpylor]

for -C7113T, C8293T, T22928C, G26660T: 181/828 in China since Apr 15,2024 I suppose it should be designated as a high prevalence.

[aviczhl2]

670 seqs now. Israel,

Prevalence in China after 5-1 is 65/259=25%

@corneliusroemer this is missed for designation.

[aviczhl2]

830, Norway, France

[Over-There-Is]

-C7113T, C8293T, T22928C, G26660T=844 G4162A, C8293T, T22928C, -G26660T=50 T3565C, G4162A, -C8293T, T22928C, G26660T=2 G1126A, G4162A, C8293T, -T22928C=16 G1126A, -G4162A, C8293T, -T22928C, G26660T=2 Totally 914 now

[FedeGueli]

already very big. @corneliusroemer

[Memorablea]

@corneliusroemer

[Over-There-Is]

881+50+2+16+2=951

[Over-There-Is]

963+57+2+17+2=1061 The designation of this branch should no more be delayed.