BA.4.1 lineage with Orf3a:G49V, S:N354D, S:R346T circulating in France (57seqs)

[FedeGueli]

Yesterday i spotted this sublineage of BA.4.1 with a double S (RBD) mutation: S:N354D, S:R346T. It is already quite big and it seems fast growing especially in France.

Defining mutations BA.4.1 + G29179A + Orf3a:G49V + S:N354D + S:346T

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_258c7_3b35d0.json?branchLabel=aa%20mutations&c=pango_lineage&label=nuc%20mutations:G29179A

Interestingly seems that the lineage circulating and growing in France is defined by a further NUC mutation:C21910A (silent: S:S116S) and it has been already exported to Italy, Belgium

A second smaller branch is defined by C29784T and this one too seems circulating through August and a sub-branch of it acquired a mutation of interest S:444R

Gisaid Query :Spike_N354D,SPike_R346T,Spike_V3G, finds 57 sequences:

Expand for EPI_ISLs

**EPI_ISL_13655828** - First sequence ( England) 30/06 EPI_ISL_13881961 EPI_ISL_13956302 EPI_ISL_14173020 EPI_ISL_14173314 EPI_ISL_14196743 EPI_ISL_14389598 EPI_ISL_14448903 EPI_ISL_14450752 EPI_ISL_14495869 EPI_ISL_14527352 EPI_ISL_14544027 EPI_ISL_14562777 EPI_ISL_14563244 EPI_ISL_14568216 EPI_ISL_14572924 EPI_ISL_14602744 EPI_ISL_14647172 EPI_ISL_14648162 EPI_ISL_14707403 EPI_ISL_14707404 EPI_ISL_14771153 EPI_ISL_14791137 EPI_ISL_14792032 EPI_ISL_14792114 EPI_ISL_14792122 EPI_ISL_14792197 EPI_ISL_14798133 EPI_ISL_14812721 EPI_ISL_14816405 EPI_ISL_14816877 EPI_ISL_14817281 EPI_ISL_14817427 EPI_ISL_14818164 EPI_ISL_14818274 EPI_ISL_14819191 EPI_ISL_14829199 EPI_ISL_14838720 EPI_ISL_14838967 EPI_ISL_14860727 EPI_ISL_14860797 EPI_ISL_14919896 **EPI_ISL_14935308** -Last sequence Denmark 06/09 EPI_ISL_14942123 EPI_ISL_14942280 EPI_ISL_14942389 EPI_ISL_14951654 EPI_ISL_14955512 EPI_ISL_14955633 EPI_ISL_14960191 EPI_ISL_14960224 EPI_ISL_14961470 EPI_ISL_14971328 EPI_ISL_14981719 EPI_ISL_14981877 EPI_ISL_14981887 EPI_ISL_14981938

CovSpectrum query : S:354D, S:346T, Orf3a:G49V finds 45 sequences https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A354D%2CS%3A346T%2COrf3a%3AG49V&

A growth advantage comparison with high transmissible BA.5.2 +Orf1b:1050N baseline finds a significant advantage, still too early to think it is reliable.

Carrying a double RBD mutations i will keep this proposed lineage especially monitored cc @corneliusroemer

PS: @AngieHinrichs could you take a look at the tree before G29179A please ? On Usher there is a reversion of both deletions in 69/70 and orf1a but i cant see them on Nextclade , so i suppose they arent real.

[AngieHinrichs]

PS: @AngieHinrichs could you take a look at the tree before G29179A please ? On Usher there is a reversion of both deletions in 69/70 and orf1a but i cant see them on Nextclade , so i suppose they arent real.

Ah, thanks for pointing that out @FedeGueli! Those are false "substitutions" that frequently appear in genome assemblies from pipelines that can't recognize deletions. I need to mask out the BA.4-specific deletions in the BA.4 branch. Those "substitutions" and "reversions" on 686, 694, 21767, and 21770 should disappear within a few days. They are causing a chunk of BA.4.6 to be misplaced elsewhere on that branch, too.

[FedeGueli]

Thx @AngieHinrichs! yeah probably in the upper side of that tree?? i will recheck in some days and publish again once updated. Thank you very much.

[AngieHinrichs]

Yep, the upper side by Nextstrain view, lower side by taxonium view. :)

[corneliusroemer]

Thanks - this one is really interesting. There's even a S:444R with 2 sequences inside 😬

I'll designate, just have to figure out whether it's a child of BA.4.1.9 (suggested by Nextclade but may be wrong).

[FedeGueli]

1 more sequence from Connecticut plus 2 from France