I am now reasonably convinced (p>0.8) that SARS-CoV-2 originated in an accidental laboratory escape from the Wuhan Institute of Virology.
1. If SARS-CoV-2 originated in a non-laboratory zoonotic transmission, then the geographic location of the initial outbreak would be drawn from a distribution which is approximately uniformly distributed over China (population-weighted); whereas if it originated in a laboratory, the geographic location is drawn from the commuting region of a lab studying that class of viruses, of which there is currently only one. Wuhan has <1% of the population of China, so this is (order of magnitude) a 100:1 update.
2. No factor other than the presence of the Wuhan Institute of Virology and related biotech organizations distinguishes Wuhan or Hubei from the rest of China. It is not the location of the bat-caves that SARS was found in; those are in Yunnan. It is not the location of any previous outbreaks. It does not have documented higher consumption of bats than the rest of China.
3. There have been publicly reported laboratory escapes of SARS twice before in Beijing, so we know this class of virus is difficult to contain in a laboratory setting.
4. We know that the Wuhan Institute of Virology was studying SARS-like bat coronaviruses. As reported in the Washington Post today, US diplomats had expressed serious concerns about the lab’s safety.
5. China has adopted a policy of suppressing research into the origins of SARS-CoV-2, which they would not have done if they expected that research to clear them of scandal. Some Chinese officials are in a position to know.
To be clear, I don’t think this was an intentional release. I don’t think it was intended for use as a bioweapon. I don’t think it underwent genetic engineering or gain-of-function research, although nothing about it conclusively rules this out. I think the researchers had good intentions, and screwed up.
This Feb. 20th Twitter thread from Trevor Bedford argues against the lab-escape scenario. Do read the whole thing, but I’d say that the key points not addressed in parent comment are:
Data point #1 (virus group): #SARSCoV2 is an outgrowth of circulating diversity of SARS-like viruses in bats. A zoonosis is expected to be a random draw from this diversity. A lab escape is highly likely to be a common lab strain, either exactly 2002 SARS or WIV1.
But, briefly, #SARSCoV2 has 6 mutations to its receptor binding domain that make it good at binding to ACE2 receptors from humans, non-human primates, ferrets, pigs, cats, pangolins (and others), but poor at binding to bat ACE2 receptors.
This pattern of mutation is most consistent with evolution in an animal intermediate, rather than lab escape. Additionally, the presence of these same 6 mutations in the pangolin virus argues strongly for an animal origin: https://biorxiv.org/content/10.1101/2020.02.13.945485v1…
…
Data point #3 (market cases): Many early infections in Wuhan were associated with the Huanan Seafood Market. A zoonosis fits with the presence of early cases in a large animal market selling diverse mammals. A lab escape is difficult to square with early market cases.
...
Data point #4 (environmental samples): 33 out of 585 environmental samples taken from the Huanan seafood market showed as #SARSCoV2 positive. 31 of these were collected from the western zone of the market, where wildlife booths are concentrated. 15⁄21http://xinhuanet.com/english/2020-01/27/c_138735677.htm…
Environmental samples could in general derive from human infections, but I don’t see how you’d get this clustering within the market if these were human derived.
One scenario I recall seeing somewhere that would reconcile lab-escape with data points 3 & 4 above is that some low-level WIV employee or contractor might have sold some purloined lab animals to the wet market. No idea how plausible that is.
Data point #3 (market cases): Many early infections in Wuhan were associated with the Huanan Seafood Market. A zoonosis fits with the presence of early cases in a large animal market selling diverse mammals. A lab escape is difficult to square with early market cases.
Given that there’s the claim from Botao Xiao’s The possible origins of 2019-nCoV coronavirus, that this seafood market was located 300m from a lab (which might or might not be true), this market doesn’t seem like it reduces chances.
We need to update down on any complex, technical datapoint that we don’t fully understand, as China has surely paid researchers to manufacture hard-to-evaluate evidence for its own benefit (regardless of the truth of the accusation). This is a classic technique that I have seen a lot in propaganda against laypeople, and there is every reason it should have been employed against the “smart” people in the current coronavirus situation.
The most recent episode of the 80k podcast had Andy Weber on it. He was the US Assistant Secretary of Defense, “responsible for biological and other weapons of mass destruction”.
Well, over time, evidence for natural spread hasn’t been produced, we haven’t found the intermediate species, you know, the pangolin that was talked about last year. I actually think that the odds that this was a laboratory-acquired infection that spread perhaps unwittingly into the community in Wuhan is about a 50% possibility… And we know that the Wuhan Institute of Virology was doing exactly this type of research [gain of function research]. Some of it — which was funded by the NIH for the United States — on bat Coronaviruses. So it is possible that in doing this research, one of the workers at that laboratory got sick and went home. And now that we know about asymptomatic spread, perhaps they didn’t even have symptoms and spread it to a neighbor or a storekeeper. So while it seemed an unlikely hypothesis a year ago, over time, more and more evidence leaning in that direction has come out. And it’s wrong to dismiss that as kind of a baseless conspiracy theory. I mean, very, very serious scientists like David Relman from Stanford think we need to take the possibility of a laboratory accident seriously.
The included link is to a statement from the US Embassy in Georgia, which to me seems surprisingly blunt, calling out the CCP for obfuscation, and documenting events at the WIV, going so far as to speculate that they were doing bio-weapons research there.
What about allegations that a pangolin was involved? Would they have had pangolins in the lab as well or is the evidence about pangolin involvement dubious in the first place?
Edit: Wasn’t meant as a joke. My point is why did initial analyses conclude that the SARS-Cov-2 virus is adapted to receptors of animals other than bats, suggesting that it had an intermediary host, quite likely a pangolin. This contradicts the story of “bat researchers kept bat-only virus in a lab and accidentally released it.”
I think it’s probably a virus that was merely identified in pangolins, but whose primary host is probably not pangolins.
The pangolins they sequenced weren’t asymptomatic carriers at all; they were sad smuggled specimens that were dying of many different diseases simultaneously.
I looked into this semi-recently, and wrote up something here.
The pangolins were apprehended in Guangxi, which shares some of its border with Yunnan. Neither of these provinces are directly contiguous with Hubei (Wuhan’s province), fwiw. (map)
1. If SARS-CoV-2 originated in a non-laboratory zoonotic transmission, then the geographic location of the initial outbreak would be drawn from a distribution which is approximately uniformly distributed over China (population-weighted); whereas if it originated in a laboratory, the geographic location is drawn from the commuting region of a lab studying that class of viruses, of which there is currently only one. Wuhan has <1% of the population of China, so this is (order of magnitude) a 100:1 update.
This is an assumption.
While it might be comparatively correct, I’m not sure about the magnitude. Under the circumstances, perhaps we should consider the possibility that there is something we don’t know about Wuhan that makes it more likely.
3. There have been publicly reported laboratory escapes of SARS twice before in Beijing, so we know this class of virus is difficult to contain in a laboratory setting.
Maybe they don’t know whether it escaped or not. Maybe they just think there is a chance that the evidence will implicate them and they figure it’s not worth the risk as there’ll only be consequences if there is definitely proof that it escaped from one of their labs and not mere speculation.
Or maybe they want to argue that it didn’t come from China? I think they’ve already been pushing this angle.
First, a clarification: whether SARS-CoV-2 was laboratory-constructed or manipulated is a separate question from whether it escaped from a lab. The main reason a lab would be working with SARS-like coronavirus is to test drugs against it in preparation for a possible future outbreak from a zoonotic source; those experiments would involve culturing it, but not manipulating it.
But also: If it had been the subject of gain-of-function research, this probably wouldn’t be detectable. The example I’m most familiar with, the controversial 2012 US A/H5N1 gain of function study, used a method which would not have left any genetic evidence of manipulation.
Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus
and
It is so effective at attaching to human cells that the researchers said the spike proteins were the result of natural selection and not genetic engineering.
I think the article just says that the virus did not undergo genetic engineering or gain-of-function research, which is also what Jim says above.
Chinese virology researcher released something claiming that SARS-2 might even be genetically-manipulated after all? After assessing, I’m not really convinced of the GMO claims, but the RaTG13 story definitely seems to have something weird going on.
Claims that the RaTG13 genome release was a cover-up (it does look like something’s fishy with RaTG13, although it might be different than Yan thinks). Claims ZC45 and/or ZXC21 was the actual backbone (I’m feeling super-skeptical of this bit, but it has been hard for me to confirm either way).
Looks like something fishy happened with RaTG13, although I’m not convinced that genetic modification was involved. This is an argument built on pre-prints, but they appear to offer several different lines of evidence that something weird happened here.
Simplest story (via R&B): It looks like people first sequenced this virus in 2016, under the name “BtCOV/4991”, using mine samples from 2013. And for some reason, WIV re-released the sequence as “RaTG13″ at a later date?
(edit: I may have just had a misunderstanding. Maybe BtCOV/4991 is the name of the virus as sequenced from miner-lungs, RaTG13 is the name of the virus as sequenced from floor droppings? But in that case, why is the “fecal” sample reading so weirdly low-bacteria? And they probably are embarrassed that it took them that long to sequence the fecal samples, and should be.)
A paper by by Indian researchers Rahalkar and Bahulikar ( https://doi.org/10.20944/preprints202005.0322.v1 ) notes that BtCoV/4991 sequenced in 2016 by the same Wuhan Virology Institute researchers (and taken from 2013 samples of a mineshaft that gave miners deadly pneumonia) was very similar, and likely the same, as RaTG13.
A preprint by Rahalkar and Bahulikar (R&B) ( doi: 10.20944/preprints202008.0205.v1 ) notes that the fraction of bacterial genomes in in the RaTG13 “fecal” sample was ABSURDLY low (“only 0.7% in contrast to 70-90% abundance in other fecal swabs from bats”). Something’s weird there.
A more recent weird datapoint: A pre-print Yan referenced ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337384/ ), whose finding (in graphs; it was left unclear in their wording) was indeed that a RaTG13 protein didn’t competently bind their Bat ACE2 samples, but rather their Rat, Mouse, Human, and Pig ACE2. It’s supposedly a horseshoe bat virus (sequenced by the Wuhan lab), so this seems hecka fishy to me.
(Sure, their bat samples weren’t precisely the same species, but they tried 2 species from the same genus. SARS-2 DID bind for their R. macrotis bat sample, so it seems extra-fishy to me that RaTG13 didn’t.).
((...oh. According to the R&B paper about the mineshaft, it was FILTY with rats, bats, poop, and fungus. And the CoV genome showed up in only one of ~280 samples taken. If it’s like that, who the hell knew if it came from a rat or bat?))
At this point, RaTG13 is genuinely looking pretty fishy to me. It might actually take evidence of a conspiracy theory in the other direction for me to go back to neutral on that.
E-Protein Similarity? Meh.
I’m not finding the Protein-E sequence similarity super-convincing in itself, because while the logic is fine, it’s very multiple-hypothesis-testing flavored.
I’m still looking into the ZC45 / ZXC21 claim, which I’m currently feeling skeptical of. Here’s the paper that characterized those: doi: 10.1038/s41426-018-0155-5 . It’s true that it was by people working at “Research Institute for Medicine of Nanjing Command.” However, someone on twitter used BLAST on the E-protein sequence, and found a giant pile of different highly-related SARS-like coronaviruses. I’m trying to replicate that analysis using BLAST myself, and at a skim the 100% results are all more SARS-CoV-2, and the close (95%) results are damned diverse. …I don’t see ZC in them, it looks like it wasn’t uploaded. Ugh. (The E-protein is only 75 amino acids long anyway. https://www.ncbi.nlm.nih.gov/protein/QIH45055.1 )
A different paper mentions extreme S2-protein similarity of early COVID-19 to ZC45 , but that protein is highly-conserved. That makes this a less surprising or meaningful result. (E was claimed to be fast-evolving, so its identicality would have been more surprising, but I couldn’t confirm it.) https://doi.org/10.1080/22221751.2020.1719902
Other
I think Yan offers a reasonable argument that a method could have been used that avoids obvious genetic-modification “stitches,” instead using methods that are hard to distinguish from natural recombination events (ex: recombination in yeast). Sounds totally possible to me.
The fact that the early SARS-CoV-2 samples were already quite adapted to human ACE2 and didn’t have the rapid-evolution you’d expect from a fresh zoonotic infection is something a friend of mine had previously noted, probably after reading the following paper (recommended): https://www.biorxiv.org/content/10.1101/2020.05.01.073262v1 (Zhan, Deverman, Chan). This fact does seem fishy, and had already pushed me a bit towards the “Wuhan lab adaptation & escape” theory.
Wuhan has <1% of the population of China, so this is (order of magnitude) a 100:1 update.
I agree that this is technically correct, but the prior for “escaped specifically from a lab in Wuhan” is also probably ~100 times lower than the prior for “escaped from any biolab in China”, which makes this sentence feel odd to me. I feel like I have reasonable priors for “direct human-to-human transmission” vs. “accidentally released from a lab”, but don’t have good priors for “escaped specifically from a lab in Wuhan”.
I agree that this is technically correct, but the prior for “escaped specifically from a lab in Wuhan” is also probably ~100 times lower than the prior for “escaped from any biolab in China”
I don’t think this is true. The Wuhan Institute of Virology is the only biolab in China with a BSL-4 certification, and therefore is probably the only biolab in China which could legally have been studying this class of virus. While the BSL-3 Chinese Institute of Virology in Beijing studied SARS in the past and had laboratory escapes, I expect all of that research to have been shut down or moved, given the history, and I expect a review of Chinese publications will not find any studies involving live virus testing outside of WIV. While the existence of one or two more labs in China studying SARS would not be super surprising, the existence of 100 would be extremely surprising, and would be a major scandal in itself.
Woah. That’s an important piece of info. The lab in Wuhan is the only lab in China allowed to deal with this class of virus. That’s very suggestive info indeed.
That’s overstating it. They’re the only BSL-4 lab. Whether BSL-3 labs were allowed to deal with this class of virus, is something that someone should research.
My understanding is that SARS-CoV-1 is generally treated as a BSL-3 pathogen or a BSL-2 pathogen (for routine diagnostics and other relatively safe work) and not BSL-4. At the time of the outbreak, SARS-CoV-2 would have been a random animal coronavirus that hadn’t yet infected humans, so I’d be surprised if it had more stringent requirements.
Your OP currently states: “a lab studying that class of viruses, of which there is currently only one.” If I’m right that you’re not currently confident this is the case, it might be worth adding some kind of caveat or epistemic status flag or something.
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Some evidence:
A 2017 news article in Nature about the Wuhan Institute of Virology suggests China doesn’t require a BSL-4 for SARS-CoV-1. “Future plans include studying the pathogen that causes SARS, which also doesn’t require a BSL-4 lab.”
Non-propagative diagnostic laboratory work including, sequencing, nucleic acid amplification test (NAAT) on clinical specimens from patients who are suspected or confirmed to be infected with nCoV, should be conducted adopting practices …. … in the interim, Biosafety Level 2 (BSL-2) in the WHO Laboratory Biosafety Manual, 3rd edition remains appropriate until the 4th edition replaces it.
Handling of material with high concentrations of live virus (such as when performing virus propagation, virus isolation or neutralization assays) or large volumes of infectious materials should be performed only by properly trained and competent personnel in laboratories capable of meeting additional essential containment requirements and practices, i.e. BSL-3.
It would be important information if it was true. But is it true?
(SARSr-CoV) makes the BSL-4 list on Wikipedia but coronaviruses are widespread in a lot of species and I can’t find any evidence that they are restricted to BSL-4 labs.
Do we have any good sense of the extent to which researchers from the Wuhan Institute of Virology are flying out across China to investigate novel pathogens or sites where novel pathogens might emerge?
I am now reasonably convinced (p>0.8) that SARS-CoV-2 originated in an accidental laboratory escape from the Wuhan Institute of Virology.
1. If SARS-CoV-2 originated in a non-laboratory zoonotic transmission, then the geographic location of the initial outbreak would be drawn from a distribution which is approximately uniformly distributed over China (population-weighted); whereas if it originated in a laboratory, the geographic location is drawn from the commuting region of a lab studying that class of viruses, of which there is currently only one. Wuhan has <1% of the population of China, so this is (order of magnitude) a 100:1 update.
2. No factor other than the presence of the Wuhan Institute of Virology and related biotech organizations distinguishes Wuhan or Hubei from the rest of China. It is not the location of the bat-caves that SARS was found in; those are in Yunnan. It is not the location of any previous outbreaks. It does not have documented higher consumption of bats than the rest of China.
3. There have been publicly reported laboratory escapes of SARS twice before in Beijing, so we know this class of virus is difficult to contain in a laboratory setting.
4. We know that the Wuhan Institute of Virology was studying SARS-like bat coronaviruses. As reported in the Washington Post today, US diplomats had expressed serious concerns about the lab’s safety.
5. China has adopted a policy of suppressing research into the origins of SARS-CoV-2, which they would not have done if they expected that research to clear them of scandal. Some Chinese officials are in a position to know.
To be clear, I don’t think this was an intentional release. I don’t think it was intended for use as a bioweapon. I don’t think it underwent genetic engineering or gain-of-function research, although nothing about it conclusively rules this out. I think the researchers had good intentions, and screwed up.
This Feb. 20th Twitter thread from Trevor Bedford argues against the lab-escape scenario. Do read the whole thing, but I’d say that the key points not addressed in parent comment are:
But apparently SARSCoV2 isn’t that. (See pic.)
One scenario I recall seeing somewhere that would reconcile lab-escape with data points 3 & 4 above is that some low-level WIV employee or contractor might have sold some purloined lab animals to the wet market. No idea how plausible that is.
Given that there’s the claim from Botao Xiao’s The possible origins of 2019-nCoV coronavirus, that this seafood market was located 300m from a lab (which might or might not be true), this market doesn’t seem like it reduces chances.
If it was a lab-escape and the CCP knew early enough, they could simply manufacture the data to point at the market as the origin.
We need to update down on any complex, technical datapoint that we don’t fully understand, as China has surely paid researchers to manufacture hard-to-evaluate evidence for its own benefit (regardless of the truth of the accusation). This is a classic technique that I have seen a lot in propaganda against laypeople, and there is every reason it should have been employed against the “smart” people in the current coronavirus situation.
The most recent episode of the 80k podcast had Andy Weber on it. He was the US Assistant Secretary of Defense, “responsible for biological and other weapons of mass destruction”.
Towards the end of the episode he casually drops quite the bomb:
The included link is to a statement from the US Embassy in Georgia, which to me seems surprisingly blunt, calling out the CCP for obfuscation, and documenting events at the WIV, going so far as to speculate that they were doing bio-weapons research there.
What about allegations that a pangolin was involved? Would they have had pangolins in the lab as well or is the evidence about pangolin involvement dubious in the first place?
Edit: Wasn’t meant as a joke. My point is why did initial analyses conclude that the SARS-Cov-2 virus is adapted to receptors of animals other than bats, suggesting that it had an intermediary host, quite likely a pangolin. This contradicts the story of “bat researchers kept bat-only virus in a lab and accidentally released it.”
I think it’s probably a virus that was merely identified in pangolins, but whose primary host is probably not pangolins.
The pangolins they sequenced weren’t asymptomatic carriers at all; they were sad smuggled specimens that were dying of many different diseases simultaneously.
I looked into this semi-recently, and wrote up something here.
The pangolins were apprehended in Guangxi, which shares some of its border with Yunnan. Neither of these provinces are directly contiguous with Hubei (Wuhan’s province), fwiw. (map)
How do you know there’s only one lab in china studying these viruses?
This is an assumption.
While it might be comparatively correct, I’m not sure about the magnitude. Under the circumstances, perhaps we should consider the possibility that there is something we don’t know about Wuhan that makes it more likely.
That’s nice to know.
shared here: https://pandemic.metaculus.com/questions/3681/will-it-turn-out-that-covid-19-originated-inside-a-research-lab-in-hubei/
Maybe they don’t know whether it escaped or not. Maybe they just think there is a chance that the evidence will implicate them and they figure it’s not worth the risk as there’ll only be consequences if there is definitely proof that it escaped from one of their labs and not mere speculation.
Or maybe they want to argue that it didn’t come from China? I think they’ve already been pushing this angle.
Not sure if you have seen this yet, but they conclude:
Are they assuming a false premise or making an error in reasoning somewhere?
First, a clarification: whether SARS-CoV-2 was laboratory-constructed or manipulated is a separate question from whether it escaped from a lab. The main reason a lab would be working with SARS-like coronavirus is to test drugs against it in preparation for a possible future outbreak from a zoonotic source; those experiments would involve culturing it, but not manipulating it.
But also: If it had been the subject of gain-of-function research, this probably wouldn’t be detectable. The example I’m most familiar with, the controversial 2012 US A/H5N1 gain of function study, used a method which would not have left any genetic evidence of manipulation.
The article says:
and
I think the article just says that the virus did not undergo genetic engineering or gain-of-function research, which is also what Jim says above.
Ah, yes: their headline is very misleading then! It currently reads “The coronavirus did not escape from a lab. Here’s how we know.”
I’ll shoot the editor an email and see if they can correct it.
EDIT: Here’s me complaining about the headline on Twitter.
Genetic engineering is ruled out, but gain-of-function research isn’t.
Chinese virology researcher released something claiming that SARS-2 might even be genetically-manipulated after all? After assessing, I’m not really convinced of the GMO claims, but the RaTG13 story definitely seems to have something weird going on.
Claims that the RaTG13 genome release was a cover-up (it does look like something’s fishy with RaTG13, although it might be different than Yan thinks). Claims ZC45 and/or ZXC21 was the actual backbone (I’m feeling super-skeptical of this bit, but it has been hard for me to confirm either way).
https://zenodo.org/record/4028830#.X2EJo5NKj0v (aka Yan Report)
RaTG13 Looks Fishy
Looks like something fishy happened with RaTG13, although I’m not convinced that genetic modification was involved. This is an argument built on pre-prints, but they appear to offer several different lines of evidence that something weird happened here.
Simplest story (via R&B): It looks like people first sequenced this virus in 2016, under the name “BtCOV/4991”, using mine samples from 2013. And for some reason, WIV re-released the sequence as “RaTG13″ at a later date?
(edit: I may have just had a misunderstanding. Maybe BtCOV/4991 is the name of the virus as sequenced from miner-lungs, RaTG13 is the name of the virus as sequenced from floor droppings? But in that case, why is the “fecal” sample reading so weirdly low-bacteria? And they probably are embarrassed that it took them that long to sequence the fecal samples, and should be.)
A paper by by Indian researchers Rahalkar and Bahulikar ( https://doi.org/10.20944/preprints202005.0322.v1 ) notes that BtCoV/4991 sequenced in 2016 by the same Wuhan Virology Institute researchers (and taken from 2013 samples of a mineshaft that gave miners deadly pneumonia) was very similar, and likely the same, as RaTG13.
A preprint by Rahalkar and Bahulikar (R&B) ( doi: 10.20944/preprints202008.0205.v1 ) notes that the fraction of bacterial genomes in in the RaTG13 “fecal” sample was ABSURDLY low (“only 0.7% in contrast to 70-90% abundance in other fecal swabs from bats”). Something’s weird there.
A more recent weird datapoint: A pre-print Yan referenced ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337384/ ), whose finding (in graphs; it was left unclear in their wording) was indeed that a RaTG13 protein didn’t competently bind their Bat ACE2 samples, but rather their Rat, Mouse, Human, and Pig ACE2. It’s supposedly a horseshoe bat virus (sequenced by the Wuhan lab), so this seems hecka fishy to me.
(Sure, their bat samples weren’t precisely the same species, but they tried 2 species from the same genus. SARS-2 DID bind for their R. macrotis bat sample, so it seems extra-fishy to me that RaTG13 didn’t.).
((...oh. According to the R&B paper about the mineshaft, it was FILTY with rats, bats, poop, and fungus. And the CoV genome showed up in only one of ~280 samples taken. If it’s like that, who the hell knew if it came from a rat or bat?))
At this point, RaTG13 is genuinely looking pretty fishy to me. It might actually take evidence of a conspiracy theory in the other direction for me to go back to neutral on that.
E-Protein Similarity? Meh.
I’m not finding the Protein-E sequence similarity super-convincing in itself, because while the logic is fine, it’s very multiple-hypothesis-testing flavored.
I’m still looking into the ZC45 / ZXC21 claim, which I’m currently feeling skeptical of. Here’s the paper that characterized those: doi: 10.1038/s41426-018-0155-5 . It’s true that it was by people working at “Research Institute for Medicine of Nanjing Command.” However, someone on twitter used BLAST on the E-protein sequence, and found a giant pile of different highly-related SARS-like coronaviruses. I’m trying to replicate that analysis using BLAST myself, and at a skim the 100% results are all more SARS-CoV-2, and the close (95%) results are damned diverse. …I don’t see ZC in them, it looks like it wasn’t uploaded. Ugh. (The E-protein is only 75 amino acids long anyway. https://www.ncbi.nlm.nih.gov/protein/QIH45055.1 )
A different paper mentions extreme S2-protein similarity of early COVID-19 to ZC45 , but that protein is highly-conserved. That makes this a less surprising or meaningful result. (E was claimed to be fast-evolving, so its identicality would have been more surprising, but I couldn’t confirm it.) https://doi.org/10.1080/22221751.2020.1719902
Other
I think Yan offers a reasonable argument that a method could have been used that avoids obvious genetic-modification “stitches,” instead using methods that are hard to distinguish from natural recombination events (ex: recombination in yeast). Sounds totally possible to me.
The fact that the early SARS-CoV-2 samples were already quite adapted to human ACE2 and didn’t have the rapid-evolution you’d expect from a fresh zoonotic infection is something a friend of mine had previously noted, probably after reading the following paper (recommended): https://www.biorxiv.org/content/10.1101/2020.05.01.073262v1 (Zhan, Deverman, Chan). This fact does seem fishy, and had already pushed me a bit towards the “Wuhan lab adaptation & escape” theory.
I agree that this is technically correct, but the prior for “escaped specifically from a lab in Wuhan” is also probably ~100 times lower than the prior for “escaped from any biolab in China”, which makes this sentence feel odd to me. I feel like I have reasonable priors for “direct human-to-human transmission” vs. “accidentally released from a lab”, but don’t have good priors for “escaped specifically from a lab in Wuhan”.
I don’t think this is true. The Wuhan Institute of Virology is the only biolab in China with a BSL-4 certification, and therefore is probably the only biolab in China which could legally have been studying this class of virus. While the BSL-3 Chinese Institute of Virology in Beijing studied SARS in the past and had laboratory escapes, I expect all of that research to have been shut down or moved, given the history, and I expect a review of Chinese publications will not find any studies involving live virus testing outside of WIV. While the existence of one or two more labs in China studying SARS would not be super surprising, the existence of 100 would be extremely surprising, and would be a major scandal in itself.
Woah. That’s an important piece of info. The lab in Wuhan is the only lab in China allowed to deal with this class of virus. That’s very suggestive info indeed.
That’s overstating it. They’re the only BSL-4 lab. Whether BSL-3 labs were allowed to deal with this class of virus, is something that someone should research.
[I’m not an expert.]
My understanding is that SARS-CoV-1 is generally treated as a BSL-3 pathogen or a BSL-2 pathogen (for routine diagnostics and other relatively safe work) and not BSL-4. At the time of the outbreak, SARS-CoV-2 would have been a random animal coronavirus that hadn’t yet infected humans, so I’d be surprised if it had more stringent requirements.
Your OP currently states: “a lab studying that class of viruses, of which there is currently only one.” If I’m right that you’re not currently confident this is the case, it might be worth adding some kind of caveat or epistemic status flag or something.
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Some evidence:
A 2017 news article in Nature about the Wuhan Institute of Virology suggests China doesn’t require a BSL-4 for SARS-CoV-1. “Future plans include studying the pathogen that causes SARS, which also doesn’t require a BSL-4 lab.”
CDC’s current interim biosafety guidelines on working with SARS-CoV-2 recommend BSL-3 or BSL-2.
WHO biosafety guidelines from 2003 recommend BSL-3 or BSL-2 for SARS-CoV-1. I don’t know if these are up to date.
Outdated CDC guidelines recommend BSL-3 or BSL-2 for SARS-CoV-1. Couldn’t very quickly Google anything current.
Do you still think there’s a >80% chance that this was a lab release?
Thank you for the correction.
Did anyone do some research?
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(SARSr-CoV) makes the BSL-4 list on Wikipedia.
But what’s the probability that animal-based coronaviruses (being very widespread in a lot of species) were restricted to BSL-4 labs?
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COVID19 and BSL according to:
W.H.O. Laboratory biosafety guidance related to the novel coronavirus (2019-nCoV)
The CDC: Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)
It would be important information if it was true. But is it true?
(SARSr-CoV) makes the BSL-4 list on Wikipedia but coronaviruses are widespread in a lot of species and I can’t find any evidence that they are restricted to BSL-4 labs.
Ok, that makes sense to me. I didn’t have much of a prior on the Wuhan lab being much more likely to have been involved in this kind of research.
Do we have any good sense of the extent to which researchers from the Wuhan Institute of Virology are flying out across China to investigate novel pathogens or sites where novel pathogens might emerge?