Thread by @LongDesertTrain

Quick BA.3.2 update. Another BA.3.2.2 (S:K356T+S:A575S branch) from South Africa via pneumonia surveillance.

This means that 40% of SARS-CoV-2 sequences from SA collected since April 1 (2/5) and 50% collected after May 1 (1/2) are BA.3.2. Its foothold seems strong there. 1/3

https://twitter.com/LongDesertTrain/status/1899647059872850369

2 interesting aspects of the new BA.3.2:
1. ORF1b:R1315C (NSP13_R392C)—This mut is in all Omicron *except* BA.3. So this may well be adaptive.

2. S:Q183H—First known antigenic spike mut seen in BA.3.2, not a major one, but one we've seen before—eg, LB.1/JN.1.9.2.1 2/3

I think the unusually long branches in the BA.3.2 tree indicate 2 things:
1. Slow growth globally—fast growth results in many identical sequences, if surveillance is sufficient

2. Undersampling—BA.3.2 most common in poorer world regions with little sequencing of late. 3/3

One quick addendum: I forgot to add that this sequence was from the North West province of South Africa, the 4th one it's been detected in.

And 5 more SA sequences (all pneumonia surveillance) were just uploaded, one another BA.3.2.2, also from North West, May 26 collection.

Since March 1, we have no sequences from the 5 provinces where BA.3.2 has not yet been detected (Northern Cape, Eastern Cape, Free State, Limpopo, Mpumalanga), so it may be established throughout the country.

Zero seqs from surrounding countries. South Africa is our sentinel.