Potential KP.3.1.1*/XDY/XDV* recombinant with additional Orf1a:T3579I and N:P279S(4, Finland)

[Over-There-Is]

Query: A13121T, G22111T, T28297C or T15837C, G19669A, G22131C by @FedeGueli
Mutations based on JN.1:
C7113T, C11001T(Orf1a:T3579I), C12616T, A13121T, G15372T, T15837C, G17334T / G19669A, del21653-21655, G22111T, G22131C, C22858T, T22928C, C23039G, G24872T / T28297C, A28958Crev, C29108T(N:P279S)
Breakpoint 1: 17334~19669
Breakpoint 2: 24872(25036?)~28297
C11001T could be homoplastic or artefactual.
T15837C is private.
3' donor could be XDV*, XBB.1.9* or their related recombinants, but only XDV* is still circulating.
There are several XDV* or XBB.1.9* subbranch with C29108T, and XDV.1> T2572C, C7056T, C12781T, T17772C, A22995Crev, T25036C, C29108T (being placed under XDV.1> A22995Crev branch, #2114) is the largest one among the current circulating branches.

Finland/THL-08417/2024|EPI_ISL_19612647|2024-10-29
Finland/THL-09182/2024|EPI_ISL_19612698|2024-10-21
Finland/THL-01134/2025|EPI_ISL_19718013|2025-01-27
Finland/THL-01127/2025|EPI_ISL_19718018|2025-01-28

@FedeGueli :
Quick snapshot of mutations

Basically it is XDY spike plus Orf9b/N from XDV.1 and Orf1ab from Kp.3.1.1

Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_e4863_c23fe0.json?f_userOrOld=uploaded%20sample&label=id:node_11868675

[FedeGueli]

I have added query , tree and sanpshot of mutations.

[FedeGueli]

@Over-There-Is could be this the KP.3.1.1 donor? : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_20c0b_14dff0.json

[Over-There-Is]

@Over-There-Is could be this the KP.3.1.1 donor? : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_20c0b_14dff0.json

I also found it but this recombinant doesn't have C5986T.

[Over-There-Is]

I don't think the tree could interpret its real evolution path so didn't attach it.

[FedeGueli]

I don't think the tree could interpret its real evolution path so didn't attach it.

yeah as usual for recombinants.

[Over-There-Is]

Neither A13121T, C22858T, G22111T, -T28297C nor -A13121T, C22858T, G22111T, T28297C give meaningful result. And C12616T, A13121T, T28297C, -C22858T, -C28958A only gives 1 result too. It means there aren't any related KP.3.1.1/XDY, XDY/XDV or KP.3.1.1/XDV recombinants being detected.

[xz-keg]

no new seqs

[FedeGueli]

dead

[Over-There-Is]

4 now, 01-28

[JosetteSchoenma]

I noticed the 2 new ones while scanning for Delta with G210T. The dates of the 2 old and the 2 new ones are 3 months apart and one of the old plus one of the new ones are from women with the same age?
EPI_ISL_19612698 and EPI_ISL_19718013
Could this be the same woman with a chronic infection infecting someone else twice, 3 months apart?