Slack / Private Message Drop — page 1054

Good idea but I probablt need to response to the what were the steps question . Here is a draft: Dear Nick, Cogent perhaps, but as I told the Intercept my initial impression and that of others about the FCS was wrong. All of the emails regarding the teleconference show the establishment of the hypotheses we later outlined in the Proximal Origins paper and then the assessment of these based on the available evidence. Opinions simply shifted as the result of analysis and the examination of new data. All of our conclusions were written in our published and peer-reviewed papers (i.e., in Nature Medicine and then updated in Cell late last year). Would you be willing to discuss the steps that took you from one conclusion to the other? Steps as follows: 1. Shortly after the teleconference we learned about the pangolin coronavirus that has a highly similar receptor binding domain- RBD. This meant that the RBD was natural. If this feature was natural then very likely that the whole virus was natural including the FCS. 2. We examined and reexamined all the hypotheses/data including the FCS - it was clear that that site was undergoing a lot of variation within the coronavirus family. 3. The insertion that generated the FCS is out-of-frame -nobody in a lab would do that. It's a minimal FCS. A researcher would insert PRAR not PRRA. 4. The proline in front of the FCS is not optimal- that's why the variants like Omicron have P681 changed to either H or R. 5. The FCS has O-linked glycans, like FCS in other coronaviruses. These are real and appear to regulate cleavage. Bottom line is no one engineered the FCS into a SARS-CoV2 progenitor. Since then more data has been published that further supports our conclusions from that initial review. For example, Since we wrote Proximal Origins we've seen betacoronaviruses that have similar sequences (almost but not quite a FCS) in that region, like RmYN02. More recent evidence - we now know the SARS-CoV-2 progenitor or at least a very close relative - it's the BANAL-20-52 bat coronavirus from Laos. This virus is extremely close to SARS-CoV-2 in all of the structural proteins. However, it carries about a 1000 synonymous mutations [mutations that affect the nucleotide sequence but not the amino acid sequence], which is strong evidence that it circulated in an animal that was not a bat before jumping to humans. Bob G. [2022-01-13 09:13:08] [Kristian Andersen] I strongly suggest _not_ giving him any details - just email him a version of Andrew's email from yesterday. He's going to twist your words and then use them later to yet again get back at you. [2022-01-13 09:14:24] [Robert Garry] Dear Nick, Cogent perhaps, but as I told the Intercept my initial impression and that of others about the FCS was wrong. All of the emails regarding the teleconference show the establishment of the hypotheses we later outlined in the Proximal Origins paper and then the assessment of these based on the available evidence. Opinions simply shifted as the result of analysis and the examination of new data. All of our conclusions were written in our published and peer-reviewed papers (i.e., in Nature Medicine and then updated in Cell late last year). Since then more data has been published that further supports our conclusions from that initial review. [2022-01-13 09:14:34] [Robert Garry] Better? [2022-01-13 09:17:28] [Kristian Andersen]