Mary Wilson
Well-known member
Aug 8, 2022
Proposal for a sublineage of BA.2.10
Earliest sequence: 2022-07-02
Countries detected: India (9 seq, all from West Bengal)
Mutations in addition to BA.2.10:
S:V83A, H146Q, Q183E, V213E, G339H, R346T, L368I, V445P, G446S, V483A, F490V, G798D, S1003I
ORF1a:K47R
ORF1b:G662S
MD3Y
ORF7a:I110T
N:T282I
nuc:C15738T, T15939C, T17859C, G28079T
S:V445P is a 2-nucleotide mutation (GTT -> CCT).
S:G798D is shared with BA.2.10.1, but Usher places this on a branch of BA.2.10 with C15738T. I think the order may actually be ambiguous, but the fact that the BA.2.10+C15738T sequences are mostly from India makes me think that Usher has probably got it right.
This lineage has so far only been detected in the state of West Bengal, India, but I think it deserves a proposal based on its exceptional total of 13 spike mutations, including 7 in the RBD. 346, 445, 446 and 490 are significant escape locations in the Bloom lab calculator, in particular knocking out a large fraction of the antibodies elicited by pre-Omicron virus that still neutralise BA.2. Somewhat surprisingly, S:Q493R is not reverted!
Also note that this is yet another highly divergent BA.2 with ORF1b:G662S, after BA.2.75 and the BA.2.10 sublineage in #898 (see the discussion in that issue).
https://github.com/cov-lineages/pango-designation/issues/915
Proposal for a sublineage of BA.2.10
Earliest sequence: 2022-07-02
Countries detected: India (9 seq, all from West Bengal)
Mutations in addition to BA.2.10:
S:V83A, H146Q, Q183E, V213E, G339H, R346T, L368I, V445P, G446S, V483A, F490V, G798D, S1003I
ORF1a:K47R
ORF1b:G662S
MD3Y
ORF7a:I110T
N:T282I
nuc:C15738T, T15939C, T17859C, G28079T
S:V445P is a 2-nucleotide mutation (GTT -> CCT).
S:G798D is shared with BA.2.10.1, but Usher places this on a branch of BA.2.10 with C15738T. I think the order may actually be ambiguous, but the fact that the BA.2.10+C15738T sequences are mostly from India makes me think that Usher has probably got it right.
This lineage has so far only been detected in the state of West Bengal, India, but I think it deserves a proposal based on its exceptional total of 13 spike mutations, including 7 in the RBD. 346, 445, 446 and 490 are significant escape locations in the Bloom lab calculator, in particular knocking out a large fraction of the antibodies elicited by pre-Omicron virus that still neutralise BA.2. Somewhat surprisingly, S:Q493R is not reverted!
Also note that this is yet another highly divergent BA.2 with ORF1b:G662S, after BA.2.75 and the BA.2.10 sublineage in #898 (see the discussion in that issue).
https://github.com/cov-lineages/pango-designation/issues/915