XDP: JN.1.4/FL.15 recombinant (25 seqs, 4 countries)

[xz-keg]

JN.1.4+C27810T(rev), G27915T, T28297C, C28846T, A28958C(rev)

Orf7b:L19F(rev)
Orf8:G8*
Orf9b:I5T
N:K229Q(rev)

JN.1.4--FL.15*
Breakpoint between 26834 and 27809

GISAID query: T28297C, C897A, C28846T, G27915T, C774T by @ryhisner ( former query:T28297C,T18453C,C774T )
No. of seqs:4 (USA)

First: EPI_ISL_18623642, USA-CA, 2023-11-7
Latest: EPI_ISL_18604137, USA-OH, 2023-11-23

usher

[xz-keg]

+1 Israel

[xz-keg]

+1 Denmark

[FedeGueli]

+2 Canada

Pleasee propose once it reaches 25

[FedeGueli]

This jumped to 22 with a batch from NYC ( hence Ryan spotted and proposed the duplicate of this , i think)

[FedeGueli]

Please propose it

[ryhisner]

You have to include C28846T in the query or else you get 3-4 unrelated sequences—and that number will probably increase as time goes on. There are really only 18 sequences in this lineage right now, not 22.
C28846T is an FL.15* mutation, so I think it's safe to call this one a JN.1/FL.15* recombinant.

[FedeGueli]

thanks @ryhisner i have edited the query cc @aviczhl2

[xz-keg]

You have to include C28846T in the query or else you get 3-4 unrelated sequences—and that number will probably increase as time goes on. There are really only 18 sequences in this lineage right now, not 22. C28846T is an FL.15* mutation, so I think it's safe to call this one a JN.1/FL.15* recombinant.

Yeah that's a thing for BA.2.86/XBB recomb islands. Recombs with similar breakpoints gather together and somethings the root and sub-branch are actually different recombs.

[xz-keg]

You have to include C28846T in the query or else you get 3-4 unrelated sequences—and that number will probably increase as time goes on. There are really only 18 sequences in this lineage right now, not 22. C28846T is an FL.15* mutation, so I think it's safe to call this one a JN.1/FL.15* recombinant.

For 4 seq withs 28846, only 1 seq without 28958( may be JN.1/other XBB.1+Orf9b:I5T recomb) , others seem to be JN.1 getting T28297C independently.

[FedeGueli]

Designated XDP via cov-lineages/pango-designation@2c80397