>96% similar

what does this mean

Not very much.

the SARS-CoV-2 genome is ~29.8K nucleotides long. 96% of that sequence is identical to the genome of RaTG13, i.e. all but ~1200 match. for reference, SARS-CoV-1 is only 82% similar to SARS-CoV-2. at a mutation rate of 8*10^-4, this means the current strains of COVID are ~97% identical to the original 2019 sequence.

so, darned close honestly. to be clear, I'm not saying RaTG13 is the source of the lab leak - it's just too different - but I am saying that it's much closer than the original SARS, and thus had no business being analyzed in a BSL-2 lab.

Sophisticated evolutionary models are needed to accurately estimated expected mean and variance in genetic distances. For example, rare events of large effect (e.g. recombination) also introduces variation beyond within-strain mutation.

I don't see how then % number means anything. Humans and apes have 4% difference. It depends on thebkind of difference, not the number of different genes

Less similar than a human and a chimp, who share 98.8% of their DNA (American Museum of Natural History).

But a human and chimp's have over 3 billion nucleotides in our genome. SARS2 only has 30 thousand, so the genetic distance between the two are at most decades, but with recombinants the timeline is much shorter

That means they were several decades of evolution in the wild away from each other.

It would take passage through billions of organisms to turn RaTG13 into SARS-CoV-2.

Which is probably what happened naturally through many, many millions of bats (and whatever intermediate animal) being infected and passing it on. Something that is well outside the scale of serial passage experiments in a lab.

DEFUSE proposed insertion of human-specific cleavage sites not serial passage.

RaTG13 differs from SARS-CoV-2 by a lot more than just an FCS

How far away would it be? Would it still take millions and millions of bats or is it now within the realm of possibility to infect humanized mice and get SARS-CoV-2 out the other end?

Yes, you're still a thousand mutations away from each other. The FCS is tiny.

Thanks.

How do you arrive at several decades and billions of organisms? You can't extrapolate the current mutation rate to the spillover event; SARS-CoV-2 was already quite fit at infecting humans and didn't need to change much. In contrast, during spillover events there's heavy selection pressure to adapt to the new host.

There's also the possibility of recombination events, which can instantly cause significant drift. Now consider the case of the Mojiang miners, who contracted and slowly succumbed to viral pneumonia in 2012 after inhaling bat guano. WIV found, like, a dozen beta-coronaviruses in that cave alone (including RaTG13.) The miners could have been exposed to several at once, which recombined and adapted quickly to their new home in human lungs. Again, unlikely to have been SARS-CoV-2, since the pandemic almost certainly would have happened already, but whatever they had was virulent enough to kill half of them.

The genetic clock was estimated from bat coronavirus mutation rates in the wild, not from SARS-CoV-2 mutation in humans.

And virulence != transmissible. They got sick by inhaling everything that was floating around in that mine. To get more people sick you'd need to take them all to that mine.

Recombination to produce a viable and more successful virus is also very rare, that is unlikely to have happened to any of those miners, much less several of them (over populations it becomes likely but there we're talking many millions of infections as well).

Don't they still collect wild bats for food in China?

If so, it seems a bit misguided to be taking issue with BSL-this-vs-that handling wild bats when BSL-fuck-all members of the public are still using them as a food source.

Pre-COVID it was already well understood that bats are viral reservoirs. It didn't prevent wet markets from selling wild bats. The labs are of focus due to GoF, in lieu of GoF there's already that level of exposure happening in the Chinese food supply.