French BA.2.9 with S:346T [170 seq, 2% in France]

[corneliusroemer]

I noticed that S:346T was growing within BA.2, particularly in France and India. There are too few sequences from India to propose a lineage, but the French cluster is very clear and localized to Auvergne-Rhone-Alpes and Bourgogne, two neighbouring regions.

The French one is a sublineage of BA.2.9 with S:346T (and ORF7a:5F). We know S:346 from BA.1.1, where it was mutated to K.

This is where it's shown up

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3db34_eb0a30.json?c=pango_lineage_usher&label=nuc%20mutations:C25624T

France/ARA-HCL022076848701/2022|EPI_ISL_12628555|2022-05-01

[FedeGueli]

227 as today. 4% of french sequences in the last two weeks
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=S%3A346T%2COrf3a%3A78Y%2Corf7a%3A5F&

[InfrPopGen]

Thanks for submitting. We've added lineage BA.2.9.4 with 230 newly designated sequences, and 34 updated designations from BA.2.9. Defining mutation(s) C27406T (ORF7a:L5F), G22599C (S:R346T).

[FedeGueli]

There is a small cluster of this sublineage with S:K444R circulating recently (august/22) in Switzerland 5 seqs.
I'll keep that monitored.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_a168_44f9e0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C4320T

[FedeGueli]

Sequences should be 7 now.
NS3_H78Y, Spike_R346T,Spike_K444R query.