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1. 2021-09-21 08:06 Kristian G. Andersen open
   Exactly. I suspect it'll be the latter.
2. 2021-09-21 08:08 Andrew Rambaut open
   Me too. But it really isn't beyond plausibility that someone went ahead and tried some of this stuff. We just need tore-convince ourselves it is coincidence.
3. 2021-09-21 08:10 Kristian G. Andersen open
   Correct - that's the problem. There's a big difference between "the lab was working on bat CoVs" to "the lab wasmodifying bat CoVs using features we see being unique to SC2".
4. 2021-09-21 08:10 Andrew Rambaut open
   Key question is - would anyone chose to put the FCS we see in SC2 in and put it out of frame.
5. 2021-09-21 08:11 Kristian G. Andersen
   Would be a very strange way to do it, but not impossible - depending on their cloning strategy.
6. 2021-09-21 08:12 Andrew Rambaut open
   If you wanted to insert an FCS you would pick the AAs you wanted, pick the codons you wanted and then insert it.
7. 2021-09-21 08:12 Andrew Rambaut open
   The alternative is that it was inserted in frame and then mutated to make it look out of frame
8. 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.
9. 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.

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