My favorite quote from the article: Fourth, for the first time it made me see the coronavirus as one of God’s biggest and funniest jokes. Think about it. Either a zoonotic virus crossed over to humans fifteen miles from the biggest coronavirus laboratory in the Eastern Hemisphere. Or a lab leak virus first rose to public attention right near a raccoon-dog stall in a wet market. Either way is one of the century’s biggest coincidences, designed by some cosmic joker who wanted to keep the debate stayed acrimonious for years to come
> biggest coronavirus laboratory in the Eastern Hemisphere.
A laboratory (and nearby university) that was carrying out risky gain of function experiments with US funding, as finally admitted to in recent congressional hearings.
I guess this meme will never die? It absolutely was not, to the point that Dr. Shi used blood samples from Wuhan as negative controls. The closest known bat viruses were collected around Yunnan (~900 miles away), and in Southeast Asia.
EDIT: And since my comment is downvoted, here's a reference from Dr. Shi herself:
> 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.
No one expected natural spillover near Wuhan. That doesn't mean it didn't happen, but the claim that the WIV was situated based on that is unequivocally false.
> A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.
I am assuming that sars-cov-2 has a human-specific furin cleavage site, and that the others are less-so.
The text below is from an article posted elsewhere on this page (which is obviously biased).
"All you really need to know about furin cleavage sites is that SARS-CoV-2 is the first and only SARS-like virus, out of many hundreds that have been described, ever to show up with a furin cleavage site in its spike gene. Sure enough, it’s an insertion, not a mutation, and it’s at the S1/S2 junction."
The Spiked artcle is dominated by impassioned rhetoric and lacks dull science.
He seeks to persuade with bombast:
All you really need to know about furin cleavage sites is that SARS-CoV-2 is the first and only SARS-like virus, out of many hundreds that have been described, ever to show up with a furin cleavage site in its spike gene. Sure enough, it’s an insertion, not a mutation, and it’s at the S1/S2 junction.
and ignores dull studies:
*Furin cleavage sites naturally occur in coronaviruses*
The spike protein is a focused target of COVID-19, a pandemic caused by SARS-CoV-2. A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.
Like many people he has studied science. As the twig was bent so he bends his view of science towards a pro fracking, Euroskeptic, Conservative House of Lords, investment banker PoV.
Furin cleavage sites are common among coronaviruses, but rare among sarbecoviruses (SARS-like viruses). The presence of the FCS is not determinative, but it's notable, especially since the EHA had proposed in DEFUSE to engineer sarbecoviruses with a human-designed FCS.
In that proposal, the WIV would have worked only on collection of novel viruses from nature, with genetic engineering at Baric's lab at UNC. DARPA also declined to fund that proposal, on safety grounds. The Times reported an intelligence leak stating the work continued with other funders at the WIV only, though I haven't seen confirmation beyond that one article.
> The investigators spoke to two researchers working at a US laboratory who were collaborating with the Wuhan institute at the time of the outbreak. They said the Wuhan scientists had inserted furin cleavage sites into viruses in 2019 in exactly the way proposed in Daszak’s failed funding application to Darpa.
> SARS-CoV-2 has continued to evolve as it moves through the population, and we have learned more about its pathogenicity and transmission determinants. As previously commented in The Lancet Microbe, one of these determinants is the unusual furin cleavage site (FCS) on its spike protein.1 While it has been proposed that the FCS might have been engineered, it is becoming clearer that natural selection is, in fact, the driving factor in its acquisition and functionality, through recombination and epistasis. [1]
I’m hardly qualified to evaluate the evidence for either argument but it seems that it’s hardly a clear cut case of engineering.
Peter Miller addressed this in the Rootclaim debate[1] so I'll quote from there:
> Even if WIV did try to create COVID, they couldn’t have. As Yuri said, COVID looks like BANAL-52 plus a furin cleavage site. But WIV didn’t have BANAL-52. It wasn’t discovered until after the COVID pandemic started, when scientists scoured the area for potential COVID relatives. WIV had a more distant COVID relative, RATG-13. But you can’t create COVID from RATG-13; they’re too different. You would need BANAL-52, or some as-yet-undiscovered extremely close relative. WIV had neither.
> Are we sure they had neither? Yes. Remember, WIV’s whole job was looking for new coronaviruses. They published lists of which ones they had found pretty regularly. They published their last list in mid-2019, just a few months before the pandemic. Although lab leak proponents claimed these lists showed weird discrepancies, this was just their inability to keep names consistent, and all the lists showed basically the same viruses (plus a few extra on the later ones, as they kept discovering more). The lists didn’t include BANAL-52 or any other suitable COVID relatives - only RATG-13, which isn’t close enough to work.
> Could they have been keeping their discovery of BANAL-52 secret? No. Pre-pandemic, there was nothing interesting about it; our understanding of virology wasn’t good enough to point this out as a potential pandemic candidate. WIV did its gain-of-function research openly and proudly (before the pandemic, gain-of-function wasn’t as unpopular as it is now) so it’s not like they wanted to keep it secret because they might gain-of-function it later. Their lists very clearly showed they had no virus they could create COVID from, and they had no reason to hide it if they did.
> COVID’s furin cleavage site is admittedly unusual. But it’s unusual in a way that looks natural rather than man-made. Labs don’t usually add furin cleavage sites through nucleotide insertions (they usually mutate what’s already there). On the other hand, viruses get weird insertions of 12+ nucleotides in nature. For example, HKU1 is another emergent Chinese coronavirus that caused a small outbreak of pneumonia in 2004. It had a 15 nucleotide insertion right next to its furin cleavage site. Later strains of COVID got further 12 - 15 nucleotide insertions. Plenty of flus have 12 to 15 nucleotide insertions compared to other earlier flu strains.
Peter goes further into it in the link. Those interested can dig in further.
Miller's claim rests on the assumption that the WIV would have published every virus it had collected. That's a facially odd claim--there's no research group in the world without unpublished work in progress, since even with no deliberate attempt to conceal, it takes time to write stuff up. We also know it to be specifically false here, since Deigin and some other authors found an unpublished merbecovirus in contamination of published datasets from agricultural sequencing on equipment shared with the WIV:
That merbecovirus is unrelated to SARS-CoV-2; but with unequivocal evidence that the WIV had at least one unpublished virus, it's hard to reject the possibility they had two.
As for previous attempts from the same authors (e.g. Pekar's "The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2"), it starts with low-quality data from the early pandemic, does some complicated math, and concludes that the pandemic originated from zoonotic transmission in the Wuhan market, "beyond reasonable doubt". It therefore wasn't a research accident, and there is no need for increased regulation of high-risk research of the type performed at the WIV.
The details can and should be criticized, and I linked a detailed rebuttal in the other post. But fundamentally, how could any model reach any conclusion with the confidence they express? Western authorities had prior warning, much more advanced surveillance, and good knowledge of where the virus might get introduced (by necessity, an airport or seaport)--and yet they succeeded in tracing almost zero cases back to their introduction. So how could anyone possibly believe that a much cruder set of tools has succeeded at the more difficult task of determining the pandemic's earliest origins?
Anecdotal as it may be, an investor in a company I used to work for was from Wuhan. He paid $80k USD to get out of the country in December 2019. They knew it was bad then and anyone who could was fleeing.
>Using data made available by the Chinese government...
They even kind of acknowledge this in the final line of the paper
> Finally, the publicly available genomic and epidemiological data from the start of the COVID-19 pandemic remain incomplete, and future data from this time could shed further light on hypotheses regarding its emergence
Not just taking into account the furin cleavage site issue, but there is every incentive for the scientific community and those in power to blame this on the wet market over the lab leak.
I mean it's damning for WIV either way. Even if the virus wasn't a lab leak, isn't the point of the institute to study these viruses ahead of an outbreak in order to protect us? It's like having a marine biologist as a life guard at the beach, you'll get some neat facts about the wild life, but if you get caught in a ripe tide we'll you're out of luck.
This aligns with my prior likely release hypothesis, informed by this excellent deep dive article that looks at a lot of the arguments for either the wet market or the lab: https://www.astralcodexten.com/p/practically-a-book-review-r...
My favorite quote from the article: Fourth, for the first time it made me see the coronavirus as one of God’s biggest and funniest jokes. Think about it. Either a zoonotic virus crossed over to humans fifteen miles from the biggest coronavirus laboratory in the Eastern Hemisphere. Or a lab leak virus first rose to public attention right near a raccoon-dog stall in a wet market. Either way is one of the century’s biggest coincidences, designed by some cosmic joker who wanted to keep the debate stayed acrimonious for years to come
> biggest coronavirus laboratory in the Eastern Hemisphere.
A laboratory (and nearby university) that was carrying out risky gain of function experiments with US funding, as finally admitted to in recent congressional hearings.
Isn't this not a coincidence at all? The research lab was put there because it was known hot spot for wild coronavirus strains.
I guess this meme will never die? It absolutely was not, to the point that Dr. Shi used blood samples from Wuhan as negative controls. The closest known bat viruses were collected around Yunnan (~900 miles away), and in Southeast Asia.
EDIT: And since my comment is downvoted, here's a reference from Dr. Shi herself:
> 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/20210727042832/https://www.scien...
No one expected natural spillover near Wuhan. That doesn't mean it didn't happen, but the claim that the WIV was situated based on that is unequivocally false.
This does not address the furin cleavage site, which I understand is not present on any other coronavirus.
This feature is the lead evidence for a lab leak.
https://en.wikipedia.org/wiki/Furin
> A 12-nt insertion at S1/S2 in the spike coding sequence yields a furin cleavage site, which raised controversy views on origin of the virus. Here we analyzed the phylogenetic relationships of coronavirus spike proteins and mapped furin recognition motif on the tree. Furin cleavage sites occurred independently for multiple times in the evolution of the coronavirus family, supporting the natural occurring hypothesis of SARS-CoV-2.
"Furin cleavage sites naturally occur in coronaviruses" - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/
Just one paper among many, not sure it's as strong evidence as you seem to think.
Overall, current evidence seems to be mostly be pointing to a natural origin, maybe linked to wildlife sold in Wuhan.
Wonder when we'll reach any sort of conclusion to this.
I am assuming that sars-cov-2 has a human-specific furin cleavage site, and that the others are less-so.
The text below is from an article posted elsewhere on this page (which is obviously biased).
"All you really need to know about furin cleavage sites is that SARS-CoV-2 is the first and only SARS-like virus, out of many hundreds that have been described, ever to show up with a furin cleavage site in its spike gene. Sure enough, it’s an insertion, not a mutation, and it’s at the S1/S2 junction."
https://www.spiked-online.com/2024/09/10/there-is-now-no-dou...
You’re seriously quoting an article on spiked-online.com as if it is a truthful and authoritative source?
No, I can’t accept that.
It's written by Matt Ridley, one of the best science writers there is.
The Spiked artcle is dominated by impassioned rhetoric and lacks dull science.
He seeks to persuade with bombast:
and ignores dull studies: ~ https://www.sciencedirect.com/science/article/pii/S187350612...Like many people he has studied science. As the twig was bent so he bends his view of science towards a pro fracking, Euroskeptic, Conservative House of Lords, investment banker PoV.
Furin cleavage sites are common among coronaviruses, but rare among sarbecoviruses (SARS-like viruses). The presence of the FCS is not determinative, but it's notable, especially since the EHA had proposed in DEFUSE to engineer sarbecoviruses with a human-designed FCS.
In that proposal, the WIV would have worked only on collection of novel viruses from nature, with genetic engineering at Baric's lab at UNC. DARPA also declined to fund that proposal, on safety grounds. The Times reported an intelligence leak stating the work continued with other funders at the WIV only, though I haven't seen confirmation beyond that one article.
> The investigators spoke to two researchers working at a US laboratory who were collaborating with the Wuhan institute at the time of the outbreak. They said the Wuhan scientists had inserted furin cleavage sites into viruses in 2019 in exactly the way proposed in Daszak’s failed funding application to Darpa.
https://www.thetimes.com/uk/article/inside-wuhan-lab-covid-p...
> SARS-CoV-2 has continued to evolve as it moves through the population, and we have learned more about its pathogenicity and transmission determinants. As previously commented in The Lancet Microbe, one of these determinants is the unusual furin cleavage site (FCS) on its spike protein.1 While it has been proposed that the FCS might have been engineered, it is becoming clearer that natural selection is, in fact, the driving factor in its acquisition and functionality, through recombination and epistasis. [1]
I’m hardly qualified to evaluate the evidence for either argument but it seems that it’s hardly a clear cut case of engineering.
[1] https://www.thelancet.com/journals/lanmic/article/PIIS2666-5...
Thank you for posting that.
Peter Miller addressed this in the Rootclaim debate[1] so I'll quote from there:
> Even if WIV did try to create COVID, they couldn’t have. As Yuri said, COVID looks like BANAL-52 plus a furin cleavage site. But WIV didn’t have BANAL-52. It wasn’t discovered until after the COVID pandemic started, when scientists scoured the area for potential COVID relatives. WIV had a more distant COVID relative, RATG-13. But you can’t create COVID from RATG-13; they’re too different. You would need BANAL-52, or some as-yet-undiscovered extremely close relative. WIV had neither.
> Are we sure they had neither? Yes. Remember, WIV’s whole job was looking for new coronaviruses. They published lists of which ones they had found pretty regularly. They published their last list in mid-2019, just a few months before the pandemic. Although lab leak proponents claimed these lists showed weird discrepancies, this was just their inability to keep names consistent, and all the lists showed basically the same viruses (plus a few extra on the later ones, as they kept discovering more). The lists didn’t include BANAL-52 or any other suitable COVID relatives - only RATG-13, which isn’t close enough to work.
> Could they have been keeping their discovery of BANAL-52 secret? No. Pre-pandemic, there was nothing interesting about it; our understanding of virology wasn’t good enough to point this out as a potential pandemic candidate. WIV did its gain-of-function research openly and proudly (before the pandemic, gain-of-function wasn’t as unpopular as it is now) so it’s not like they wanted to keep it secret because they might gain-of-function it later. Their lists very clearly showed they had no virus they could create COVID from, and they had no reason to hide it if they did.
> COVID’s furin cleavage site is admittedly unusual. But it’s unusual in a way that looks natural rather than man-made. Labs don’t usually add furin cleavage sites through nucleotide insertions (they usually mutate what’s already there). On the other hand, viruses get weird insertions of 12+ nucleotides in nature. For example, HKU1 is another emergent Chinese coronavirus that caused a small outbreak of pneumonia in 2004. It had a 15 nucleotide insertion right next to its furin cleavage site. Later strains of COVID got further 12 - 15 nucleotide insertions. Plenty of flus have 12 to 15 nucleotide insertions compared to other earlier flu strains.
Peter goes further into it in the link. Those interested can dig in further.
[1]=https://www.astralcodexten.com/p/practically-a-book-review-r...
Miller's claim rests on the assumption that the WIV would have published every virus it had collected. That's a facially odd claim--there's no research group in the world without unpublished work in progress, since even with no deliberate attempt to conceal, it takes time to write stuff up. We also know it to be specifically false here, since Deigin and some other authors found an unpublished merbecovirus in contamination of published datasets from agricultural sequencing on equipment shared with the WIV:
https://pubmed.ncbi.nlm.nih.gov/36865340/
That merbecovirus is unrelated to SARS-CoV-2; but with unequivocal evidence that the WIV had at least one unpublished virus, it's hard to reject the possibility they had two.
That is interesting information.
Perhaps the answer is that both events happened - the furin cleavage escaped the lab on a precursor, which found BANAL-52 in the market.
Relevant paper.
https://www.cell.com/cell/fulltext/S0092-8674(24)00901-2
The paper itself was already submitted and briefly discussed, https://news.ycombinator.com/item?id=41593098
As for previous attempts from the same authors (e.g. Pekar's "The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2"), it starts with low-quality data from the early pandemic, does some complicated math, and concludes that the pandemic originated from zoonotic transmission in the Wuhan market, "beyond reasonable doubt". It therefore wasn't a research accident, and there is no need for increased regulation of high-risk research of the type performed at the WIV.
The details can and should be criticized, and I linked a detailed rebuttal in the other post. But fundamentally, how could any model reach any conclusion with the confidence they express? Western authorities had prior warning, much more advanced surveillance, and good knowledge of where the virus might get introduced (by necessity, an airport or seaport)--and yet they succeeded in tracing almost zero cases back to their introduction. So how could anyone possibly believe that a much cruder set of tools has succeeded at the more difficult task of determining the pandemic's earliest origins?
Anecdotal as it may be, an investor in a company I used to work for was from Wuhan. He paid $80k USD to get out of the country in December 2019. They knew it was bad then and anyone who could was fleeing.
The header to this study should read:
>Using data made available by the Chinese government...
They even kind of acknowledge this in the final line of the paper
> Finally, the publicly available genomic and epidemiological data from the start of the COVID-19 pandemic remain incomplete, and future data from this time could shed further light on hypotheses regarding its emergence
Interesting, very much at odds with Matt Ridley's analysis here: https://www.spiked-online.com/2024/09/10/there-is-now-no-dou...
Not just taking into account the furin cleavage site issue, but there is every incentive for the scientific community and those in power to blame this on the wet market over the lab leak.
Matt Ridley is a journalist with hardly any qualification to conduct an analysis.
It's interesting to read this study... the degree of complexity of the analysis reminds me of a overcomplicated codebase.
Would love to see completely independent analysis before trusting such a large codebase is bug-free.
I mean it's damning for WIV either way. Even if the virus wasn't a lab leak, isn't the point of the institute to study these viruses ahead of an outbreak in order to protect us? It's like having a marine biologist as a life guard at the beach, you'll get some neat facts about the wild life, but if you get caught in a ripe tide we'll you're out of luck.
They didn’t talk about the furin site at all? Hmm
> Team member Ed Holmes at the University of Sydney says
> He was an honorary visiting professor at Fudan University in Shanghai, China, from 2019-2021
Real good timing on his part.
[0]https://en.wikipedia.org/wiki/Edward_C._Holmes
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So we still live in 2020? Hey, that shit is done with, get over it.