JN.1+S:V1104L emerging in India(Designated JN.1.11, 16 and 5 countries with Orf1a:T2283I and S:F456L )

[aviczhl2]

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 branch 4 and https://github.com/sars-cov-2-variants/lineage-proposals/issues/1262

JN.1+G17334T,G24872T(S:V1104L)

GISAID query: G24872T, G17334T,C28958A No. of seqs: 21(India 20 UK 1)

First: EPI_ISL_18694669, India-GJ, 2023-12-7 Latest: EPI_ISL_18725672, India-MH, 2024-1-1

20/790=2.5% in India seqs from 2023-12. From GJ, KA and MH.

+C7113T,T22928C(Orf1a:T2283I,S:F456L) GISAID query: C7113T,T22928C,T3565C No. of seqs: 6(India 5 UK 1)

Note that due to artefacts usher places those seqs on different branches. Some with S:V483G artefact are placed together, some with artefacts around S:16 are placed together, and seqs with other artefacts are placed in other places.

@AngieHinrichs

current usher

[corneliusroemer]

Also found this one - it's a bit tricky to designate due to the artefacts, there's now an Israeli sequence as well though with 456L hCoV-19/England/CLIMB-CM7YMUES/2023|EPI_ISL_18735395|2023-12-29

And two Texas seqs without 456L:

hCoV-19/USA/TX-HMH-M-136910/2023|EPI_ISL_18743029|2023-12-27
hCoV-19/USA/TX-HMH-M-136429/2023|EPI_ISL_18743507|2023-12-15

[corneliusroemer]

I've designated via the non-Indian sequences with 1104L for now as JN.1.11, the 456L would be a sublineage in the future

[AngieHinrichs]

Yep, it's currently placed on a messy reversion branch within JN.1.1 instead of JN.1. When the 2024-01-11 build finishes I will do some pruning & re-optimization on the tree, and then hopefully in tomorrow's 2024-01-12 build JN.1.11 will be in the right place.

[aviczhl2]

The S:F456L branch is 10 now.

[FedeGueli]

456L 15 now

[aviczhl2]

Countries for F456L branch: India, UK, USA, Israel, Singapore

[FedeGueli]

I've designated via the non-Indian sequences with 1104L for now as JN.1.11, the 456L would be a sublineage in the future

@corneliusroemer could you reopen this one to track properly the 456L branch please?

[Over-There-Is]

JN.11> A12889G> T3055C> T22926C or JN.11.1> T3055C?