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The latest example of a potential new variant evolving in a long-term chronic infection has been detected by the diligent work of those collecting and sequencing samples in South Africa.

As Ryan H describes on this thread, it is descended from the BA.3 lineage, which last in circulation about 3 years ago. So presumably it has been evolving in a chronic case since then, and recently managed to transmit to other people. The latest sample is from a different province and with one added Spike mutation (K356T).

https://threadreaderapp.com/thread/1899647059872850369.html
#COVID19 #BA_3
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Thread by @LongDesertTrain on Thread Reader App

@LongDesertTrain: Do you remember BA.3—the weakling cousin of BA.1 & BA.2 that seemed to take the worst from each & had weaker ACE2 binding than even the ancestral Wuhan Virus? After 3 years, BA.3 is back....…
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#COVID19 #ba_3
Mike Honey
Here’s the frequency of the BA.3 samples in the context of all the recent samples from South Africa. Optimistically, we can hope that it has already gone extinct, as there have been >35 samples collected since it was last detected.

In the context of global sampling, there are still thousands of samples reported each week, so it seems unlikely to be spreading widely, yet.
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Mike Honey
Meanwhile, the wastewater surveillance from NICD in South Africa showed a wild, wild spike in recent months – on the scale of the original Omicron wave (just prior to the start of their data).

Hopefully that is just a coincidence, but it is quite puzzling what might’ve driven that.
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Mike Honey
Here’s the general variant picture for South Africa. LP.8.1.* rose to dominance in recent months, perhaps in sync with that wastewater spike. But LP.8.1.* hasn’t caused large waves elsewhere.
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Mike Honey
Here’s the lifecycle of BA.3.*, from it’s emergence in Nov 2022 to it’s apparent extinction around 6 months later (from my “Archive” dataviz). It only ever briefly reached 2% frequency in South Africa and then Poland, and was insignificant elsewhere.
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Mike Honey
If this new BA.3 saltation is successful, it would quite likely be another “reset” of the immunity landscape (like BA.2.86/JN.1), with most people suddenly being susceptible. With the current healthcare settings, this would likely drive another big wave.

It would be an incredible piece of luck for SARS-CoV-2. But with billions of infections leading to millions of chronic infections in every year since 2022, we are giving the virus endless “free spins”.
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