Chat message

Slack / Private Message Drop, p.1000 [SLACK_001214] · slack_pm:msg:10431

Date: 2021-09-21 08:25
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

Recipients on this medium are inferred from channel membership, not per-message addressing.

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.

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-09-21 08:14 Kristian G. Andersen open

Again, it depends on cloning strategy - if the use restriction enzymes and there would be an easy way to insert anFCS with PCR utilizing REs already present in the sequence, then it could be a way to do it. Not the optimal way, for sure, but sometimes ease trumps perfection.
2021-09-21 08:16 Andrew Rambaut open

Would you pick CGG for example? Would you consider what codon to use for an R or just pick one arbitrarily.
2021-09-21 08:21 Kristian G. Andersen open

CGG would be an unusual choice IMO - not a 'optimized' R and sorta middle-of-the-pack as it comes to usage in human genomes. Very rare, of course, in viruses because it's a CpG.
2021-09-21 08:24 Andrew Rambaut open

And you have 6 codons to chose from.
2021-09-21 08:25 Kristian G. Andersen

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.
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.
2021-09-21 08:26 Andrew Rambaut open

Yup.
2021-09-21 08:27 Kristian G. Andersen open

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.
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?

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