XDN: JN.1.1/JD.1* or XCP recombinant(37 seqs, 2 countries)

[aviczhl2]

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1158

JN.1.1--JD.1 or XCP (thanks @JosetteSchoenma pointing out possibility of XCP) Breakpoint likely between 24379 and 24989 Very few JD.1 or XCP seqs have 24378T, so may between 23605 and 24377 with little chance.

Additional mutations: C280T

C280T from a JN.1.1 branch

GISAID query: T28282,A6183,T22926,-27810,-28958(edited) No. of seqs : 20(UK 16 USA 4) First: EPI_ISL_18552726, UK, 2023-11-21 (credit to @JosetteSchoenma ) Latest: EPI_ISL_18743268, USA, 2023-12-29

usher

[FedeGueli]

Some trouble in the transfer

[JosetteSchoenma]

Like I mentioned in the other issue, the one without a date is the first one. I discovered it on the 1st of December, when all the other ones weren't submitted to GISAID yet. 🙃

The date for EPI_ISL_18552726 is 2023-11-21 (only 2023 on GISAID).

Plus, alternative query from @FedeGueli C11747T, C11812A, C14425T.

It misses one bad sequence from England which might be different. No S:F486P for example.

Other issue: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1158

[aviczhl2]

It misses one bad sequence from England which might be different. No S:F486P for example.

That seq certainly belongs to this branch, at least on usher. Just with some missing coverage.

[JosetteSchoenma]

It misses one bad sequence from England which might be different. No S:F486P for example.

That seq certainly belongs to this branch, at least on usher. Just with some missing coverage.

It could very well belong here, but I wouldn't really in Usher for that.

[aviczhl2]

There exists new seqs without C11812A for this recomb. Change query.

[aviczhl2]

It seems that one seq of this recomb, EPI_ISL_18707947(the 14425-missing-coverage-seq) is removed due to submitter's request. So despite 3 new seqs were added yesterday, currently it is 22 on GISAID.

[FedeGueli]

this is growing faster than JN.1 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=T28282%2CC14425%2CA6183&analysisMode=CompareToBaseline& still very small to conclude anything but interesting to keep in mind.

[aviczhl2]

It misses one bad sequence from England which might be different. No S:F486P for example.

Seems that the seq is now retracted by submitter.

[aviczhl2]

+14 UK today, total=36 now. @corneliusroemer

[aviczhl2]

1 seq without 14425T appears(re-appear), change query.

Happen to find that the original query captures 2 new unrelated seqs, so -2 , and +1 for cover the seq without 14425T, so the actual toll being 35.

[FedeGueli]

Thank you

[aviczhl2]

2 more from UK today.

[corneliusroemer]

XDN