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Sure, scientists can continue to debate the fine points of these issues. The evidence doesn't hinge on the two lineages argument. The following review paper lis

Sure, scientists can continue to debate the fine points of these issues. The evidence doesn't hinge on the two lineages argument. The following review paper lists a bunch of other reasons why a zoonotic spillover is more likely including genomic structure, similarity to other endemic coronaviruses which had zoonotic origins, epidemiological evidence surrounding the seafood market, etc. https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf https://www.cell.com/cell/pdf/S0092-8674(21)00991-0.pdf Notice that the review seriously considers the possibility of a lab leak, indicating that this wasn't some off-limits topic even back in 2021. The Lancet letter cites evidence of a natural origin and condemns conspiracy theories. I think that's still largely consistent with the current consensus. Since none of the known samples at the WIV were related to SARS-CoV-2, by definition the truth of the lab leak hypothesis would imply a conspiracy and coverup. I don't think "strongly condemning" something is the same as suppressing public debate about it.

toomim 3y ago
That article has biased interpretations of the data. It discounts circumstantial evidence of a lab origin, while foregrounding circumstantial evidence of zoonotic origin. Neither theory has direct evidence. Nobody has found covid at WIV, and nobody found an animal reservoir that could prove zoonotic origin. All we have are two pieces of circumstantial evidence: (1) Lab origin: Covid was discovered close to the WIV, while it was researching gain-of-function on coronaviruses. (2) Zoonotic origin: Covid was discovered in a wet market, where past coronaviruses have been known to evolve and leap to humans. Yet, that article completely discounts (1) as evidence, while calling the evidence of it occurring near WIV "a coincidence": > There is currently no evidence that SARS-CoV-2 has a laboratory origin. There is no evidence that any early cases had any connection to the WIV, in contrast to the clear epidemiological links to animal markets in Wuhan, nor evidence that the WIV possessed or worked on a progenitor of SARS-CoV-2 prior to the pandemic. The suspicion that SARS-CoV-2 might have a laboratory origin stems from the coincidence that it was first detected in a city that houses a major virological laboratory that studies coronaviruses That is a biased interpretation. Then it goes on to say that (2) does count as evidence, even though there's no reservoir animal that could make the direct connection: > We contend that although the animal reservoir for SARS-CoV2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Certainly, if you discount all the evidence coming from your opposition, and foreground all the evidence that agrees with you, it's going to look like your side is right.
- fasterik 3y ago
  It's not circumstantial evidence in the case of the market, there is direct evidence. You're ignoring the fact that contact tracing of early cases pointed to employees of the market and people who visited the market, and that SARS-CoV-2 was found in environmental samples from the market. On the other hand, there is no contact tracing and no biological sample that leads to the WIV or its employees.
  - tripletao 3y ago
    There's no question that the market was a major cluster, but that doesn't mean it was necessarily the point of introduction. SARS-CoV-2 must have been introduced to other continents at airports or seaports, but that's not where the first major clusters were found there. SARS-CoV-2 has relatively low IFR, and symptoms easily confused with other respiratory illnesses. This means that even with advance warning and good surveillance, many generations of cryptic spread are possible before someone gets sick enough to get tested. I've seen many fine-grained geographic arguments, both for and against unnatural origin, but would generally consider them to be noise given that early under-ascertainment. As to the environmental samples, virus was definitely present in the market, since infected humans were present. A few samples with raccoon dog DNA were found with a few SARS-CoV-2 reads; but almost all the SARS-CoV-2 in that market must have come from infected humans, and there's no evidence those reads didn't too. The correlation between SARS-CoV-2 presence and raccoon dog presence is negative, and that correlation is most positive for non-susceptible animal species; so I again think that's noise. This is from Jesse Bloom's analysis at https://www.biorxiv.org/content/10.1101/2023.04.25.538336v1 https://www.biorxiv.org/content/10.1101/2023.04.25.538336v1
  - toomim 3y ago
    That's direct evidence that covid was in the market, but only circumstantial evidence for where it originated. The market was both (1) close to the lab and (2) a place where nature contacts humans. The lab origin theory says it originated in the lab, and then an infected WIV employee came to the market for lunch or dinner and created a super-spreader. The zoonotic theory says an animal brought it or a precursor to the market, where it possibly mutated and jumped to humans. The existence of covid in the market provides circumstantial evidence for both theories.
tripletao 3y ago
> Notice that the review seriously considers the possibility of a lab leak, indicating that this wasn't some off-limits topic even back in 2021. I don't think you've been following this debate for very long? The authors of the paper you've linked have worked aggressively and prolifically to destroy the reputations of anyone who suggests that SARS-CoV-2 might have arisen from a research accident. One of them described Yuri Deigin's early summary of the evidence for that as a "Turner Diary-esque manifesto". (The Turner Diaries is a novel popular among violent white supremacists, notably including Timothy McVeigh, the Oklahoma City bomber.) https://twitter.com/angie_rasmussen/status/1346232208206381058 https://twitter.com/angie_rasmussen/status/13462322082063810... Their paper includes a strawman of that evidence in order to refute it. If you've mistaken that for serious consideration, then I can't believe you're familiar with the people involved here. Is there a specific piece of evidence for zoonosis that you consider strong, and would be willing to discuss? You mentioned the "two lineages", and I explained why I thought it was weak; but then you dropped it, and mentioned many other pieces of evidence. If we change the topic with each response then this just becomes a Gish gallop, which isn't productive. > I don't think "strongly condemning" something is the same as suppressing public debate about it. Perhaps you don't, but Facebook did--articles like that Lancet correspondence were the justification for the ban that they applied until May 2021. Without the tremendous reputational risks taken by a small number of scientists (Yuri Deigin, Alina Chan, Richard Ebright, etc.), that false consensus could easily have held.
- fasterik 3y ago
  I have no doubt you're more immersed in these debates than I am. I'm just a casual bystander who (admittedly, maybe too credulously) accepts the mainstream view on the topic. However, given that you're primarily citing Twitter threads rather than scientific papers, my heuristic alarm bells are going off. Has anybody published a good summary of the case for the lab leak in any reputable journal or biorxiv that I can take a look at?
  - tripletao 3y ago
    I linked to Alex Washburne's criticism of Pekar (the "two lineages" paper) on biorxiv above, and I believe that's generally sound. (Note that he's got a different preprint alleging genomic evidence that SARS-CoV-2 was assembled using BsaI and BsmBI, which I believe is quite wrong.) That Twitter criticism is from a pseudonymous account, but it's clearly some kind of relevant academic. Prominent journals have been unfortunately willing to publish low-quality work in support of natural zoonosis; I assume you don't think pangolins are the proximal host, but it took Nature more than a year to correct "Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins". David Relman published a note back in 2020, which doesn't say much but does refute the arguments of "Proximal origin": https://www.pnas.org/doi/pdf/10.1073/pnas.2021133117 https://www.pnas.org/doi/pdf/10.1073/pnas.2021133117 There's no more recent summary that I'd recommend. The most notable development since then is perhaps the absence of notable developments; there's still very little evidence on either side, and these arguments often devolve into whether the PRC is covering up a research accident or covering up zoonotic origin. If SARS-CoV-2 did arise from a research accident, then the evidence confirming that may be an intelligence matter (like a leaked document) rather than new science. For example, the Sverdlovsk anthrax incident wasn't confirmed to be a lab accident until the fall of the Soviet Union. Alina Chan's book is written for a popular audience, but well-referenced into the scientific literature. Jesse Bloom does excellent work, but his papers address particular narrow questions, nothing like a summary.

toomim 3y ago

That article has biased interpretations of the data. It discounts circumstantial evidence of a lab origin, while foregrounding circumstantial evidence of zoonotic origin. Neither theory has direct evidence. Nobody has found covid at WIV, and nobody found an animal reservoir that could prove zoonotic origin. All we have are two pieces of circumstantial evidence: (1) Lab origin: Covid was discovered close to the WIV, while it was researching gain-of-function on coronaviruses. (2) Zoonotic origin: Covid was discovered in a wet market, where past coronaviruses have been known to evolve and leap to humans. Yet, that article completely discounts (1) as evidence, while calling the evidence of it occurring near WIV "a coincidence": > There is currently no evidence that SARS-CoV-2 has a laboratory origin. There is no evidence that any early cases had any connection to the WIV, in contrast to the clear epidemiological links to animal markets in Wuhan, nor evidence that the WIV possessed or worked on a progenitor of SARS-CoV-2 prior to the pandemic. The suspicion that SARS-CoV-2 might have a laboratory origin stems from the coincidence that it was first detected in a city that houses a major virological laboratory that studies coronaviruses That is a biased interpretation. Then it goes on to say that (2) does count as evidence, even though there's no reservoir animal that could make the direct connection: > We contend that although the animal reservoir for SARS-CoV2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Certainly, if you discount all the evidence coming from your opposition, and foreground all the evidence that agrees with you, it's going to look like your side is right.

fasterik 3y ago
It's not circumstantial evidence in the case of the market, there is direct evidence. You're ignoring the fact that contact tracing of early cases pointed to employees of the market and people who visited the market, and that SARS-CoV-2 was found in environmental samples from the market. On the other hand, there is no contact tracing and no biological sample that leads to the WIV or its employees.
- tripletao 3y ago
  There's no question that the market was a major cluster, but that doesn't mean it was necessarily the point of introduction. SARS-CoV-2 must have been introduced to other continents at airports or seaports, but that's not where the first major clusters were found there. SARS-CoV-2 has relatively low IFR, and symptoms easily confused with other respiratory illnesses. This means that even with advance warning and good surveillance, many generations of cryptic spread are possible before someone gets sick enough to get tested. I've seen many fine-grained geographic arguments, both for and against unnatural origin, but would generally consider them to be noise given that early under-ascertainment. As to the environmental samples, virus was definitely present in the market, since infected humans were present. A few samples with raccoon dog DNA were found with a few SARS-CoV-2 reads; but almost all the SARS-CoV-2 in that market must have come from infected humans, and there's no evidence those reads didn't too. The correlation between SARS-CoV-2 presence and raccoon dog presence is negative, and that correlation is most positive for non-susceptible animal species; so I again think that's noise. This is from Jesse Bloom's analysis at https://www.biorxiv.org/content/10.1101/2023.04.25.538336v1 https://www.biorxiv.org/content/10.1101/2023.04.25.538336v1
- toomim 3y ago
  That's direct evidence that covid was in the market, but only circumstantial evidence for where it originated. The market was both (1) close to the lab and (2) a place where nature contacts humans. The lab origin theory says it originated in the lab, and then an infected WIV employee came to the market for lunch or dinner and created a super-spreader. The zoonotic theory says an animal brought it or a precursor to the market, where it possibly mutated and jumped to humans. The existence of covid in the market provides circumstantial evidence for both theories.

tripletao 3y ago

> Notice that the review seriously considers the possibility of a lab leak, indicating that this wasn't some off-limits topic even back in 2021. I don't think you've been following this debate for very long? The authors of the paper you've linked have worked aggressively and prolifically to destroy the reputations of anyone who suggests that SARS-CoV-2 might have arisen from a research accident. One of them described Yuri Deigin's early summary of the evidence for that as a "Turner Diary-esque manifesto". (The Turner Diaries is a novel popular among violent white supremacists, notably including Timothy McVeigh, the Oklahoma City bomber.) https://twitter.com/angie_rasmussen/status/1346232208206381058 https://twitter.com/angie_rasmussen/status/13462322082063810... Their paper includes a strawman of that evidence in order to refute it. If you've mistaken that for serious consideration, then I can't believe you're familiar with the people involved here. Is there a specific piece of evidence for zoonosis that you consider strong, and would be willing to discuss? You mentioned the "two lineages", and I explained why I thought it was weak; but then you dropped it, and mentioned many other pieces of evidence. If we change the topic with each response then this just becomes a Gish gallop, which isn't productive. > I don't think "strongly condemning" something is the same as suppressing public debate about it. Perhaps you don't, but Facebook did--articles like that Lancet correspondence were the justification for the ban that they applied until May 2021. Without the tremendous reputational risks taken by a small number of scientists (Yuri Deigin, Alina Chan, Richard Ebright, etc.), that false consensus could easily have held.

fasterik 3y ago
I have no doubt you're more immersed in these debates than I am. I'm just a casual bystander who (admittedly, maybe too credulously) accepts the mainstream view on the topic. However, given that you're primarily citing Twitter threads rather than scientific papers, my heuristic alarm bells are going off. Has anybody published a good summary of the case for the lab leak in any reputable journal or biorxiv that I can take a look at?
- tripletao 3y ago
  I linked to Alex Washburne's criticism of Pekar (the "two lineages" paper) on biorxiv above, and I believe that's generally sound. (Note that he's got a different preprint alleging genomic evidence that SARS-CoV-2 was assembled using BsaI and BsmBI, which I believe is quite wrong.) That Twitter criticism is from a pseudonymous account, but it's clearly some kind of relevant academic. Prominent journals have been unfortunately willing to publish low-quality work in support of natural zoonosis; I assume you don't think pangolins are the proximal host, but it took Nature more than a year to correct "Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins". David Relman published a note back in 2020, which doesn't say much but does refute the arguments of "Proximal origin": https://www.pnas.org/doi/pdf/10.1073/pnas.2021133117 https://www.pnas.org/doi/pdf/10.1073/pnas.2021133117 There's no more recent summary that I'd recommend. The most notable development since then is perhaps the absence of notable developments; there's still very little evidence on either side, and these arguments often devolve into whether the PRC is covering up a research accident or covering up zoonotic origin. If SARS-CoV-2 did arise from a research accident, then the evidence confirming that may be an intelligence matter (like a leaked document) rather than new science. For example, the Sverdlovsk anthrax incident wasn't confirmed to be a lab accident until the fall of the Soviet Union. Alina Chan's book is written for a popular audience, but well-referenced into the scientific literature. Jesse Bloom does excellent work, but his papers address particular narrow questions, nothing like a summary.