6 ms·

>96% similar what does this mean

epgui 3y ago
Not very much.
sterlind 3y ago
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.
- uiberto 3y ago
  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.
- wedernoch 3y ago
  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
nsvd 3y ago
Less similar than a human and a chimp, who share 98.8% of their DNA (American Museum of Natural History).
- baja_blast 3y ago
  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
lamontcg 3y ago
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.
- peteradio 3y ago
  DEFUSE proposed insertion of human-specific cleavage sites not serial passage.
  - lamontcg 3y ago
    RaTG13 differs from SARS-CoV-2 by a lot more than just an FCS
    - peteradio 3y ago
      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?
      - lamontcg 3y ago
        Yes, you're still a thousand mutations away from each other. The FCS is tiny. The mutations are spread all over the entire genome--although the main areas are in spike RBD (which suggests that RaTG13 may not be able to use ACE2 at all). The PRRAR FCS that SARS-CoV-2 uses is also a previously-unknown-to-humans FCS and not one a human scientist would have naively guessed would work.
        peteradio 3y ago
        Thanks.
- 3y ago

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.

uiberto 3y ago
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.
wedernoch 3y ago
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

nsvd 3y ago

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

baja_blast 3y ago
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

lamontcg 3y ago

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.

peteradio 3y ago
DEFUSE proposed insertion of human-specific cleavage sites not serial passage.
- lamontcg 3y ago
  RaTG13 differs from SARS-CoV-2 by a lot more than just an FCS
  - peteradio 3y ago
    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?
    - lamontcg 3y ago
      Yes, you're still a thousand mutations away from each other. The FCS is tiny. The mutations are spread all over the entire genome--although the main areas are in spike RBD (which suggests that RaTG13 may not be able to use ACE2 at all). The PRRAR FCS that SARS-CoV-2 uses is also a previously-unknown-to-humans FCS and not one a human scientist would have naively guessed would work.
      - peteradio 3y ago
        Thanks.
3y ago