KP.2.3/KP.3.3 recombinant (29 seqs, 5 places, 20 with S:R346T)

[xz-keg]

From sars-cov-2-variants/lineage-proposals#2049

It seems that a lot of new DeFLiRT+DeFLuQE recombinants are submitted these days.
Among them, this seems a very interesting one, it loses S:R346T during recomb in exchange for S:Q493E, but gains S:R346T independently afterwards.

KP.2.3--KP.3.3

Breakpoint between 22001 and 22598

Additional mutations: C4891T, C5310T, C6471A,A18642C,del21653_21655

Orf1a:T1682I, T2069N
S:S31-

C4891T, C5310T, C6471A,A18642C,del21653_21655 from a KP.2.3 branch

GISAID query: C4891T, C22000A, G28884C
No. of seqs: 22(USA-CA,UT,TX,NY)

First: EPI_ISL_19339481, Texas, 2024-7-10
Latest: EPI_ISL_19433553, Utah, 2024-9-16

GISAID query for S:R346T sub-branch: C4891T, C22000A, G28884C,G22599C (15 seqs)

Usher places it on a flip-flop reversion branch. It shouldn't have Orf1a:A690V.

https://nextstrain.org/fetch/raw.githubusercontent.com/aviczhl2/lineage_proposal_jsons/main/kp_2_3_kp_3_3_recomb.json?label=id:node_5516374

[DailyCovidCases]

This branch has slowed down a lot now. You can close this issue @aviczhl2

[FedeGueli]

Not slow, what we should wait for is for appearing in numbers outside the Utah Cluster.

[corneliusroemer]

I don't really trust those Texas/Utah clusters - the losing and regaining S:R346T is a bit add as well. Would only designate if it clearly spreads more widely, with more labs involved.

[xz-keg]

27,England.
The S:R346T branch spreads to NY too.