BA.2.75.4 (S:L452R) Sublineage with S:K444T, S:D574V, & ORF1a:K4014R (168 seq, Jan 22)

[ryhisner]

Description
Sub-lineage of: BA.2.75.4
Earliest sequence: 2022-9-6, Singapore (Traveler from India)— EPI_ISL_14917768
Most recent sequence: 2022-11-3, England — EPI_ISL_15758527, EPI_ISL_15758586
Countries circulating:
Number of Sequences: 20
GISAID Query: Spike_K444T, Spike_D574V, Spike_L452R, NSP8_K72R
CovSpectrum Query: Nextcladepangolineage:BA.2.75.4* & S:K444T & S:D574V
Substitutions on top of BA.2:75.4
Spike: K444T, D574V
ORF1a: K4014R
Nucleotide: G8602A, A22893C, A12306G, A23283T, A26612T

USHER Tree
Note that though there are only 18 sequences on this tree (after subtracting duplicates), this is because Usher, rather comically, places two sequences from this lineage on the BA.2.76 tree.
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BA.2.75.4%20(L452R)%20%2B%20K444T%20%2B%20D574V%20%2B%20ORF1aK4014R%20-%20subtreeAuspice1_genome_6549_42b950.json

Evidence
This clearly originated in India, but only slowly spread internationally. It seemed to appear in Australia (perhaps in travelers), then disappear for a month, only to return in the last couple weeks. The third and fourth sequences from England were uploaded yesterday, but nothing so far from continental Europe. One week ago the first two sequences from the USA were uploaded from Virginia.

The spike profile is certainly interesting, but it may be held back by the lack of any mutation at S:R346, S:348, and S:K356. R346T/S/I in particular has seemed to be a very easy mutation to pick up for most lineages, so it wouldn’t be surprising to see one of those appear in this lineage eventually, assuming it isn’t driven to extinction before that can happen.

Genomes

Genomes

EPI_ISL_14917768, EPI_ISL_15357083, EPI_ISL_15357195, EPI_ISL_15357479, EPI_ISL_15358813, EPI_ISL_15363268, EPI_ISL_15469952, EPI_ISL_15474716, EPI_ISL_15573126, EPI_ISL_15580487, EPI_ISL_15609536, EPI_ISL_15617479, EPI_ISL_15654506, EPI_ISL_15705620, EPI_ISL_15705952, EPI_ISL_15731803, EPI_ISL_15732455, EPI_ISL_15732513, EPI_ISL_15758527, EPI_ISL_15758586

[ryhisner]

This seemed to vanish for a while but has recently reappeared, and after 12 sequences were uploaded over the past two days (mostly South Korea but one each from Belgium and Japan), it now stands at 56 sequences.

[ryhisner]

Still a lot of this one in South Korea, and strangely, 12 sequences from North Carolina, USA, were uploaded last week.

[ryhisner]

15 sequences from South Korea uploaded three days ago (Thursday, Jan 19) and one uploaded today from Hawaii, USA. Total now 168 sequences.

[InfrPopGen]

Thanks for submitting. We've added lineage BR.5 with 59 newly designated sequences, and 0 updated. Defining mutations A12306G (ORF1a:K4014R), A23283T (S:D574V), A26612T (following A22893C (S:K444T)).