GK.2.1/XBB.1.5 recombinant with additional S:P1162S (43 seqs, 11 countries)

[aviczhl2]

From sars-cov-2-variants/lineage-proposals#700

XBB.1.5(with 17124 but without 10204)+C27059T+C28005T(Orf8:P38S), T22928C(S:F456L),G22927T(S:L455F),C22624T,A25045G
+C15755G(Orf1b:S763C),G23093A,C23741T(S:V511I),C7417T,C25046T(S:P1162S)

C15755G,G23093A,C23741T,C27059T,C28005T,T22928C,G22927T,C22624T,A25045G are from GK.2.1
C7417T,C25046T are private mutations.

XBB.1.5--GK.2.1
Breakpoint between 12468 and 15754.

GISAID query: C7417T,C25046T,C15755G
No. of seqs: 31(Canary Islands 2 UK 14 Spain 3 Switzerland 2 USA 2 South Korea 1 Norway 1 Ireland 1 Israel 1 Italy 4 )
9-CLIMB seqs currently not on GISAID.

First: EPI_ISL_18119219, Italy, 2023-5-18
Latest: CLIMB-CM7YGPFT, UK, 2023-8-21

usher

[aviczhl2]

Detected in France and Belgium. 36 on GISAID and 7 additional CLIMB seqs. Total 43.

[corneliusroemer]

Thanks! This matches GK.2.1 in particular due to the presence of 25045G

For the 5' side, XBB.1.5 is indeed the most likely donor, but more due to exclusion of all other possible donors, not due to the presence of any particular signature mutations
FY.4.2 has 7417T but also 6777 mutated which this recombinant doesn't so seems excluded based on that.https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=405G%2C9866T%2C12467.%2C11750.%2C10204.%2C5720.%2CC12789.%2CA8001.%2CC6740.%2CA3662.%2CC2710.%2CG2513.%2CG6536.%2CC4234.%2C1670.%2CC920.%2CT5338.%2CC2695.%2CC7119.%2CC7164.%2CA10042.%2C7417T%2C6777.&
Potential donors: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=405G%2C9866T%2C12467.%2C11750.%2C10204.%2C5720.%2CC12789.%2CA8001.%2CC6740.%2CA3662.%2CC2710.%2CG2513.%2CG6536.%2CC4234.%2C1670.%2CC920.%2CT5338.%2CC2695.%2CC7119.%2CC7164.%2CA10042.&

[corneliusroemer]

Oh it actually matches this small branch of XBB.1.5.68 with 7417T:

https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_3dd2f_1c52b0.json?label=id:node_7290583

Or these 3 sequences at the bottom just before FY.4.2 - though none of them are cmopatible due to extra ORF1a mutations

https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_3dd2f_1c52b0.json?label=id:node_7290583

So I'll leave it open as XBB for the parent side

[FedeGueli]

Thx @corneliusroemer this seems fast

[JosetteSchoenma]

XCL