BA.2 sub-lineage with S:I1221T dominant in Hong Kong

[bitbyte2015]

A significant portion of sequences from the BA.2 branch beginning with ORF1a:T1543I have an additional mutation S:I1221T. It is the second largest branch of BA.2 with a spike amino acid substitution after S:G798D (#428)

Of the 103 sequences available, 10 have N:A55S and 5 have S:I210T. 68 sequences are from Hong Kong. What sets this one apart from #428 is that it makes up 60/76 of Hong Kong BA.2 collected after January 20 and 60/105 overall. It is difficult to ascertain the advantage of acquiring this mutation in the TM domain but this lineage appears to be responsible for a significant portion of Hong Kong's new cases which are surging.

[FedeGueli]

I checked yesterday it is 85% of BA.2 sequences in HK. Given the hard epi situation there, maybe a designation could help tracking it outside Hong Kong.
@chrisruis @corneliusroemer

[AngieHinrichs]

I believe @chrisruis has designated this as BA.2.2 but starting with Orf1ab:T4087I. At that node it becomes almost 100% Hong Kong with a few samples in England; at the S:I1221T node it's still mostly U.K. with a smattering of other countries including Hong Kong. Here is a view from the UCSC/UShER tree, colored by country, hovering the mouse over Hong Kong to show where the Hong Kong samples are (larger circles):

https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-430.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:T25224C

[FedeGueli]

Thank you @AngieHinrichs .

@chrisruis @bitbyte2015 could you close this one?

[chrisruis]

Thanks All