XCH: GK.1.1/XBB.1.9.1* Recombinant (FLip+T573I+S704L) ( copied back from the main repo)

[FedeGueli]

ALL copied by original issue of Ryan Hisner (cov-lineages/pango-designation#2173) to complete here the recombinant panorama . (it is not a proposal)

Description
Recombinant Between: GK.1.3 (XBB.1.5.70.1.3) and XBB.1.9.1* (Most likely. It could also be XBB.1.16)
Earliest sequence: 2023-6-9, USA, Colorado — EPI_ISL_17856744
Most recent sequence: 2023-7-25, Australia (NSW) — EPI_ISL_18073787; Spain (Basque) — EPI_ISL_18056891
Countries circulating: Australia (3), USA (2), France (1), Spain (1)
Number of Sequences: 7
GISAID AA Query: Not possible
GISAID Nucleotide Query: G25947C, T28297C, C28657T
CovSpectrum Query: [3-of: G25947C, C27741T, T28297C, C28657T] & [4-of: A1124G, C1973T, A2163C, C7564T, T8737C, G12467T, A16856G, C23673T] & !A25045G & !C25658T & !C27059T & !C28005T
Breakpoints:
First Breakpoint: 23673-25044 (S:704-S:1161)
Second Breakpoint: 28297-28656 (N:8-N:128)

Private Mutations: ORF3a:Q185H (G25947C)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/GK.1.3_XBB.1.9.1_Recomb__7_seq.json?c=gt-nuc_25947&label=id:node_3098784

image
Evidence
Given wide geographic spread and that this recombination joins together the magic FLip combo of S:L455F & S:F456L (not to mention S:S704L) with the advantageous ORF9b:I5T, I think this one is worth flagging. The five most recently collected sequences in this lineage, all collected between July 18-25, have S:T573I and three additional synonymous nucleotide mutations (G9220A, T9952C, C26907T).

At first, this looks simply like a GK.1.3 that picked up three nucleotide mutations: G25947C (ORF3a:Q185H), C27741T (syn), T28297C (ORF9b:I5T). But it's missing four synonymous nucleotides that all GK.1.3 possess: A25045G, C25658T, C27059T, & C28005T. However, it retains the synonymous C28657T, which is found in all GK.1 but is rare elsewhere.

There are zero XBB* sequences (other than the ones in this lineage) returned by the following CovSpectrum search query:

Nextcladepangolineage:XBB* & [2-of: C28657T, G25947C, C27741T] & T28297C & !A25045G & !C25658T & !C27059T & !C28005T

But CovSpectrum returns 541 other results for the search query below:

Nextcladepangolineage:XBB* & [1-of: C27741T, G25947C] & T28297C & !A25045G & !C25658T & !C27059T & !C28005T

Any lineage with sequences matching this description could be the partner recombinant. Here is the breakdown of the 541 sequences returned.

XBB.1.9.1* — 344 (63.6%)
XBB.1.16* — 108 (20.0%)
XBB.1.9.2* — 66 (12.2%)
XBB.1.22* — 14 (2.6%)
XBB.1.9.6* — 3 (0.55%)
XBB.1.42* — 3 (0.55%)
XBB.1.5* — 2 (0.37%)
XBB.1.9 — 1 (0.18%)

So this is probably a GK.1.3 recombinant with an XBB.1.9.1* lineage of some sort, but it could be any of the others listed above as well.

Genomes

Genomes
EPI_ISL_17856744, EPI_ISL_17976216, EPI_ISL_18046369, EPI_ISL_18056891, EPI_ISL_18060735, EPI_ISL_18066425, EPI_ISL_18073787

[FedeGueli]

XCH