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JN.1+M:L46F+S:F456L(318 seqs, 15 countries, 17% Shanxi, 17% Hubei, 10% Henan, 11% Heilongjiang, 1 with S:R346T) #2531
Comments
Thank you great work |
+1 Japan |
+1 UK |
+1 Taiwan |
+8 from Fujian, Anhui, Hubei and Taiwan. |
To me it seems really a fastg lineage, likely less than FLiRT tough. @corneliusroemer |
14/81=17% in the 4-1 Shanxi batch. |
ping @corneliusroemer this is fast |
+22. 16/207=8% in Hubei seqs from 2024.3.20. |
+1 South Korea with the same situation of Hong Kong seqs(share mut+ no coverage at 456) |
fast growing and prevalent, ping @corneliusroemer |
90, Canada |
It got FLiRT! : EPI_ISL_19045970 @corneliusroemer this one is to watch |
153, New Zeland, France, |
19/189=10% in Hubei seqs after 4-1 |
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& |
189, Qatar, |
251 seqs now |
17/153=11% in Heilongjiang seqs after 2024-4 |
@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 |
+3 South Korea, it starts expanding outside China |
Hong_Kong/HKU-240503-042/2023|EPI_ISL_19093478|2023-12-17 |
thx for the analysis |
274, Netherlands, Ireland (both via GBW) |
imopressive fast , @corneliusroemer when you will be back this is one of the first to need a designation |
Some sequences from Liaoning and Shanxi got 4162 reverted, but I don't think they're true |
Multiple cities, Liaoning 05-10 13/101 |
*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: |
349 |
But some sequences have reversions on 4162 and 3565, and they could still be identified by G1126A. |
From branch 26 of sars-cov-2-variants/lineage-proposals#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
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