Hong Kong: Omicron BA.2 with S:I1221T mutation at 100% of recent sequences *6 UPDATES*

BA.2, BA.2.2, Coronavirus, Deaths, Elderly, Genome, Hong Kong, Hospitalization, Infection, Omicron, Revaccination, Transmission, UK, Vaccine Breakthrough, Vaccine Waning

A catchup post looking at the BA.2 variant with mutation S:I1221T. The combination is found in  most of the recent BA.2 sequences from Hong Kong, so the mutation may be significant.

This mutational combination seems to have first been mentioned by Raj Rajnarayana on Twitter on the 4th March 2022, although it was originally reported to Github by @bitbyte2015 weeks earlier.



Cov-Spectrum.org shows the I1221T Spike mutation in 100% of Hong Kong BA.2 sequences.


The majority of BA.2 & S:I1221T sequences are from Hong Kong, with the UK making up the second largest proportion. Other countries have just a handful of examples so far. 


BA.2 with I1221T currently has a relative growth advantage of about 35%:

Age demographics show that it seems to concentrated in the elderly



Tom Peacock isn’t convinced that it is responsible for the unusual infection situation in Hong Kong though


There are some more technical details on Github:

“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.”


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

UPDATE 1 – 5th March 2022 – Hong Kong Covid-19 statistics

We have machine translated the Hong Kong government’s Covid-19 stats for 5th March and added them below.

5th_wave_statistics – ENGLISH


Detail from that report – click to expand:



Hong Kong deaths statistics dated 4th March 2022. As with many other countries across the globe, the pandemic is once again hitting the elderly very hard.


UPDATE 2 – 5th March 2022 – Local situation report

From a local situation report for Hong Kong dated 5th March 2022. The case fatality rate for unvaccinated over-80s is nearly 9%, a figure reminiscent of the CFR rates for the original outbreak in Wuhan. This is certainly not a “mild” variant for the elderly.




UPDATE 3 – 5th March 2022 – population size & vaccination status

The population of Hong Kong is around 7,600,000, with 13,508,738 vaccine doses administered.

UPDATE 4 – 5th March 2022 – the case fatality rate seems out of sync with other countries in the region

The case fatality rate in Hong Kong seems completely out of sync with others countries in the region that are also seeing large Covid waves. Click to expand.

UPDATE 5 – 7th March 2022 – “outbreak has torn through hundreds of nursing homes”

Hong Kong reported 25,150 new coronavirus infections and 280 deaths on Monday (Mar 7), as authorities struggle to contain a worsening COVID-19 outbreak that has torn through hundreds of nursing homes and hit many of the city’s unvaccinated elderly.

More in the Channel News Asia report

UPDATE 6 – 9th March 2022 – Hong Kong BA.2 variant with S:I1221T designated BA.2.2


Hong Kong: Omicron BA.2 with S:I1221T mutation designated BA.2.2


We’ll update this post again when we have more news. 

Whilst you’re waiting, please feel free to watch this entirely unconnected video about Ukraine and redistribute it:



Video download link


** This post was originally published on March 5, 2022 **