JN.1+S:A67V(39 seqs, 11 countries ,60% Chongqing)

[xz-keg]

JN.1+C5512T,G2782T,C21762T(S:A67V)

GISAID query: C5512T,G2782T,C21762T,C18894T
No. of seqs: 19(China 6(Chongqing 5 Liaoning 1), UK 1 France 1 Oman 1 Japan 1 Poland 1 Singapore 2(1 from Saudi Arabia) USA 6(2 from Italy, CO,CA,MD,NY 1 each)

First:EPI_ISL_18819543, 2023-11-28, Japan,
Latest: EPI_ISL_18926252, 2024-2-16, Chongqing

This lineage seems extremely widely distributed, suggesting circulating in undersampled regions.
It also takes 5/5 of Chongqing seqs in 2024.

usher

[Memorablea]

Please refer to the testing number.So, it shouldn't be 100% Chongqing？

[xz-keg]

Please refer to the testing number.So, it shouldn't be 100% Chongqing？

Unfortunately nobody knows what other seqs look like. Based on existing seqs it is 100%.

[HynnSpylor]

Oh I intended to propose it about 6 hours ago, but failed for the poor network!

Chongqing updates very new 5 seqs, all of them on the branch. Despite it could be a cluster, there is another one detected in Liaoning Province, which is more than 1,000 km from Chongqing, indicating the spread in China.

Genomes:
EPI_ISL_18651177, EPI_ISL_18678962, EPI_ISL_18815387, EPI_ISL_18819543, EPI_ISL_18835379, EPI_ISL_18847565,
EPI_ISL_18854014, EPI_ISL_18869787, EPI_ISL_18876905, EPI_ISL_18881153, EPI_ISL_18886344, EPI_ISL_18886394,
EPI_ISL_18900903, EPI_ISL_18909539, EPI_ISL_18926250-18926254,

[xz-keg]

Oh I intended to propose it about 6 hours ago, but failed for the poor network!

Chongqing updates very new 5 seqs, all of them on the branch. Despite it could be a cluster, there is another one detected in Liaoning Province, which is more than 1,000 km from Chongqing, indicating the spread in China.

Genomes: EPI_ISL_18651177, EPI_ISL_18678962, EPI_ISL_18815387, EPI_ISL_18819543, EPI_ISL_18835379, EPI_ISL_18847565, EPI_ISL_18854014, EPI_ISL_18869787, EPI_ISL_18876905, EPI_ISL_18881153, EPI_ISL_18886344, EPI_ISL_18886394, EPI_ISL_18900903, EPI_ISL_18909539, EPI_ISL_18926250-18926254,

There is another JN.1+S:A67V branch achieving high local prevalence in another undersampled area of Assam, India, #1293.

[FedeGueli]

One scientist of the Chongqing lab that seequenced this has opened an issue on the Pango report, i suggest to track this in the main repo: @aviczhl2 if you have suggestions/better queries / trees put them in the main page proposal Thank you!

cov-lineages/pango-designation#2498

[xz-keg]

One scientist of the Chongqing lab that seequenced this has opened an issue on the Pango report, i suggest to track this in the main repo: @aviczhl2 if you have suggestions/better queries / trees put them in the main page proposal Thank you!

cov-lineages/pango-designation#2498

I think his proposal is a general JN.1+S:A67V containing 10+ separate lineages?

[HynnSpylor]

2 more in CO, US

[FedeGueli]

One scientist of the Chongqing lab that seequenced this has opened an issue on the Pango report, i suggest to track this in the main repo: @aviczhl2 if you have suggestions/better queries / trees put them in the main page proposal Thank you!
cov-lineages/pango-designation#2498

I think his proposal is a general JN.1+S:A67V containing 10+ separate lineages?

thank you for noticing and thanks for reopening this one. we could comment here and there transfer our findings to the issue opened by the lab.

[xz-keg]

thank you for noticing and thanks for reopening this one. we could comment here and there transfer our findings to the issue opened by the lab.

He says 6/10 of his samples are from this branch. So I change the prevalence to 60%.

Consider Chongqing has 30 million pop, a single branch getting 60% is quite amazing in regions with such size.

[HynnSpylor]

+2 in Henan Province, China

[FedeGueli]

27 +2 Henan + 4 Germany please propose it once reaches 40.

[FedeGueli]

It seems that the other issue is now aligned with this. closing this then