Potential BA.2.75*/BQ.1* recombinant (41 seqs as of 2023-01-28)

[c19850727]

Description

Recombinant between: BA.2.75* and BQ.1* (without S:R346T)
Earliest sequence: 2022/11/04 (US-TX)
Most recent sequence: 2022/11/26 (Canada-NB)
Countries circulating: US-TX (3/6), Canada-NB (2/6), France (1/6)
Potential breakpoint: Spike NTD (22193-22330)

Mutation profile (private mutations are in yellow color):

Private mutations: C7303T, C12952T, C13965T, C15277T (ORF1b:H604Y)
GISAID query: C7303T, C12952T, C13965T, C15277T

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41807_99a4b0.json?branchLabel=none&c=gt-nuc_12952&l=scatter&label=id:node_8931725&scatterY=gt

Genomes:
EPI_ISL_15841842, EPI_ISL_15853687, EPI_ISL_15893272, EPI_ISL_15951145, EPI_ISL_15976945, EPI_ISL_15977006

[silcn]

There are also a couple of private mutations in the BQ.1* part: C23625T = S:A688V and T23773C. The first suggests the parent might be a BQ.1.8.2, though the regions of geographic circulation don't match up.

[FedeGueli]

Hi @silcn there were also a group of BQ.1.1 sequences with S:A688V i tracked them in the BQ.1 diversity issue with @corneliusroemer but never checked if they were monophyletic

[FedeGueli]

One more sequence with NSP12_H613Y, Spike_G339D,Spike_i210V, -E_T11A, NSp8_N118S

total count now 7

[c19850727]

10 sequences as of 2022-12-05. Newly found in Canada-ON and US-CA.

[FedeGueli]

12 seqs as today with NSP12_H613Y, Spike_G339D,Spike_i210V, -E_T11A, NSp8_N118S

[FedeGueli]

Now we are at 18seqs with Ireland and California accounting for the last six

[c19850727]

19 sequences as of 2022-12-25. Newly found in Ireland.

[FedeGueli]

22 seqs as today. From Nevada and Maryland last sequences came

[FedeGueli]

one more from England

[FedeGueli]

One more from California

[c19850727]

25 sequences as of 2023-01-05.

[FedeGueli]

30 sequences as today. last sequences from Uk,Usa, Denmark

[FedeGueli]

34 sequences as today, new ones from England 3 and Denmark 1

[FedeGueli]

38 as today

[c19850727]

37 sequences as of 2023-01-20. Newly found in the Netherlands.

[FedeGueli]

@c19850727 saka my query finds 38 : NSP12_H613Y, Spike_G339D,Spike_i210V, -E_T11A, NSp8_N118S ,
my last samples are NDL NDL TX MD DK EN EN correct?

[c19850727]

Hi @FedeGueli I just double checked the usher tree and it seems you are right. There were one sequence (England/BRBR-3267E1FC/2022) with a N at 13965 that has been missed in my query but still got caught by yours.

BTW as of today there are 41 sequences (using a new and simplied query: C12952T, T23773C, C15277T)

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XBP with 4 newly designated sequences, and 0 updated designations. Defining mutations C15277T (ORF1b:H604Y), A22190G (S:I210V), C12952T, T23773C (following A22893C, T22942A, G27038A, C28312T, G28330A).

[JosetteSchoenma]

XBP