Private channel session 1610

14 messages over 1h 53m, 2021-09-21 – 2021-09-21.

A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.

2021-09-21 15:25 Kristian G. Andersen open PDF p.1002

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 Edward C. Holmes open PDF p.1002

I'll get onto it. I'm also going to have to chat to the intelligence folk.
2021-09-21 16:02 Robert F. Garry open PDF p.1002

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 littleelbow 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 andSC2 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 previouslyundiagnosed NTD and RBD changes by design.
2021-09-21 16:05 Kristian G. Andersen open PDF p.1002

Yup, all important points Bob. As for the glycans - do you have the coordinates?
2021-09-21 16:06 Kristian G. Andersen open PDF p.1002

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 Robert F. Garry open PDF p.1002

For SC2 to laos bat 52 its N 30, 74 and 370.
2021-09-21 16:25 Robert F. Garry open PDF p.1003

SC1 coming
2021-09-21 16:37 Edward C. Holmes open PDF p.1003

I'd love to know what a 'human specific furin cleavage site' is.
2021-09-21 16:48 Kristian G. Andersen open PDF p.1003

It's not "PRRAR", that's for sure.
2021-09-21 16:48 Kristian G. Andersen open PDF p.1003

@Robert Garry - I'm using NetNGlyc and since N-linked glycans are easy to predict I think I have what I need
2021-09-21 16:51 Robert F. Garry open PDF p.1003

for sc1 the ones I have my eye on are N 29, 73 and maybe 227
2021-09-21 16:52 Robert F. Garry open PDF p.1003

variable with close bat viruses like KY417150
2021-09-21 17:14 Kristian G. Andersen open PDF p.1003

@Robert Garry what are the key N-linked sites for the DC-SIGN/L-SIGN stuff? I have my eye focused on residue 370 in SC2 (357 in SC1) since that is a FULLY conserved N-linked glycan across _all_ sarbecos, _except_ in SC2 because residue 372 changes from a fully conserved T to an A (via a single A>G transition in the first codon position). In the RBD there are three N-linked glycans in SC2/BANAL, so two are conserved, one is not.
2021-09-21 17:19 Kristian G. Andersen open PDF p.1003

We have _some_ information about what this particular residue does in SC2: https://pubmed.ncbi.nlm.nih.gov/34289344/