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BA.2 sub-lineage with S:I1221T dominant in Hong Kong #430

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bitbyte2015 opened this issue Feb 8, 2022 · 4 comments
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BA.2 sub-lineage with S:I1221T dominant in Hong Kong #430

bitbyte2015 opened this issue Feb 8, 2022 · 4 comments
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BA.2.2

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@bitbyte2015
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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)

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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
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FedeGueli commented Mar 6, 2022 •
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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
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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):
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https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-430.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:T25224C

@FedeGueli
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Thank you @AngieHinrichs .

@chrisruis @bitbyte2015 could you close this one?

@chrisruis
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Thanks All

@chrisruis chrisruis added this to the BA.2.2 milestone Mar 7, 2022
@aviczhl2 aviczhl2 mentioned this issue Jul 18, 2023
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@AngieHinrichs @bitbyte2015 @chrisruis @FedeGueli