> As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers.

Where did you read that? Kinney explicitly asserts the opposite, but I can't figure out what he's referring to. Someone else linked to Figure S9 from their 2017 PLOS Pathogens paper, which indeed seems not to contain the site in the final assembly. I've edited my other comment here to reflect that.

Nope - the restriction sites aren't in the final assembly in that paper. These authors just don't understand the tools remotely well enough to have written their paper. It will never be published.

https://twitter.com/alchemytoday/status/1583361758903013376

Yeah, I think Kinney is wrong here. Someone else found a survey paper noting the theoretical possibility of using BsaI and BsmBI in a way that leaves the sites in the final genome, but I haven't seen anyone who actually did that. So I'm leaning to a false discovery here.

Another good twitter thread on it this morning:

https://twitter.com/acritschristoph/status/15834864034169692...

And Francois Balloux seems to have deleted his twitter account this morning.

As far as I can tell, WIV (and other) researchers have left other restriction sites in final genomes, but not BsaI and BsmBI sites. That makes sense given the typical use of those two enzymes. So I'm inclined to agree there's nothing obviously special about that combination of restriction sites and spacings, which increases my concern that this is just a false discovery.

Jesse Bloom said he'd try reproducing with a wider range of natural viruses and potential synthetic assembly strategies. Unless and until that still gets an interesting p value, I'd agree this is oversold.