French BA.2.9 sublineage with S:W64R (21752C) with global circulation (~5% in France, 597 seqs)

[FedeGueli]

S:W64R is one of the BA.2 mutations we are seeing popping up in different lineages convergently ,
it was highlighted first by @corneliusroemer last week and today by @RajLABN with a tweet (https://twitter.com/RajlabN/status/1524768961228947456?s=20&t=cgGTMkJ_c9yPlK7-CONs3A)

Here i want to propose one BA.2.9 sublineasge carrying S:W64R

Nr sequences: 533
First sequence: 15/2022
Countries: France 292 seqs, Uk 110 seqs, 72 Denmark 48 Germany , Spain , Israel , Usa , Hong Kong)
EPI_ISLs:
contributors (18).csv

Growth advantage seems solid vs current BA.2 baseline (39%)

Cov-spectrum overview

Usher tree for this branch is clear:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_32212_d83eb0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C241T,T670G,C2790T,C3037T,G4184A,C4321T,C9344T,A9424G,C9534T,C9866T,C10029T,C10198T,G10447A,C10449A,C12880T,C14408T,C15714T,C17410T,A18163G,C19955T,A20055G,C21618T,T22200G,G22578A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,C22792T,G22813T,T22882G,G22992A,C22995A,A23013C,A23040G,A23055G,A23063T,T23075C,A23403G,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C25624T,C26060T,C26270T,C26577G,G26709A,C26858T,A27259C,G27382C,A27383T,T27384C,C27807T,A28271T,C28311T,G28881A,G28882A,G28883C,A29510C

[corneliusroemer]

Globally, two nuc mutations are responsible for S:W64R: 21752C and 21752A, in this case it's C.

Pretty clear from the timeline that this lineage seems to have started off in France:

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF3a%3AH78Y&nucMutations=21752C&pangoLineage=BA.2*&

[FedeGueli]

Thx @corneliusroemer i dint know that! thank you very much

[InfrPopGen]

Thanks for submitting. We've added lineage BA.2.9.3 with 609 newly designated sequences, and 124 updated designations from BA.2.9. Defining mutation(s) T21752C (S:W64R).