New BA.5.2.1 sublineage with S:346S circulating in USA (121 Seqs)

[FedeGueli]

Thx to @shay671 and @c19850727 who first spotted a " creepy sequence" (=with heavily mutated spike) in this tree i identified a new growing sublineage of the high transmissible BA.5.2.1 branch characterized by S:346S mutation.

It is defined by the following mutations:
Orf1a:K2589R
then G26196A
then Orf1b:K1957R
then S:346S+24079C

Tree is already showing quite interesting diversity suggesting a more sustained circulation than what could be seen by number of sequences (62)
Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_208e_1d1ea0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:A8031G

CovSpectrum finds just 40 sequences in just 3 countries but this sublineage is mainly from US:
contributors (6).csv

Covspectrum overview
https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?variantQuery=NextcladePangoLineage%3ABA.5.2.1*+%26+Orf1a%3AK2589R+%26+G26196A+%26+Orf1b%3AK1957R+%26+S%3A346S+%26+24079C&aaMutations1=S%3A346S&nucMutations1=28330G&

Relative Growth advantage vs BA.5.2.1 baseline in Usa in the last two months from sequences ratio between the two:

Link to Growth Advantage tool:
https://cov-spectrum.org/explore/United%20States/AllSamples/Past2M/variants?variantQuery=NextcladePangoLineage%3ABA.5.2.1*+&variantQuery1=NextcladePangoLineage%3ABA.5.2.1*+%26+Orf1a%3AK2589R+%26+G26196A+%26+Orf1b%3AK1957R+%26+S%3A346S+%26+24079C&analysisMode=CompareToBaseline&

cc @corneliusroemer in #865

[FedeGueli]

69 seqs as today

[FedeGueli]

114 Sequences as today and keeping its growth advantage vs BA.5 baseline

@corneliusroemer @chrisruis @InfrPopGen maybe this has to be monitored closely.
(See NY State in the comparison tool:
https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?variantQuery=NextCladePangoLineage%3ABA.5*&aaMutations1=Orf1a%3AK2589R%2Corf1b%3AK1957R%2CS%3A346S&nucMutations1=G26196A%2C24079C&analysisMode=CompareToBaseline&)

also vs BA.5.2*
https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?variantQuery=NextCladePangoLineage%3ABA.5.2*&aaMutations1=Orf1a%3AK2589R%2Corf1b%3AK1957R%2CS%3A346S&nucMutations1=G26196A%2C24079C&analysisMode=CompareToBaseline&

[FedeGueli]

121 sequences displayed on Usher as today:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f4c3_ed7ca0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A8031G

It is still mainly a New York (state) sublineage even if i would not define simply a cluster: there are already 6 main branches representing together 75% of samples of this sublineage:

[corneliusroemer]

This deserves designation now - it has tripled in numbers in 2 weeks and growth advantage over BA.5.2.1 is stably positive.