Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

CK.1.1 sublineage with S:V1264L (111 seqs mainly in Japan, still circulating even shows growth advantage) #2271

Closed
HynnSpylor opened this issue Sep 6, 2023 · 2 comments

Comments

@HynnSpylor
Copy link
Contributor

HynnSpylor commented Sep 6, 2023

*Transferred from sars-cov-2-variants/lineage-proposals#666
Defining mutations:
CK.1.1>C26907T>A27753C>G25352T (S:V1264L)
GISAID query: A24129G, G25352T, A27753C
Earliest seq: 2023-02-24 (Japan- EPI_ISL_17265415)
Most recent seq: 2023-08-18 (Japan- EPI_ISL_18122853)
Countries detected: Japan (108), South Korea (1), US (1)

Usher Tree:
QQ截图20230907002601
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3126b_8a6d50.json?c=gt-S_1264

In recent 3 months, almost (~98%) CK.1.1 (with SGTF and S:Y144-) seqs got S:V1264L. It seems very strange that an old BA.5* lineage can still circulate in Japan- Even it shows a 14% growth advantage:
QQ截图20230907001316
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=S%3AV1264L&nextcladePangoLineage=CK.1.1*&

And it becomes the biggest BA.5* lineages in past 3 months:
QQ截图20230907002634

If we carefully analyze the Usher Tree, the ORF8:P38S may be another key mutations- the branch has increased and circulated since Jun 2023. 7 seqs further get S:L176F.

Despite it can not compete with XBB* outside Japan, it still deserves a further tracking.

Genomes:
EPI_ISL_17265415, EPI_ISL_17280829, EPI_ISL_17281014, EPI_ISL_17281546, EPI_ISL_17295219, EPI_ISL_17295221,
EPI_ISL_17387955, EPI_ISL_17388093, EPI_ISL_17388167, EPI_ISL_17463107, EPI_ISL_17495667, EPI_ISL_17495682,
EPI_ISL_17540021, EPI_ISL_17540023, EPI_ISL_17540025-17540027, EPI_ISL_17540176, EPI_ISL_17558606, EPI_ISL_17629485,
EPI_ISL_17630994, EPI_ISL_17631063, EPI_ISL_17631079, EPI_ISL_17637599-17637600, EPI_ISL_17652270, EPI_ISL_17880076,
EPI_ISL_17881491, EPI_ISL_17881691, EPI_ISL_17882706, EPI_ISL_17882776, EPI_ISL_17883773, EPI_ISL_17952860,
EPI_ISL_17973117, EPI_ISL_17973136, EPI_ISL_17980792, EPI_ISL_17982143, EPI_ISL_17985835, EPI_ISL_18006526,
EPI_ISL_18006568-18006569, EPI_ISL_18007023, EPI_ISL_18013331, EPI_ISL_18013347, EPI_ISL_18033119, EPI_ISL_18044112,
EPI_ISL_18051431, EPI_ISL_18051668, EPI_ISL_18051720, EPI_ISL_18056120, EPI_ISL_18060297, EPI_ISL_18060307,
EPI_ISL_18064876, EPI_ISL_18065198, EPI_ISL_18065265, EPI_ISL_18065270, EPI_ISL_18065290-18065291, EPI_ISL_18065909,
EPI_ISL_18066504, EPI_ISL_18067291, EPI_ISL_18067296, EPI_ISL_18067316, EPI_ISL_18071617, EPI_ISL_18082342,
EPI_ISL_18082733, EPI_ISL_18082764, EPI_ISL_18082768, EPI_ISL_18082773, EPI_ISL_18097036, EPI_ISL_18097142,
EPI_ISL_18097384, EPI_ISL_18097395, EPI_ISL_18097408, EPI_ISL_18097447, EPI_ISL_18106312, EPI_ISL_18106326-18106331,
EPI_ISL_18106335, EPI_ISL_18106337-18106339, EPI_ISL_18118051, EPI_ISL_18122670, EPI_ISL_18122733, EPI_ISL_18122817,
EPI_ISL_18122853, EPI_ISL_18122908, EPI_ISL_18122931, EPI_ISL_18122965, EPI_ISL_18122986, EPI_ISL_18127362,
EPI_ISL_18127575, EPI_ISL_18128140, EPI_ISL_18134206, EPI_ISL_18139646, EPI_ISL_18139662, EPI_ISL_18141048,
EPI_ISL_18146244, EPI_ISL_18164744, EPI_ISL_18164943, EPI_ISL_18214715, EPI_ISL_18214761, EPI_ISL_18215757,
EPI_ISL_18223426, EPI_ISL_18226568

@FedeGueli
Copy link
Contributor

I think that the deletion S:Y144- (from CK.1.1) has its role in its success. We already saw that in BQ.1 when it had hit the wall fo the double BA.5/BA.5+346T recent immunity S:Y144- became widespread in the tree and Yunlong Cao confirmed with his lab tests its importance. So my idea that the whole CK.1.1 managed to find in Japan its niche ( as we saw for other lineages in Australia, Philippines , New Zealand islands could permit that) and when BA.5 specific immunity started to wane it got the right mutation at residue 1264 that we already saw in "last warriors"(meaning more resilient lineages) as BA.2.38.3/BH.1 in India one of the last stepwise BA.2 to resist to saltations/recombinants in India.

@HynnSpylor
Copy link
Contributor Author

1 more seq in Shanghai, China

@HynnSpylor HynnSpylor changed the title CK.1.1 sublineage with S:V1264L (110 seqs mainly in Japan, still circulating even shows growth advantage) CK.1.1 sublineage with S:V1264L (111 seqs mainly in Japan, still circulating even shows growth advantage) Sep 7, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants