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Repository for suggesting new lineages that should be added to the current scheme
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BQ.1.1 sublineage with S:Y144-, S:S256L (210 seqs, Europe, Asia, Australia) #1403

Closed Sinickle closed 1 year ago

Sinickle commented 1 year ago

Description Sub-lineage of: BQ.1.1 Earliest sequence: 2022-10-12, Indonesia --- EPI_ISL_15812519 Most recent sequence: 2022-11-26, Australia — EPI_ISL_15982517 Countries circulating: Australia (26), Indonesia (15), Germany (5), Singapore (3), Japan (2), UK (2), Austria (1), France (1), Netherlands (1), Number of Sequences: 56 GISAID Query: Spike_K444T,Spike_F486V,Spike_R346T,Spike_S256L,Spike_y144del CovSpectrum Query: s:256l & s:444t & s:486v & s:346t & s:144- Substitutions on top of BQ.1.1 Spike: Y144del, S256L Nucleotides: T21992-,A21993-,T21994-, C22329T

USHER Trees https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33441_d00980.json?c=gt-S_256 image

Evidence I'm proposing these because I notice that in my spike-protein-only BQ.1* sublineage tracking collection, I noticed that it seems S:144- lineages seem to be picking up an additional NTD mutation, and these are appearing towards the top in measured growth advantage.

@alurqu proposed one of these in https://github.com/cov-lineages/pango-designation/issues/1400. I've proposed another one with S:153I in #1402

I believe that these lineages follow the prediction in the paper "Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution" that BQ.1.1 needs to pick up NTD mutations to further evade immunity. S:144- can be clearly measured to provide growth advantage already. I believe that these additional NTD mutations may enhance its immune evasion and provide a further growth advantage to what is already a contender for the most fit spike protein at the moment. Even if these mutations were not previously beneficial, its possible that they will now be advantageous due to removing a proportion of remaining immunity that now may be comparatively larger if S:144- has taken out a substantial amount of non-overlapping antibodies.

S:256L has been sequenced over 1000 times in the last 6 months, notably being a part of CM.9, a BA.2.3.20 sublineage, as well as in XBC.

Genomes: 45 seqs - 1402Genomes.txt

Sinickle commented 1 year ago

S:256L has come up on a few different BQ.1 lineages. Usher is still putting the vast majority with this particular spike profile on the same single branch though.

FedeGueli commented 1 year ago

@Sinickle is not already designated BQ.1.1.31?

Sinickle commented 1 year ago

@FedeGueli you're right!! I think the designation came after I created the issue, but regardless, it's designated so I'll close the issue now.