I've said there was no evidence of recent recombination in SARS-CoV-2. That turns out to not be quite right, though it doesn't affect the receptor binding domain. Rather, the S1/S2 cleavage site of SARS-CoV-2 may have been acquired from an HKU9-like virus in the last few decades.https://twitter.com/arambaut/status/1268695688151523329 …
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Yea I fully agree with Andrew’s analysis. But RaTG13 still has the ancestral sequence from the end of RBD to S1/S2 (and also ancestral S2). So it should still have the ancestral cleavage site. Suggests to me the furin site acquisition is after the SARS2/RaTG13 lineages split.
Ah, sorry - the furin site acquisition is still unknown. While RmYN02 has an insertion at the S1/S2 boundary, it isn't actually a polybasic site - it just shows that bat viruses 'mess around' with this part of the protein. Bill's post show how these sites can be gained in bats.
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Yep agreed. Also btw it’s making me crazy that people are saying RmYN02 has a polybasic cleavage site! Spike evolution is impressively modular, something we are thinking a lot about now.
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Another thing, RmYN02 has a strange cleavage site. I would love to know where it came from but the origin of the "new" region of its spike very clearly hasn't been sampled. It's out of nowhere (from our perspective). The S1/S2 boundary is in the recombinant region.
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