4 ms·

There's little question that most of SARS-CoV-2's genome evolved naturally in bats, especially the spike given its close identity to BANAL-52. I believe that SA

There's little question that most of SARS-CoV-2's genome evolved naturally in bats, especially the spike given its close identity to BANAL-52. I believe that SARS-CoV-2 is very unlikely to have been derived in a laboratory from any known virus, including RaTG13. I'm not sure how you'd distinguish between a novel naturally-evolved virus and a laboratory chimera of two such viruses, though. The WIV had the biggest program in the world to sample novel coronaviruses from nature. In DEFUSE, they sought DARPA funding to make chimeras of such viruses, with novel FCSs. That proposal was rejected for safety concerns, but we don't know what work continued with other funders. https://theintercept.com/2021/09/23/coronavirus-research-grant-darpa/ https://theintercept.com/2021/09/23/coronavirus-research-gra... Your links above support the possibility that SARS-CoV-2 is natural. They don't exclude that it's unnatural, though.

mikeyouse 5y ago
I mean, sure anything's possible -- but WIV had the biggest program to sample coronaviruses because there are so many coronaviruses in China and they've had epidemics caused by zoonotic spillover in the past. The reason there were funding proposals of all sorts to study bat coronaviruses is because literally everyone in virology was terrified of a bat coronavirus like covid19. I don't think "the west" fully appreciates how much SARS changed research in China. > I'm not sure how you'd distinguish between a novel naturally-evolved virus and a laboratory chimera of two such viruses, though. BLAST sequencing against known viruses would do the trick. (https://www.viprbrc.org/brc/blast.spg?method=ShowCleanInputPage&decorator=reo https://www.viprbrc.org/brc/blast.spg?method=ShowCleanInputP...) You could come up with a conspiracy theory to say they were hiding their most dangerous pathogens as part of a defense program so we wouldn't have access to the sequences of the progenitor viruses -- but the fact that we had staff helping in WIV and literally no intelligence has come out to that effect blunts the theory in my view. I'm 99%:1% confident it was natural spillover and probably 75%:25% that no lab had ever seen the virus before the first people got sick. Sars cov2 was a bat virus -- so it needed an intermediate mammal host with human-like ace2 receptors to spread to humans. So WIV would have had to have developed this unnaturally, which we would be able to "see" in the DNA or it happened naturally. Those two things don't seem remotely 50:50 likely to me.
- tripletao 5y ago
  By "two such viruses", I meant two novel, unpublished viruses. I don't think that requires any great conspiracy from the WIV, just the normal delays between sampling, sequencing, and publishing. RaTG13 was sampled in 2013, but the full genome wasn't published until after the pandemic. And interesting odds. In your p = 24% case where it's natural spillover but a lab had seen the virus before people got sick, are you assuming that a researcher got infected with a naturally-evolved virus, whether directly from an animal on a sampling trip or from a culture in the lab? It's hard to see why they'd be concealing their prior knowledge of the virus otherwise. I'd personally bet maybe 20% lab-manipulated (by a DEFUSE-like path), 50% naturally-evolved but accidentally released by researchers, 30% true natural. I'm less sure that SARS-CoV-2 needed a non-bat animal host given BANAL-52's spike, though that leaves the question of how BANAL-52 got so closely-adapted to human ACE2 rather mysterious. (I wonder if SARS-CoV-2 but with the BANAL-52 spike would infect humanized mice? I guess that's exactly the kind of curiosity that might have started this pandemic...) As to the abundance of coronaviruses, I assume you're aware that the closest bat viruses have been collected far from Wuhan, and Dr. Shi herself didn't expect spillover in Wuhan: > We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province. https://web.archive.org/web/20201206204844/https://www.sciencemag.org/sites/default/files/Shi%20Zhengli%20Q%26A.pdf https://web.archive.org/web/20201206204844/https://www.scien... SARS-1 emerged far from the bat caves too, but wildlife trafficking there was quickly identified as the likely conduit. I understand there's some debate as to whether civet cats (and not some other animal) were actually the proximal host for SARS-1, but that's still much stronger evidence of zoonosis than we have for SARS-CoV-2.
- pengaru 5y ago
  > cov2 was a bat virus -- so it needed an intermediate mammal host with human-like ace2 receptors to spread to humans. My understanding is that bats like the chinese horseshoe have perfectly suitable ACE2 receptors for getting infected by sars-cov-2 as-is, and that the main reason for wanting an intermediate host is to explain how the virus got in contact with humans because humans don't really interface physically with bats, but I'm totally out of my depths here. The article linked below makes it sound like the virus can infect a wide variety of mammals, including bats and humans, with or without the now famous furin cleavage site, so it doesn't seem like the smoking gun lab-leak proponents like to brandish it as. https://www.news-medical.net/news/20200420/ACE2-receptor-expression-by-SARS-CoV-2-across-different-animal-species.aspx https://www.news-medical.net/news/20200420/ACE2-receptor-exp...

mikeyouse 5y ago

I mean, sure anything's possible -- but WIV had the biggest program to sample coronaviruses because there are so many coronaviruses in China and they've had epidemics caused by zoonotic spillover in the past. The reason there were funding proposals of all sorts to study bat coronaviruses is because literally everyone in virology was terrified of a bat coronavirus like covid19. I don't think "the west" fully appreciates how much SARS changed research in China. > I'm not sure how you'd distinguish between a novel naturally-evolved virus and a laboratory chimera of two such viruses, though. BLAST sequencing against known viruses would do the trick. (https://www.viprbrc.org/brc/blast.spg?method=ShowCleanInputPage&decorator=reo https://www.viprbrc.org/brc/blast.spg?method=ShowCleanInputP...) You could come up with a conspiracy theory to say they were hiding their most dangerous pathogens as part of a defense program so we wouldn't have access to the sequences of the progenitor viruses -- but the fact that we had staff helping in WIV and literally no intelligence has come out to that effect blunts the theory in my view. I'm 99%:1% confident it was natural spillover and probably 75%:25% that no lab had ever seen the virus before the first people got sick. Sars cov2 was a bat virus -- so it needed an intermediate mammal host with human-like ace2 receptors to spread to humans. So WIV would have had to have developed this unnaturally, which we would be able to "see" in the DNA or it happened naturally. Those two things don't seem remotely 50:50 likely to me.

tripletao 5y ago
By "two such viruses", I meant two novel, unpublished viruses. I don't think that requires any great conspiracy from the WIV, just the normal delays between sampling, sequencing, and publishing. RaTG13 was sampled in 2013, but the full genome wasn't published until after the pandemic. And interesting odds. In your p = 24% case where it's natural spillover but a lab had seen the virus before people got sick, are you assuming that a researcher got infected with a naturally-evolved virus, whether directly from an animal on a sampling trip or from a culture in the lab? It's hard to see why they'd be concealing their prior knowledge of the virus otherwise. I'd personally bet maybe 20% lab-manipulated (by a DEFUSE-like path), 50% naturally-evolved but accidentally released by researchers, 30% true natural. I'm less sure that SARS-CoV-2 needed a non-bat animal host given BANAL-52's spike, though that leaves the question of how BANAL-52 got so closely-adapted to human ACE2 rather mysterious. (I wonder if SARS-CoV-2 but with the BANAL-52 spike would infect humanized mice? I guess that's exactly the kind of curiosity that might have started this pandemic...) As to the abundance of coronaviruses, I assume you're aware that the closest bat viruses have been collected far from Wuhan, and Dr. Shi herself didn't expect spillover in Wuhan: > We have done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don't think the spillover from bats to humans occurred in Wuhan or in Hubei Province. https://web.archive.org/web/20201206204844/https://www.sciencemag.org/sites/default/files/Shi%20Zhengli%20Q%26A.pdf https://web.archive.org/web/20201206204844/https://www.scien... SARS-1 emerged far from the bat caves too, but wildlife trafficking there was quickly identified as the likely conduit. I understand there's some debate as to whether civet cats (and not some other animal) were actually the proximal host for SARS-1, but that's still much stronger evidence of zoonosis than we have for SARS-CoV-2.
pengaru 5y ago
> cov2 was a bat virus -- so it needed an intermediate mammal host with human-like ace2 receptors to spread to humans. My understanding is that bats like the chinese horseshoe have perfectly suitable ACE2 receptors for getting infected by sars-cov-2 as-is, and that the main reason for wanting an intermediate host is to explain how the virus got in contact with humans because humans don't really interface physically with bats, but I'm totally out of my depths here. The article linked below makes it sound like the virus can infect a wide variety of mammals, including bats and humans, with or without the now famous furin cleavage site, so it doesn't seem like the smoking gun lab-leak proponents like to brandish it as. https://www.news-medical.net/news/20200420/ACE2-receptor-expression-by-SARS-CoV-2-across-different-animal-species.aspx https://www.news-medical.net/news/20200420/ACE2-receptor-exp...