BQ.1.2 Sublineage with S:K147E, S:∆186-187, S:N188Y, S:R346T, S:V445A, ORF8:C90* (10 seq, April 8)

[ryhisner]

Description
Sub-lineage of: BQ.1.2
Earliest sequence: 2023-1-27, Nigeria — EPI_ISL_17038850
2nd-earliest sequence: 2023-3-20, Ireland — EPI_ISL_17325799
Most recent sequence: 2023-3-29, England — EPI_ISL_17423437 + 6 other sequences
Countries circulating: England (7), Ireland (1), Nigeria (1), USA (1)
Number of Sequences: 10
GISAID AA Query: Spike_I666V, Spike_V445A, NS8_C90stop
GISAID Nucleotide Query: A22001G, G26951C, C28163A
CovSpectrum Query: Nextcladepangolineage:BQ* & [3-of: A22001G, G22599C, T22896C, G26951C, C28163A]
Substitutions on top of BQ.1.2:
Spike: K147E, N188Y, R346T, V445A (7/9 also have N703Y)
ORF8: C80*
Nucleotide: A22001G, G22599C, T22896C, G26951C, C28163A (and 7/9 with A23558G)

AA Deletions: S:∆186-187
Nucleotide Deletions: ∆22119-22124

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BQ.1.2_K147E_186-187del_V445A_N703Y_subtreeAuspice1_genome_20228_197cf0.json

Evidence
The first sequence in this lineage was in late January in Nigeria. No further sequences appeared until very recently, when nine more have been uploaded—seven from England, one from Ireland, and one from Illinois, USA. It's hard to tell for certain due to lack of surveillance and low-quality sequencing, but this lineage could be much more common in the region around Nigeria than elsewhere. The recent spate of cases could be a fluke, but the number of spike mutations, the rare (out-of-frame) spike deletion, and the large differences between the sequences from four geographically widespread locations combine to make this an intriguing lineage.

All seven sequences from England almost certainly have both R346T and N703Y but three are missing coverage in one or both of those areas. The sequence from Nigeria has >6% NNN's.

Genomes

Genomes

EPI_ISL_17038850, EPI_ISL_17325799, EPI_ISL_17384968, EPI_ISL_17423308, EPI_ISL_17423360-17423361, EPI_ISL_17423369, EPI_ISL_17423392, EPI_ISL_17423410, EPI_ISL_17423437

[thomasppeacock]

Recommending this as it seems (a late) example of a great convergence lineage and I think its good to continue to try and keep tabs on those.

[InfrPopGen]

Thanks for submitting. We've added lineage BQ.1.2.2 with 7 newly designated sequences, and 0 updated. Defining mutations C28163A (ORF8:C90*), A22001G (S:K147E), T22896C (S:V445A), G26951C (following 22599C (S:R346T)).

[corneliusroemer]

Thanks @InfrPopGen!