4 ms·

> Isn’t some of the so-called gain of function research (and I do mean in the broadest sense) effectively controlled evolution over many cycles such that it evo

> Isn’t some of the so-called gain of function research (and I do mean in the broadest sense) effectively controlled evolution over many cycles such that it evolves the correct mutations? Yeah, this is called passaging but it's very unlikely (nearly impossible) that it was used here -- you'd have to start with a very close predecessor, much closer than Ratg13, and the work in cell cultures usually ends up deleting the FCS since it's not a very stable mutation unless being actively selected for. So to perform the subculturing necessary to gain all of the various mutations that set sars cov2 apart would surely destroy it's ability to infect humans. (https://www.news-medical.net/news/20210208/Furin-cleavage-SARS-CoV-2-spike-deletions-mostly-suppressed-within-infected-airway-epithelium-says-study.aspx https://www.news-medical.net/news/20210208/Furin-cleavage-SA...) > And though I know the paper was retracted, what about those HIV-1 inserts? That the paper was retracted should tell you enough, but what was missed at the time is that ratg13, which was unambiguously of natural origin also has the same alleged HIV-1 inserts (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7033698/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7033698/). So it's pretty clear that the 'HIV-1 inserts' are just a common feature of ratg13-like coronaviruses. > Either way, empirically we have no conclusive evidence of natural origin (of the stages between the original bat coronavirus and the original Wuhan variant) nor of a lab leak. Right, but this is actually strongly suggestive of natural origin. We know what lab manipulation looks like and sars cov2 has none of these signs - in this case the absence of evidence actually is instructive.

nradov 5y ago
Thanks for the explanation. There is a hypothesis that the virus was modified in a lab by passaging it through transgenic animals that had more human-like respiratory systems. So that could account for its ability to infect humans. I don't necessarily believe that really happened (seems far fetched), but it's there any way to completely disprove that hypothesis?
- mikeyouse 5y ago
  I wasn't familiar with that theory, so leaning on others here (I'm taking out the cites since it really muddles the readability but they're in the source file). This all makes sense to me; > A specific laboratory escape scenario involves accidental infection in the course of serial passage of a SARSr-CoV in common laboratory animals such as mice. However, early SARSCoV-2 isolates were unable to infect wild-type mice. Although murine models are useful for studying infection in vivo and testing vaccines, they often result in mild or atypical disease in hACE2 transgenic mice. These findings are inconsistent with a virus selected for increased pathogenicity and transmissibility through serial passage through susceptible rodents. Although SARS-CoV-2 has since been engineered and mouse-adapted by serial passage, specific mutations in the spike protein, including N501Y, are necessary for such adaptation in mice. Notably, N501Y has arisen convergently in multiple SARS-CoV-2 variants of concern in the human population, presumably being selected to increase ACE2 binding affinity. > If SARS-CoV-2 resulted from attempts to adapt a SARSr-CoV for study in animal models, it would likely have acquired mutations like N501Y for efficient replication in that model, yet there is no evidence to suggest such mutations existed early in the pandemic. Both the low pathogenicity in commonly used laboratory animals and the absence of genomic markers associated with rodent adaptation indicate that SARS-CoV-2 is highly unlikely to have been acquired by laboratory workers in the course of viral pathogenesis or gain-of function experiments. Basically if you wanted to study sars cov2 in transgenic mice with adapted hACE2 receptors, there are obvious mutations that you would engineer into the virus to make it more stable and pathogenic. None of these mutations existed in the first samples. But importantly, when covid was spreading in humans, these same mutations naturally appeared through convergent evolution in several variants. Contrary to many claims, the virus wasn't close to being optimized for pathogenicity which would've been the ostensible purpose of GoF research. It really "acts" like it was recently passed to an intermediate host, then fairly quickly began to infect humans. [https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf]
salawat 5y ago
I do mot understand the assertion that one would "see evidence of lab tampering". No-see-ums are a thing.
- mikeyouse 5y ago
  The strongest version of the lab-created theory (in my view) is that they were studying coronaviruses / performing GoF research to understand the danger of coronaviruses. In that case, there would be zero point to using less efficient inserts or using esoteric seamless recombinant techniques to hide restriction sites. The mere fact that we can make genetic modifications that are well hidden doesn't add any information to the story since there's no evidence at all of anyone in the lab using those techniques and the resulting virus has a bunch of strange mutations that both made it more pathogenic in some respects and much less in others -- but the hard to predict ones made it more pathogenic and the easily missed ones made it less pathogenic. It's not solely the presence/absence of restriction sites that would indicate a lab-engineered virus. All scientists are basically using the same set of tools in terms of computation models and molecular techniques -- so when you see a spike protein that is "optimized for ACE2 binding" as many breathless people claimed -- you can tell that it actually isn't all that well optimized, and the genetics / stats package that would have been used to design the variant actually indicate several better options if you were trying to achieve high-efficiency ACE2 binding [see the discussion paragraph here: https://journals.asm.org/doi/10.1128/JVI.00127-20 https://journals.asm.org/doi/10.1128/JVI.00127-20] There are other indicators as well -- the additional proline in the FCS makes no sense from an engineering standpoint since it could very easily corrupt nearby helices, block the protease activity, or mess up binding through misfolding. Any competent engineer would have used a different amino acid there if they were trying to find a spacer -- or would have added another arginine to the beginning of the sequence to roughly double the odds of cleavage. So you have to simultaneously believe they're very competent at the molecular engineering needed to silently design viruses, but incompetent enough to use inefficient inserts and miss obvious, readily predictable areas to make it more pathogenic. Until we find a precursor virus or a whistleblower, we're down to weighing probabilities and I'd put "engineering using seamless recombination" very, very low on the list.. like below 0.01%.
  - 5y ago

nradov 5y ago

Thanks for the explanation. There is a hypothesis that the virus was modified in a lab by passaging it through transgenic animals that had more human-like respiratory systems. So that could account for its ability to infect humans. I don't necessarily believe that really happened (seems far fetched), but it's there any way to completely disprove that hypothesis?

mikeyouse 5y ago
I wasn't familiar with that theory, so leaning on others here (I'm taking out the cites since it really muddles the readability but they're in the source file). This all makes sense to me; > A specific laboratory escape scenario involves accidental infection in the course of serial passage of a SARSr-CoV in common laboratory animals such as mice. However, early SARSCoV-2 isolates were unable to infect wild-type mice. Although murine models are useful for studying infection in vivo and testing vaccines, they often result in mild or atypical disease in hACE2 transgenic mice. These findings are inconsistent with a virus selected for increased pathogenicity and transmissibility through serial passage through susceptible rodents. Although SARS-CoV-2 has since been engineered and mouse-adapted by serial passage, specific mutations in the spike protein, including N501Y, are necessary for such adaptation in mice. Notably, N501Y has arisen convergently in multiple SARS-CoV-2 variants of concern in the human population, presumably being selected to increase ACE2 binding affinity. > If SARS-CoV-2 resulted from attempts to adapt a SARSr-CoV for study in animal models, it would likely have acquired mutations like N501Y for efficient replication in that model, yet there is no evidence to suggest such mutations existed early in the pandemic. Both the low pathogenicity in commonly used laboratory animals and the absence of genomic markers associated with rodent adaptation indicate that SARS-CoV-2 is highly unlikely to have been acquired by laboratory workers in the course of viral pathogenesis or gain-of function experiments. Basically if you wanted to study sars cov2 in transgenic mice with adapted hACE2 receptors, there are obvious mutations that you would engineer into the virus to make it more stable and pathogenic. None of these mutations existed in the first samples. But importantly, when covid was spreading in humans, these same mutations naturally appeared through convergent evolution in several variants. Contrary to many claims, the virus wasn't close to being optimized for pathogenicity which would've been the ostensible purpose of GoF research. It really "acts" like it was recently passed to an intermediate host, then fairly quickly began to infect humans. [https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf]

salawat 5y ago

I do mot understand the assertion that one would "see evidence of lab tampering". No-see-ums are a thing.

mikeyouse 5y ago
The strongest version of the lab-created theory (in my view) is that they were studying coronaviruses / performing GoF research to understand the danger of coronaviruses. In that case, there would be zero point to using less efficient inserts or using esoteric seamless recombinant techniques to hide restriction sites. The mere fact that we can make genetic modifications that are well hidden doesn't add any information to the story since there's no evidence at all of anyone in the lab using those techniques and the resulting virus has a bunch of strange mutations that both made it more pathogenic in some respects and much less in others -- but the hard to predict ones made it more pathogenic and the easily missed ones made it less pathogenic. It's not solely the presence/absence of restriction sites that would indicate a lab-engineered virus. All scientists are basically using the same set of tools in terms of computation models and molecular techniques -- so when you see a spike protein that is "optimized for ACE2 binding" as many breathless people claimed -- you can tell that it actually isn't all that well optimized, and the genetics / stats package that would have been used to design the variant actually indicate several better options if you were trying to achieve high-efficiency ACE2 binding [see the discussion paragraph here: https://journals.asm.org/doi/10.1128/JVI.00127-20 https://journals.asm.org/doi/10.1128/JVI.00127-20] There are other indicators as well -- the additional proline in the FCS makes no sense from an engineering standpoint since it could very easily corrupt nearby helices, block the protease activity, or mess up binding through misfolding. Any competent engineer would have used a different amino acid there if they were trying to find a spacer -- or would have added another arginine to the beginning of the sequence to roughly double the odds of cleavage. So you have to simultaneously believe they're very competent at the molecular engineering needed to silently design viruses, but incompetent enough to use inefficient inserts and miss obvious, readily predictable areas to make it more pathogenic. Until we find a precursor virus or a whistleblower, we're down to weighing probabilities and I'd put "engineering using seamless recombination" very, very low on the list.. like below 0.01%.
- 5y ago