BQ.1.2.2 (BQ.1.2 + K147E, ∆186-187, N188Y, R346T, V445A) Sublineage w/ S:A484K, S:V486A, ORF7a:∆71-82, + 4x ORF1ab

[ryhisner]

Description—First sequence spotted by @c19850727 (Sakaguchi Hitoshi) and @hynnspylor (here)

Sub-lineage of: BQ.1.2.2 Earliest sequence: 2023-7-24, USA, Delaware — EPI_ISL_18115437, EPI_ISL_18115438 Most recent sequence: 2023-8-2, Finland — EPI_ISL_18106489 Countries circulating: USA (2), Finland (1) Number of Sequences: 3 GISAID AA Query: Spike_E484K, Spike_F486A GISAID Nucleotide Query: G8368A, A17824G CovSpectrum Query: Nextcladepangolineage: Substitutions/Deletions on top of BQ.1.2.2 Spike: A484K, V486A ORF7a: ∆71-82 (frameshift) ORF1a L580F, L730F ORF1b: V464F, T1453A Nucleotide: C2003T, C2453T, G8368A, G14857T, A17824G, T23011A, G23012A, C23013A (reversion), T23019C, A25983G Nucleotide Deletions: ∆27605-27639

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BQ.1.2.2_A484K_V486A.json?c=gt-S_484&label=id:node_3628803

Evidence BQ.1.2.2 already possessed an interesting spike profile, with spike mutations K147E, ∆186-187, N188Y, R346T, and V445A. These three have added the 2-nucleotide A484K as well as V486A. The two sequences from the USA both seem to have great coverage throughout the whole genome, whereas the one from Finland is missing quite a bit of coverage. It's hard to know for certain if the additional mutations in the two US sequences—S:T547I, S:V1228L, ORF1a:T708I, ORF1b:A2222V (nucleotides C2388T, C20132T, C20719T, C23202T, C23557T, G25244T)—are truly absent from the Finnish sequence or if they were just not picked up in sequencing.

Notably, this branch features three consecutive nucleotide mutations, all to A—T23011A, G23012A, C23013A. The mutations relative to BA.2 at S:484 and 486 are pictured below.

In the two sequences from the US state of Delaware, there's also a very odd synonymous mutation C23557T, which is adjacent to the A23558G mutation that forms S:I666V. Peculiarly, according to the study "Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories" by P. Simmonds, the nucleotide context in which C23557T occurs is easily the least favorable one for C->T mutations.

Genomes

Genomes

EPI_ISL_18115437, EPI_ISL_18115438, EPI_ISL_18106489

[FedeGueli]

@ryhisner edited to credit hynnspylor who independently discovered it at the same time with Saka here : https://github.com/cov-lineages/pango-designation/issues/2068#issuecomment-1680316776

[FedeGueli]

Please propose in the main page if reaches 5 adding one more country.

[Sinickle]

Not sure if S:V486A will have some sort of epistatic effect, but S:A484K looks like a definite win for BQ.1

[Over-There-Is]

Substitutions/Deletions on top of XBB.1.5:

[FedeGueli]

@Over-There-Is now corrected

[FedeGueli]

Designated JH.2 via https://github.com/cov-lineages/pango-designation/commit/9043731f6746aade7f24fddc96892b661bf06797