BA.5.2.1 with S:1020S with growth in Czechia [250 seq of which 100 in CZ 2022-09-05]

[corneliusroemer]

Looking at where S:1020S was occurring I noticed that the share of a lineage was growing rather fast in Czechia over the last few weeks. There are 4 AA mutations on top of BA.5.2.1, 3 of which are in ORF1a/b which is quite a lot.

S:A1020S
ORF1a:L1507F
ORF1a:T3940I
ORF1b:S220N

Share of this lineage as proportion of BA.5.2.1 in Czechia:

Could this be a sequencing artefact? Or a single super spreading event? I'm a bit puzzled by the peaks and troughs in share.

The solution is simple: We never designated a BA.5.2.1 + S:1020S but only certain branches of it. As a result, there are already 2 related lineages with BA.5.2.1 + S:1020S: BF.5 and BF.3.

Now to clean up, we should probably designate this one as close to the polytomy as possible to prevent us from having to designate ever more BA.5.2.1 + S:1020S.

Usher tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6f40_61e4a0.json?branchLabel=back-mutations&c=pango_lineage_usher

[corneliusroemer]

I guess the lineage should start here, or one nucleotide further inwards - as that's where it stops being predominantly South African.

It's ~240 sequences in this part of the Usher tree.

[corneliusroemer]

covSpectrum agrees and since C4784T commonly occurs in BA.5.2.1 without S:1020S - it appears that the occurrence here is homoplasic.

So it's actually good we didn't designate all S:1020S with one lineage.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=4784T&nextcladePangoLineage=BA.5.2.1&

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AA1020S&nucMutations=4784T&nextcladePangoLineage=BA.5.2.1*&

[InfrPopGen]

Thanks for submitting. We've added lineage BF.23 with 136 newly designated sequences, and 34 updated designations from BA.5.2.1. Defining mutation C4784T (ORF1a:L1507F).