Hi David,

thank you for your question. Yes, I am aware of Segreto's paper and indeed we have not found evidence for the predicted O-methylation in the furin cleavage site. My take on this is however quite the opposite.

Let me explain;

The main argument I have advanced in the blog post is that when we look at the genome, we can put a certain propability on plausible 'scenarios' how the virus came to be; especially with respect to the question whether the virus was engineered or not. In that regard, not much has changed. Since any engineer could not have had an advanced knowledge of whether the site would be glycosylated or not, it is unlikely they would have chosen to engineer a furin cleavage site like the one we observe.

What has changed however is that indeed, the evidence for an immune-system selected furin cleavage site has decreased; meaning that in theory it is possible for this site to also have evolved in more cell-culture based scenarios. So the lack of predicted (but not observed) O-glycosylation does not change our estimates on 'intentional design', but it cannot be used as an argument against some evolution in cell culture dishes. (It can also not be used for it).

Now we know from other papers [https://zenodo.org/record/5075888#.YSSurN9CSUn] done in the meantime that cell culture of SARS-CoV-2 in Vero-E6 cells (which the WIV and pretty much every coronavirus researcher uses) leads reliably to loss furin cleavage site; so I am still not giving 'cell culture based evolution scenarios' a very high probability.

Another thing that has become more supportive of some of the original arguments put forward in the blog is the totally misplaced 'proline' in the furin cleavage site. (The one I said nobody would ever engineer in). As it turns out, it is exactly this proline that the delta variant has mutated away into an arginine, and low-and-behold, the spike protein suddenly is cleaved much for efficiently in the FCS, which causes the delta variant to be so much more infectious and virulent.

So this strikes first against the idea that: 'The virus was optimized for humans', and second 'the FCS was engineered'; clearly neither of these arguments has turned out true.

So engineering seems really out of the picture at this point.

Another thing I might add; I have had several conversations and discussions with lab leak proponents, including both Yuri and Segreta, and I asked them to walk me through scenarios they believed are possible w.r.t lab leak; in Segreta's case, it was a version of 'RATG13 and SARS-CoV-2 ancestors were both partly engineered and part of GoF research towards creating an attenuated pan-coronavirus vaccine that has gone wrong', which is based on some hileriously cherry-picked snippets of science that do not really go well together. (it's a good twitter thread here: https://twitter.com/PhilippMarkolin/status/1413817168823738379) Either way, let's just say that I have not heard of any lab leak scenario that seems either plausible or has any definitive evidence supporting it even from the most staunch proponents. Now that does not mean lab leak didn't happen, it all about how we inform our baysian estimates in the lack of compelling evidence.

The moment a lab-notebook shows up explaining how SARS-CoV-2 was engineered, or a whisleblower comes forward explaining what experiments were done in the lab, or we find the intermediate animal host, likelyhoods shift dramatically. But after all this time, it seems unlikely either of those things will come forward; so I expect this topic to remain uncertain and unresolved for a long time.

Hope that answers your question?