Putative host origins of RNA insertions in SARS-CoV-2 genomes

Hey Tom - great analysis, as always! As for the insertion in Omicron, I think we have to be careful what we can and cannot conclude. A lot of people take this as meaning that Omicron has an “insertion of human origin”, which I don’t think we can conclude with any sort of confidence (although I think it’s a very plausible hypothesis).

What I think we can reasonably conclude is that the insertion is more likely to be host-derived than SARS-CoV-2 derived. However, given how short the stretch of homology is, what that host is exactly is unknowable IMO. Could certainly be human, but could also be a range of other things - including virus, bacteria, mammalian, etc.

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