XDN: JN.1.1/JD.1 recombinant (20 seqs, 2 countries)

[aviczhl2]

This is the 5th non-singlet recomb of BA.2.86*. I thought it was a singlet but @FedeGueli found there's already one being removed by usher.

JN.1.1--JD.1
Breakpoint between 24379 and 24989

Additional mutations: C280T, C11812A,

C280T from a JN.1.1 branch
C11812A is private mutations

GISAID query: C11812A, T28282C, C280T
No. of seqs : 2(UK)
EPI_ISL_18552726, 2023
EPI_ISL_18592162, 2023-11-26

usher

[aviczhl2]

+1 Wales

[aviczhl2]

It seems that seqs of this branch weren't added to usher despite I put it on recombinants.tsv @AngieHinrichs.

[AngieHinrichs]

Thanks for the heads-up. It is a little more complicated for COG-UK sequences because they tend to be present in all three of GISAID, COG-UK and INSDC, and I need to make sure that the INSDC accession is not excluded. I will work on it and hopefully they'll be added tomorrow (2023-12-20).

[aviczhl2]

+1 Wales.

Oh I find them actually on usher.

[aviczhl2]

+3 Wales

[aviczhl2]

+1 England

[aviczhl2]

There's one more seq without 14425T. Change query.

[JosetteSchoenma]

Since we discussed this one in the private group after I spotted it at the 1st of December, I got some extra info.

The date for EPI_ISL_18552726 is 2023-11-21 (not on GISAID).

Alternative query from @FedeGueli
C11747T, C11812A, C14425T

6 extra ones showed up yesterday. Will compare results later.

I got another breakpoint, so I will have a better look at that too.

It gained Orf8:8G* !

[aviczhl2]

+4 USA

[FedeGueli]

Please propose it.

[FedeGueli]

Designated XDN via cov-lineages/pango-designation@cd3327a