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1. 2021-09-21 08:24 Andrew Rambaut open
   And you have 6 codons to chose from.
2. 2021-09-21 08:25 Kristian G. Andersen open
   Correct. Key here too is that if you were to 'optimize' the FCS sequence (as is commonly done for these types ofexperiments) you would _not_ end up with the FCS sequence we see, including the CGG codons. But again, itdoesn't really tell us much.
3. 2021-09-21 08:26 Kristian G. Andersen open
   What I think we have to look _very_ closely at are all the specific sites they talk about in the grant and then compare across our alignments - is SC2 unique in those positions compared to, say, the BANAL viruses? Does it flip back toSARS1 at some of these positions, etc.
4. 2021-09-21 08:26 Andrew Rambaut open
   Yup.
5. 2021-09-21 08:27 Kristian G. Andersen
   I'll get some of this started later today - it's important to get the insights irrespective of what it's going to end upshowing.
6. 2021-09-21 08:28 Andrew Rambaut open
   Would there be any reason to pick the SARS2 backbone for doing these? Assuming they had the genome sequence way back at the start?
7. 2021-09-21 08:30 Kristian G. Andersen open
   Well, in the grant they specifically talk about *new* viruses - so a SC2 precursor could have been one of those "low risk" viruses they talk about and then they started fiddling with it.
8. 2021-09-21 08:34 Andrew Rambaut open
   They would have selected it from candidates by genome sequencing it. I guess they would have seen an ACE-2 binding RBD and thought that is the one to try an FCS in?
9. 2021-09-21 08:37 Andrew Rambaut open
   Or they just were selecting viruses by seeing if they could get any to culture and then worry about genome sequencing?

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