A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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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.
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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".
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Key question is - would anyone chose to put the FCS we see in SC2 in and put it out of frame.
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Would be a very strange way to do it, but not impossible - depending on their cloning strategy.
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2021-09-21 08:12
Andrew Rambaut
If you wanted to insert an FCS you would pick the AAs you wanted, pick the codons you wanted and then insert it.
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The alternative is that it was inserted in frame and then mutated to make it look out of frame
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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.
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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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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.