A thread on #Omicron sub-lineages BA.1, BA.1.1, BA.2, and BA.3. Here, we go back to original papers and highlight what we currently know about them in the geographic location where Omicron emerged and caused the first large wave of infections in the world.
The BA.1, BA.2, and BA.3 were originally identified in southern Africa - the BA.2 and BA.3 share many not all of the characteristic mutations of BA.1/Omicron and both having many unique mutations of their own nature.com/articles/s4158… 
At present BA.1.1 and BA.2 are growing in prevalence in many places in the world, in South Africa, it seems to be around 25% of the most recent samples (sampled on the week starting at 10 Jan-17 Jan).
In some of the provinces the prevalence of BA.1.1 and BA.2 reach around 40%.
The increase of BA.1.1 & BA.2 is associated with a decrease in infections in SA. I would like to request that when countries present an increase of sub-lineages of #Omicron they present with total infections as this avoid panic and put the pandemic in perspective.
We are currently characterizing the biological characteristics of the sub-lineages BA.1.1 and BA.2. Luckily, we already have solid results on BA.1.1. neutralization as this was the virus outgrown by @sigallab in their recent Nature paper - nature.com/articles/s4158…
There is of course a lot of work needed to better characterize BA.1.1, BA.2, and BA.3. We in South Africa, are alerted but not too concerned given the Omicron wave is decreasing fast here. Of course, we will keep advancing science and communicate as more results emerge.
Original descriptions of the Omicron sub-lineages paper Open access at Nature - nature.com/articles/s4158… - All South Africa data is public at @GISAID - Thanks @houzhou @moir_monika @sigallab @rjlessells for keeping an eye on the sub-lineages of Omicron in SA!
These sub-lineages
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