XEL: KS.1.1.2/JN.1* recombinant (56 seqs, 10 countries, >5% South Korea)

[xz-keg]

There seems to be a KS.1.1/JN.1* recombinant, with KS.1.1 Spike ( except for S:A1087S>A reversion)

KS.1.1--JN.1

Breakpoint between 22929 and 24820

Additional mutations: C6701T, C19716T, T25510C, C29311T

Orf1a:L2146F, Orf3a:S40P

C6701T, C19716T from a KS.1.1.2 branch,
One of T25510C, C29311T from a JN.1* branch, the other is private. (There exists a KP.3.2.3 branch containing both, but that brings unnecessary G24872T so not possible)

GISAID query: T25510C, C29311T,C19716T,T3565C
No. of seqs: 6(USA 1 Netherlands 1 South Korea 2 Ireland 1 Israel 1)

First: EPI_ISL_19257990, South Korea, 2024-6-17
Latest: EPI_ISL_19300800, Israel, 2024-7-21

usher

[FedeGueli]

S:A1087S is reverted so not exactly KS.1.1 spike, KS.1.1 S1 you likely were meaning

[xz-keg]

S:A1087S is reverted so not exactly KS.1.1 spike, KS.1.1 S1 you likely were meaning

Yeah and I realize the other donor is not KP.3.2.3 due to not having V1104L.

[FedeGueli]

ah good spot!

[xz-keg]

9, Russia

[FedeGueli]

+1 NY

[xz-keg]

14, China

[xz-keg]

+17 in the recent South Korean batch, also in Canada, France and Japan

[xz-keg]

17/359=5% prevalence in South Korea

[FedeGueli]

56 another batch from South Korea where it is around 5%, please propose it

[FedeGueli]

KS.1.1 donor now designated KS.1.1.2 via. cov-lineages/pango-designation@c542eb9#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1277

then this recombinant designated XEL via cov-lineages/pango-designation@d247018