BA.5 + C1627T sublineage (On usher identified as BA.5.2 No28330G) sublineage with orf1a:R207C, orf1a:Q3922R, E:S50G and S:262S (175seqs, 5% prevalence in Philippines , spread to 6 continents NA/SA)

[FedeGueli]

S:A262S is a mutation that seems to be growing in the last weeks, here i want to propose a sublineage of BA.5 in the branch with C1627T that leads to BA.5.2* pre A28330G.

Defining mutations:
C1627T + Orf1a:R207C+ Orf1a:Q3922R+ G29422T + E:S50G + S:A262S

As can be seen by this usher tree (big blue point are from Eswatini) all this tree is disseminated with sequences coming from Eswatini suggesting that this entire branch could have evolved in South Africa or Eswatini

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c532_51aee0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:G22346T

First sequence: Eswatini/ILRI_M03297/2022|EPI_ISL_13149302|2022-05-03
102 Sequences on CovSpectrum:
contributors.csv
(120 already on Usher plus 2 from Denmark and 3 from 3 different american states uploaded today to Gisaid,
while yesterday was one from Austria,one from Singapore, and two from California)
Last sequence: hCoV-19/Denmark/DCGC-561360/2022 | EPI_ISL_14393203

18 Countries:

Interestingly it seems to have a significant prevalence in Philippines around 4-5% in the past two months:

And this seems reasonable after looking at its growth advantage in Philippines vs BA.5 baseline

At global level its early apparent advantage is still there also vs dominant BA.5.2 lineage:
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?variantQuery=NextCladePangoLineage%3ABA.5.2*&variantQuery1=NextcladePangolineage%3ABA.5+%26+C1627T+%26+orf1a%3AR207C%26orf1a%3AQ3922R%26G29422T%26E%3AS50G+%26S%3A262S&analysisMode=CompareToBaseline&

Covspectrum query : https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=+C1627T+%26+orf1a%3AR207C%26orf1a%3AQ3922R+%26+E%3AS50G+%26+ORF3a%3A197V&variantQuery1=NextCladePangoLineage%3ABA.5.2*&

(Edited)

Gisaid Query: NSP2_R27C,NSP7_Q63R,Spike_A262S

[FedeGueli]

Using Gisaid query NSP2_R27C, E_S50G ,Spike_A262S i found 129 viruses but interestingly 14 of them are from last week indicating a good growth rate for this lineage

[FedeGueli]

@corneliusroemer @chrisruis @InfrPopGen @thomaspeacock i count 13seqs on Gisaid with collection day after 1st of August and from 5 countries: Usa(4seqs 2states), denmark (4seqs, 3 regions) , Australia (2seqs,2regions),
Israel,Uk and Austria (1 seqs).
56 seqs out of 129 has been collected after 16th of July.
Said that
I propose a fast designation of this lineage due a likely high prevalence in Philippines and rapid spread from there.

[FedeGueli]

5 more uploads: 2 Usa (2 different states), 1 Denmark, 1 Canada, 1 Czechia

[FedeGueli]

On Usher are displayed 160 seqs of this sublineage:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22a1f_bb6810.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C884T

[FedeGueli]

Big upload yesterday from Eswatini, mainly may sequences, confirms early circulation of this sublineage there and big upload also from Philippines , mainly july samoples. plus sequences from Us and Uk.

@InfrPopGen @corneliusroemer @chrisruis i think this deserves a designation.

[FedeGueli]

175 seqs as today on Usher but yesterday there was a big upload from Eswatini (Sequences from May) and Philippines (sequences mainly from July) plus some Uk and Us samples

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28cfe_df3010.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C884T

[InfrPopGen]

Thanks for submitting. We've added lineage BA.5.10 with 47 newly designated sequences, and 3 updated designations from BA.5. Defining mutation G22346T (S:A262S).

[FedeGueli]

Thx a lot @InfrPopGen

[FedeGueli]

@InfrPopGen very timely designation there was an upload today of new 15 sequences sampled in South Korea and Japan related to travel to Philippines.