Slack / Private Message Drop — page 1002

Yup - I'm getting all the full length genomes first and then we can cut alignments out from there. Getting them annotated too - future Kristian will thank present Kristian. [2021-09-21 11:09:02] [Kristian Andersen] Alright, first attempt at an annotated alignment with relevant sequences. Am I missing anything? Any other sequences mentioned in the grant I should include? @Robert Garry, once I have the coordinates of the N-linked glycs I'll include those in the alignment as well. Once we have all of those annotated, I'll create Spike alignments, including AA and NT versions. [shared file(s): 2021.09.21_alignment-full.geneious] [2021-09-21 11:45:41] [Robert Garry] excellent! [2021-09-21 13:59:31] [Eddie Holmes] What also annoys me is that Peter should have seen this coming and it is worse than he was suggesting a few days ago. He's a jackass. We still have no evidence for SC2 in that lab and they must have sequenced it first. But it is very striking that a bat-derived CoV with an FCS turns up in a city that was on a grant proposing to muck around with FCSs in bat-derived CoVs. [2021-09-21 14:00:43] [Eddie Holmes] I might see if I can talk to Linfa about it. [2021-09-21 15:25:59] [Kristian Andersen] Getting Linfa's take on this would be great - he's on the grant too and he also hasn't mentioned anything about this. [2021-09-21 15:27:37] [Eddie Holmes] I'll get onto it. I'm also going to have to chat to the intelligence folk. [2021-09-21 16:02:14] [Robert Garry] Some of the most valuable info is going to come from sorting out the parallels btwn SC1 and SC2. It's ironic that two KEY pieces surfaced in the past few weeks- the hubel civet viruses and the BANAL bat viruses. With SC1 and a little elbow grease you'll see the adaptions from bat to civet to human and then human to human. With SC2 we'll have all the same genomes except the intermediate host (and I think a good assumption that there is one). In both SC1 and SC2 you've got highly similar N-glycan changes in the NTD followed by very similar and specific RBD changes. It's possible the NTD changes opened the door for the RBD changes. Put the FCS aside - nobody did these previously undiagnosed NTD and RBD changes by design. [2021-09-21 16:05:51] [Kristian Andersen] Yup, all important points Bob. As for the glycans - do you have the coordinates? [2021-09-21 16:06:11] [Kristian Andersen] I'm done with my Zoom calls so I'll focus on this for the rest of the day/night. [2021-09-21 16:24:57] [Robert Garry] For SC2 to laos bat 52 its N 30, 74 and 370.