4 ms·

thanks, i see what you are saying regarding the binding sites, clearly they are quite different. but, the similarities seem greater than possible by chance, an

by yters 6y ago

thanks, i see what you are saying regarding the binding sites, clearly they are quite different. but, the similarities seem greater than possible by chance, and i am not sure how that could happen. maybe a variant of sars mutated into sars2? the sites are at least similar enough that researchers are trying to use sars vaccines to engineer sars2 vaccine

DiogenesKynikos 6y ago
What do you mean that they're more similar than is possible by chance? Instead of reading conspiracy blogs, go read scientific papers. If you don't understand them, then there is really good introductory course material on virology available from several universities.
- yters 6y ago
  Looking at the ACE2 alignment from the article, it looks like there are 55 spots where the sequences have different proteins. Of those 55 spots, 7 of them are identical between the bat and sars2. On the other hand, I count 20 matches between sars and sars2. Using a uniform distribution over the 20 proteins, and saying the probability of two proteins matching is 1/20, then the binomial probability of getting 7 or more matches out of 55 is 0.02, whereas the probability of getting 20 or more matches is less than 0.000001. I can see 0.02 being achieved by chance, but 0.000001 seems pretty unlikely to happen by accident. So, there is some sort of non accidental relationship between sars and sars2. Maybe 1) sars2 is descended from sars, or maybe 2) it is lab engineered. If the bat coronavirus is likely the more proximate ancestor to sars2 than sars, then #1 seems unlikely, which makes #2 the more plausible hypothesis. Also, to return to your argument about restricting our 'lab origin' hypothesis to known viruses, it seems that if WIV found a very effective bat coronavirus, and intend to create a bioweapon from it, this is exactly the situation when they would not share the sequence. I do not understand why you think people creating a bioweapon would want to share their materials with the world. You may also find this other article by the same author interesting, pointing out the evidence strongly points to RaTG13 being faked. https://nerdhaspower.weebly.com/ratg13-is-fake.html https://nerdhaspower.weebly.com/ratg13-is-fake.html There is also this interesting tweet from Jonathan Jacobs that the sample data for RaTG13 does not match the assembled genome. https://twitter.com/bioinformer/status/1252813532850081792 https://twitter.com/bioinformer/status/1252813532850081792
  - DiogenesKynikos 6y ago
    > So, there is some sort of non accidental relationship between sars and sars2. Yeah, they're both betacoronaviruses. You've just discovered something called "common descent." Charles Darwin published about it in 1859. I'm sorry, but this is getting comical. You really have to step back and learn some basics about biology before you go on this dive into conspiracy theories.
    - yters 6y ago
      Hmm, still not following. Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I blasted sars2 against sars and against ratg13. 88% coverage for the first and 99% for the second, so ratg13 seems to be a much more recent ancestor. - sars2 v. sars: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WE9PBF114 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WE9PB... - sars2 v. ratg13: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WGNJGT114 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WGNJG... Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13? Apologies for being dense :) As you notice, I'm pretty new to bioinformatics. Just trying to understand what your argument is. UPDATE: Sorry, I see a mistake I've been making that is confusing. I should be referring to Bat_CoV_ZC45 and Bat_CoV_ZXC21, not ratg13. ratg13 is the one that also has a close match to ace2, but the author claims is a forgery. The bat coronaviruses also seem to be more evolutionarily close to sars2 than sars, and they don't have the ace2 binding sites.
      - DiogenesKynikos 6y ago
        > Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I'm saying that it's complete nonsense to say that there's a (1/20)^7 chance of 7 amino acids matching. We're talking about viruses that are descended from a common ancestor, not random, independently distributed coin flips. > ratg13 seems to be a much more recent ancestor. RaTG13 is not an ancestor of SARS-CoV-2. The two viruses share a common ancestor. > Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13? ACE2 is a human protein. Neither SARS-CoV-2 nor SARS-CoV have ACE2. If you're talking about the RBD of the S protein, then note that the RBDs of SARS-CoV-2 and SARS-CoV are only 73% homologous, which is a pretty massive difference. Stepping back for a second, you're diving down the conspiracy-theory rabbit hole with very little prior knowledge of the subject. That's just going to make you easy prey to a lot of nonsense. Really, instead of reading blogs that claim to have found the secret truth about SARS-CoV-2, listen to what respected virologists have to say about it. Do some basic background reading on virology and coronaviruses. Read some review articles from scientific journals.

by yters 6y ago

DiogenesKynikos 6y ago

What do you mean that they're more similar than is possible by chance? Instead of reading conspiracy blogs, go read scientific papers. If you don't understand them, then there is really good introductory course material on virology available from several universities.

yters 6y ago
Looking at the ACE2 alignment from the article, it looks like there are 55 spots where the sequences have different proteins. Of those 55 spots, 7 of them are identical between the bat and sars2. On the other hand, I count 20 matches between sars and sars2. Using a uniform distribution over the 20 proteins, and saying the probability of two proteins matching is 1/20, then the binomial probability of getting 7 or more matches out of 55 is 0.02, whereas the probability of getting 20 or more matches is less than 0.000001. I can see 0.02 being achieved by chance, but 0.000001 seems pretty unlikely to happen by accident. So, there is some sort of non accidental relationship between sars and sars2. Maybe 1) sars2 is descended from sars, or maybe 2) it is lab engineered. If the bat coronavirus is likely the more proximate ancestor to sars2 than sars, then #1 seems unlikely, which makes #2 the more plausible hypothesis. Also, to return to your argument about restricting our 'lab origin' hypothesis to known viruses, it seems that if WIV found a very effective bat coronavirus, and intend to create a bioweapon from it, this is exactly the situation when they would not share the sequence. I do not understand why you think people creating a bioweapon would want to share their materials with the world. You may also find this other article by the same author interesting, pointing out the evidence strongly points to RaTG13 being faked. https://nerdhaspower.weebly.com/ratg13-is-fake.html https://nerdhaspower.weebly.com/ratg13-is-fake.html There is also this interesting tweet from Jonathan Jacobs that the sample data for RaTG13 does not match the assembled genome. https://twitter.com/bioinformer/status/1252813532850081792 https://twitter.com/bioinformer/status/1252813532850081792
- DiogenesKynikos 6y ago
  > So, there is some sort of non accidental relationship between sars and sars2. Yeah, they're both betacoronaviruses. You've just discovered something called "common descent." Charles Darwin published about it in 1859. I'm sorry, but this is getting comical. You really have to step back and learn some basics about biology before you go on this dive into conspiracy theories.
  - yters 6y ago
    Hmm, still not following. Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I blasted sars2 against sars and against ratg13. 88% coverage for the first and 99% for the second, so ratg13 seems to be a much more recent ancestor. - sars2 v. sars: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WE9PBF114 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WE9PB... - sars2 v. ratg13: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WGNJGT114 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WGNJG... Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13? Apologies for being dense :) As you notice, I'm pretty new to bioinformatics. Just trying to understand what your argument is. UPDATE: Sorry, I see a mistake I've been making that is confusing. I should be referring to Bat_CoV_ZC45 and Bat_CoV_ZXC21, not ratg13. ratg13 is the one that also has a close match to ace2, but the author claims is a forgery. The bat coronaviruses also seem to be more evolutionarily close to sars2 than sars, and they don't have the ace2 binding sites.
    - DiogenesKynikos 6y ago
      > Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I'm saying that it's complete nonsense to say that there's a (1/20)^7 chance of 7 amino acids matching. We're talking about viruses that are descended from a common ancestor, not random, independently distributed coin flips. > ratg13 seems to be a much more recent ancestor. RaTG13 is not an ancestor of SARS-CoV-2. The two viruses share a common ancestor. > Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13? ACE2 is a human protein. Neither SARS-CoV-2 nor SARS-CoV have ACE2. If you're talking about the RBD of the S protein, then note that the RBDs of SARS-CoV-2 and SARS-CoV are only 73% homologous, which is a pretty massive difference. Stepping back for a second, you're diving down the conspiracy-theory rabbit hole with very little prior knowledge of the subject. That's just going to make you easy prey to a lot of nonsense. Really, instead of reading blogs that claim to have found the secret truth about SARS-CoV-2, listen to what respected virologists have to say about it. Do some basic background reading on virology and coronaviruses. Read some review articles from scientific journals.