BQ.1.1.38 sublineage with S:A348S - 41 sequences South Africa, Denmark, Nyc - as 24-02-23

[FedeGueli]

BQ.1.1.38, (spotted by @ryhisner very early months ago) is accordingly to Collection24 ( the covspectrum collection of all the designated lineages) the fastest among the BQ* descendants along with the italian BQ.1.1.37 ( the one defined by ins:S:247SAE S:248D )

https://cov-spectrum.org/collections/24

BQ.1.1.38 is mainly split in two : the uppper part of the tree defined by a branch with S:A701V is internationally spread while the bottom part of the tree is largely made by samples from south africa from mutliple branches showing high diversity pointing at some sort of sustained circulation there:

While weighing BQ.1.1.38 we should be aware that the "international branch with S:A701V is much slower than the rest of the lineage, suggesting maybe a founder effect for its wider spread in other countries

https://cov-spectrum.org/explore/World/AllSamples/from=2022-12-15&to=2023-02-04/variants?aaMutations=S%3AA701V&nextcladePangoLineage=BQ.1.1.38*&nextcladePangoLineage1=BQ.1.1.38*&analysisMode=CompareToBaseline&

So i noticed immediately the branch defined by S:A348S and digging into it i spotted that its sublineages acquired more Spike mutations as S:T470I (1seq) or S:S494P (4 seqs)

Defining mutations : BQ.1.1.38 > C421T > S:A348S (G22604T)

Usher Tree:

Gisaid query: Spike_A348S,Spike_N856S,N_E136D

Sequences : 14 EPI_ISL_16376011-16376013, EPI_ISL_16376016, EPI_ISL_16578154, EPI_ISL_16580278, EPI_ISL_16649783, EPI_ISL_16713768, EPI_ISL_16749592, EPI_ISL_16750770, EPI_ISL_16750826, EPI_ISL_16750870, EPI_ISL_16750897, EPI_ISL_16823490,

Countries: Even if it is just 14 sequences it has been already exported to Denmark and NYC

[corneliusroemer]

Yep, also noticed this due to high predicted "combined fitness" of ACE2 binding and immune escape per Bloom lab calculator as implemented in Nextclade.

Thanks for looking at the Usher tree, looks pretty clean so should enable us to go and designate a few lineages. We're getting very few sequences from Africa recently so it makes sense to designate there even with only relatively few sequences, so far.

[FedeGueli]

Thx @corneliusroemer

[FedeGueli]

@corneliusroemer it jumped to 23 with just South African sequences .

[FedeGueli]

26 sequences as today.

prevalence of this lineage could be very roughly estimated in 4% in the most recent samples. SA is experiencing a rise in positivity rate and cases maybe it should be good designate this one to easily disentangle which are the drivers of the possible surge (very likely XBB.1.5 that went from 10% to 40% very rapidly)

[FedeGueli]

26 sequences. it is clearly losing the game versus XBB.1.5 in SAF. Interestingly these two last sequences both have S:N440R.

[FedeGueli]

41 sequences . Its prevalence in February hanging around 1%, likely it cannot compete with XBB.1.5 but clearly fast enough to keep circulating there.

@corneliusroemer

[FedeGueli]

it seems dead or better saying killed by XBB.1.5. @corneliusroemer dunno if it makes sense to designate it. (i suggest to close this)

[FedeGueli]

@corneliusroemer designated it: EW.3 https://github.com/cov-lineages/pango-designation/commit/911be6085b5055e1d11a4968a2b6f74a09072c00