BM.4.1.1 with S:444T (15 seqs, Australia, Austria, US as of 2022-10-10)

[corneliusroemer]

Came across a BA.2.75 that had S:346T, S:486S and S:444T which looks like a combination that could be quite fit.

GISAID query: Spike_R346T, Spike_F486S,Spike_K444T

Found 3 sequences that cluster together on 3 continents - so worth monitoring:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38bf3_f4f710.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A22893C

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A346T%2CS%3A444T%2CS%3A486S&nextcladePangoLineage=BA.2.75*&

Australia/NSW-ICPMR-32565/2022|EPI_ISL_14789037|2022-08-17
Austria/LB-R00097-S304/2022|EPI_ISL_14841062|2022-08-30
hCoV-19/USA/CA-CDC-LC0881994/2022|EPI_ISL_15103933|2022-09-10

[ryhisner]

I'e been surprised K444T hasn't been found much in BA.2.75. There were a couple sequences earlier with R346T and K444T (and I think one other additional RBD mutation I can't remember), but it never went anywhere. Maybe this one will catch fire.

[corneliusroemer]

A fourth one has been uploaded:

hCoV-19/USA/IL-CDC-LC0881226/2022 | EPI_ISL_15102898

They all share: ORF1b:Q2425R in addition to S:444T.

[FedeGueli]

8 sequences of this one as today

[corneliusroemer]

And apparently and extra S:452R has appeared in this as well?

So the other one looks quite designatable already (already 15 sequences)

These are the two with S:L452R as well:

hCoV-19/South_Korea/KDCA129119/2022|EPI_ISL_15281174|2022-09-16 hCoV-19/Austria/LB-R00104-S295/2022|EPI_ISL_15259739|2022-09-26

Spike_R346T, Spike_F486S,Spike_K444T,Spike_L452R

[corneliusroemer]

@ryhisner the reason could be that BA.2.75 already has S:446S - making S:444 less beneficial in addition

[Sinickle]

13 sequences on CH.1.1.

With 7 convergent RBD mutations, it won't be surprising if this is one of the fastest growing variants.

[FedeGueli]

for CH.1.1 NSP16_Q28R,Spike_K444T,Spike_L452R should work well.

3 out 4 sequences sampled in South Korea with travel history come from Thailand so likely it emerged there.

[xiaoxi-wu-tfs]

May I ask how does the CH.1* pango-lineages got named and how did you decide the initials? Thanks!

[FedeGueli]

May I ask how does the CH.1* pango-lineages got named and how did you decide the initials? Thanks!

Initials are progressive so.it was the first avaible at the time of designation. The exact moment of designation is once a commit was created for it and you can find in the comments above. In this case was a double designation : CH.1 with S:K444T and its sublineage CH.1.1 with S:L452R