NJ.1 (S:F59L,R346T,F456L+Orf3a:K16N+S:K478T) with S:N185S (5), and further S:T22N, M153I (3)

[xz-keg]

Most seqs on this JN.1.11+S:R346T branch are dropouts from KP.2*. However, there seems to be a real branch hiding inside.

JN.1.11+C7979T, A12463G,T21737C,G22599C, T22928C(S:F59L,R346T,F456L)+G25440T(Orf3a:K16N)+C20436T, C21381T,A22995C(S:K478T rev)

All seqs have C7979T,A12463G have G17334T but not C7113T, this means it shall be a descendant directly from JN.1.11. And these two mutations do not appear in other lineages so small chance of recombinant.

And the S:K478T rev sub-branch is particularly interesting as it harbors recent GBW seqs from both China and India as well as USA local seq.

GISAID query: C7979T, A12463G,C20436T
GISAID query for S:N185S sub-branch: A12463G,C20436T,A22116G
GISAID query for S:T22N,M153I further sub-branch: A12463G,C20436T,A22116G,C21627A
No. of seqs: 6(Canada 1 USA 5(1 from China, 2 from India))

First: EPI_ISL_19264665, 2024-7-9,Canada
Latest: EPI_ISL_19427404, 2024-9-9, USA from China

usher

[FedeGueli]

this is a sublineage of branch 61 of #1089 ! then proposed in Pango cov-lineages/pango-designation#2542 , but better to trrack the 478T sublineage here, not worth reopening the old things. thx for spotting it.

[FedeGueli]

i was tracking this too with C7979T, A12463G,C21381T but your query catches one more.

[xz-keg]

No further seqs

[xz-keg]

+2 USA-NJ, with additional S:N185S, T22N and M153I

[FedeGueli]

+1 Colorado

[xz-keg]

designated NJ.1 via cov-lineages/pango-designation@608685e

[FedeGueli]

Worth tracking its sublineages

[FedeGueli]

no new seqs closing it