BA.2 with ORF1b:S959P [50% in India, 3% of global BA.2]

[corneliusroemer]

I think it's worth designating BA.2 with ORF1b:S959P

It doesn't seem to be in a currently designated sublineage of BA.2

It makes up a large fraction of all BA.2 in India, about 3% of all global BA.2

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF1b%3AS959P&pangoLineage=BA.2*

It's also very common in Australia, New Zealand and Japan.

[chrisruis]

Thanks @corneliusroemer I agree this is worth designating. The mutation was a bit jumpy in older UShER trees which is why I haven't added it before. But it now looks much cleaner. So we've added this as BA.2.10 in v1.2.140

[FedeGueli]

Orf1b:S959P is still around in XDV.1 and it is still the one acquired with BA.2.10 here, going to be BJ.1 then , recombining w BA.2.75 to become XBB >> XBB.1.19.1 >> GW.5 and then recombining again with FL.13.4* to become XDE and then recombining with JN.1 to become XDV and then XDV.1 .
We usually thought that Orf1b:S959P could have been deleterious but with such of a story of recombinations being conserved and then successful i doubt it is .
I am not sure but could be the oldest, not belonging to defining BA.2 mutations, to be around?