BA.5.6 with S:R346T and S:H146Y circulating in England (27 Sequences)

[olias120676]

The undesignated BA.5.6 with S:R346T hasn't shown much growth. However a branch with S:H146Y has 27 sequences all in England, first of which appeared on August 26th, suggesting fairly rapid growth

GISAID query: Spike_H146Y, nsp1_S34T, Spike_R346T
Cov-Spectrum query: S:H146Y, ORF1a:S34T, S:R346T (link)

USHER tree:
https://nextstrain.org/fetch/raw.githubusercontent.com/olias120676/jsons/main/2022092601.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:T365A,C21998T,G29254T

Defining mutations on top of BA.5.6:
S:R346T
S:H146Y
ORF1a:S34T (nsp1_S34T)
T365A
T15537C

List of IDs:
EPI_ISL_14858770
EPI_ISL_14858787
EPI_ISL_14919393
EPI_ISL_14995186
EPI_ISL_15021129
EPI_ISL_15020809

[FedeGueli]

Welcome back Dave. i have added this one to collection # 26 on covspectrum to see how it goes and def it goes very well, still quite far behind BQ.1 but the fastest of the unproposed lineages tracked there:https://cov-spectrum.org/collections/26

[corneliusroemer]

Looks like the parent without 146Y was more common in Romania - while the child is growing in England.

I'd probably designate the parent too - as S:346T is known to confer a significant growth advantage and we may regret not designating it.

[Lukas67]

We found our first sequence of BA.5.6 with S:R346T with Nanopore WGS and submitted to GISAID.

EPI_ISL_15137796

[corneliusroemer]

All the English ones are from one lab so could well be clustered.

Still only 66 BA.5.6 with S:346T and this will likely be outrun by the various novel variants so not of big priority in my view.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A346T&nextcladePangoLineage=BA.5.6*&

[FedeGueli]

30 seqs as today

[corneliusroemer]

An interesting other tiny lineage with S:445A popped up in the outer one. I'd now designate the outer one with S:346T.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_12753_99a5d0.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G22599C

[FedeGueli]

Now this grew to 47 with Spike_H146Y, nsp1_S34T, Spike_R346T , i think it is worth designating it @InfrPopGen

[corneliusroemer]

I would designate the outer one with 346T still, not the inner one (yet)

[InfrPopGen]

Thanks for submitting. We've added lineage BA.5.6.3 with 11 newly designated sequences, and 0 updated designations. Defining mutation G22599C (S:R346T) (following G18984T (ORF1b:M1839I)). This is the parent of the lineage proposed here. Designation of the child lineage may follow, possibly after it has grown a little more.