XEK: KP.2.3/XEC Recombinant(45 seqs, 12 countries)

[Fearuncle]

Big thanks to @Over-There-Is From: https://github.com/sars-cov-2-variants/lineage-proposals/issues/2023 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ed35_40f680.json?f_userOrOld=uploaded%20sample KP.2.3 / XEC recombinant Query: C3505T, T5701C, C9286T

Break point: 9286/~15402 Mutations based on JN.1: C593T(Orf1a:H110Y), C3505T, T5701C(private), C7113T(Orf1a:T2283I), C9286T / C18657T, C19716T, C21627A(S:T22N), T21738C(S:F59S), T22928C(S:F456L), C23039G(S:Q493E), G24872T(S:V1104L), C25006T, C28291A(Orf9b:P3H), G28884C(N:R204P)

5' donor: KP.2.3> C9286T> C593T> C3505T, A15402G(=JN.1+C593T, C3505T, C7113T, C9286T / A15402G, G17334T, C22000A, G22599C, T22928C, G24872T, G25593T, C28714T, 3 seqs, DE 2, NL 1) 3' donor: XEC(=JN.1+C18657T, C19716T, C21627A, T21738C, T22928C, C23039G, G24872T, C25006T, C28291A, G28884C)

Earliest sequence: 07-19 Denmark EPI_ISL_19332668 Latest sequence: 09-02 England, United Kingdom EPI_ISL_19406440 Regions detected: UK 5, Austria 3, Germany 3, Sweden 2, Denmark 1, Netherlands 1, Ukraine 1

Sequences: EPI_ISL_19332668, EPI_ISL_19364165, EPI_ISL_19368841, EPI_ISL_19368849, EPI_ISL_19372478, EPI_ISL_19373085, EPI_ISL_19381036, EPI_ISL_19381934, EPI_ISL_19385623, EPI_ISL_19389047, EPI_ISL_19389054, EPI_ISL_19390181, EPI_ISL_19406420, EPI_ISL_19406440, EPI_ISL_19410161, EPI_ISL_19410789

And 1 sequence seem also related to this branch: EPI_ISL_19378121(potential contaminated)

[xz-keg]

7 countries including Ukraine.

[xz-keg]

+2 netherlands +2 Slovenia, 20 now.

[Fearuncle]

now in 8 countries

[Over-There-Is]

Also in United States now.

[Over-There-Is]

Break point: 9286/~15402

The left slash here should be a right slash to avoid the tilde forming delete line , like this: ~without slash~ /~left slash/~ \~right slash\~. My typo. Sorry.

[Fearuncle]

9 countries

[Fearuncle]

In Croatia EPI_ISL_19416657

[Over-There-Is]

27, US-NJ

[FedeGueli]

+2 netherlands +2 Slovenia, 20 now.

one of the two samples from Netherlands seems a recombinant with KP.3.1.1 getting Orf1a:S4286C , C12616T and
EPI_ISL_19413561

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice4_genome_test_56317_be12f0.json?label=id:node_7053962

Query (if real): C2110A, C12616T ,G561A,

Interesting it shares 4 Nucs (C12616T ,G561A, G15372T, G17334T, ) in orf1ab with a GBW KP.3.1.1 sample from Cuba collected in July (EPI_ISL_19240845)

First spotted by @ryhisner

Edited this has no 31del as i wrote above , sorry.

[Over-There-Is]

31, Ireland +2

[Fearuncle]

Now 38

[Fearuncle]

Places #2 on collection 42

[FedeGueli]

ping @corneliusroemer this is shown as the third branch of XEC instead it is a recombinant and it seems fast

[xz-keg]

It is much faster than XEC.

[FedeGueli]

It is much faster than XEC.

yeas apaprently yes. i remember i spotted that branch when proposing the orf1a:I1367L branch and it was something like two seqs when the proposed brannch was--20? 30? now this will already reach out and overtake that branch in the next week or soon

[Fearuncle]

now in france

[Mydtlwn]

Please designate it as soon as possible! We should not delay any more.

[Mydtlwn]

@corneliusroemer

[corneliusroemer]

Interesting, thanks! So there's a single breakpoint here and it's essentially an XEC with some 5' from a KP.2.3 branch, correct?

[xz-keg]

Interesting, thanks! So there's a single breakpoint here and it's essentially an XEC with some 5' from a KP.2.3 branch, correct?

Yeah

[FedeGueli]

Interesting, thanks! So there's a single breakpoint here and it's essentially an XEC with some 5' from a KP.2.3 branch, correct?

yeah it took back orf1a:T2283I from Jn.1.11.1

[Fearuncle]

it is now #1 in Collection 42

[Fearuncle]

[FedeGueli]

This, XEC and MV.1 seems able to breakaway from the bunch of fast lineages, but MC.10 + 435S is climbing and it is likely as fast or only slighty slower than them.

[Fearuncle]

now 4 with S:F2L and ORF3a:L95F

[FedeGueli]

now 4 with S:F2L and ORF3a:L95F

S:F2L popped up also in another lineage (#2083 could be convergent at this point cc @ryhisner

[FedeGueli]

Designated XEK via https://github.com/cov-lineages/pango-designation/commit/ba3711a5615956ed97150288eb68356aa0fe7cdd