Talk:SARS-CoV-2/Archive 10

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Guangdong Phylogenetic Analysis

The following addition by @Rotideypoc41352: to the Reservoir and Origin section insinuates a conclusion that is neither supported in nor by the referenced paper:

A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 showed that the virus type most closely related to the bat coronavirus was most abundant in Guangdong, China, and designated type "A". The predominant type among samples from Wuhan, "B", is more distantly related to the bat coronavirus than the ancestral type "A".

This implies that Guangdong Province may be considered as an alternative location (to Wuhan) for the initial outbreak, since the "A" cluster is marginally closer to the outgroup, RaTG13. Forster et al., on the other hand, suggest that type "B" exhibits a potential founder effect due to the relative propensity of types "A" and "C" to spread abroad. Note that 17 of the 43 cases of type "A" occur outside of East Asia altogether as opposed to six cases in Guangdong and five cases in Wuhan. All six cases in Guangdong occurred in Shenzhen, as well, which Wikipedia describes as "busiest in China when it comes to border crossings;" one viral lineage traced in the paper even follows a Canadian infected with the type "B" variant who travels to Ottawa from Wuhan via Guangdong Province. Furthermore, only four Guangdong cases make up the ancestral T-allele node that the phylogenetic analysis predicts is equally close to RaTG13 as the ancestral C-allele node made up of three Americans and a Chinese national who was not in Guangdong. Four cases and a median network algorithm do not a substitute for Wuhan make, and Forster et al. never made this claim. This selection should either be rewritten to better represent the source cited or stricken from the article. At the very least, the claims should be qualified and disassociated from Guangdong. Vachaknu (talk) 10:59, 30 May 2021 (UTC)

Honestly, the edit request I fulfilled more than a year ago should just be updated with info from more recent review articles. I kept trying to fix the Reservoir section in general because Asifwhale completely changed the meaning of the sentences without updating the sources, but I burned out. Rotideypoc41352 (talk · contribs) 14:11, 30 May 2021 (UTC)

Burnout is understandable given the controversy surrounding SARS-CoV-2 articles here on Wikipedia, and I appreciate your effort to improve this section. I also agree that an update is overdue since the articles cited are, by and large, more than a year old - a cursory search easily turned up three more recent academic sources relevant to the phylogenetic analysis of SARS-CoV-2 origins. If there is an appetite to update the section as a whole, I am willing to lend a hand. If not, I intend to submit an edit request within the week regarding the excerpt above since it is currently misleading. Vachaknu (talk) 22:00, 30 May 2021 (UTC)

@Vachaknu: use Sallard et al 2012, not the others you found per WP:MEDRS. Another reason the article needs updating: any biomedical information citing a primary source (as defined in WP:MEDDEF) should be updated to summarize a more recent literature review or systematic review from reputable, independent journals (or other medical reliable source). Rotideypoc41352 (talk · contribs) 23:12, 30 May 2021 (UTC)

References

Discussion of 4th origin hypothesis

Continuing discussion here after revert by @Hemiauchenia:, regarding the following text from the Reservoir and zoonotic origin section, changes emphasized:

All available evidence suggests that SARS‑CoV‑2 has a natural animal origin and is not genetically engineered. Nevertheless, early in the pandemic, conspiracy theories spread on social media claiming that the virus was bio-engineered by China at the Wuhan Institute of Virology. While some scientists, including David Relman and former CDC director Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute, the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".

A few topics for discussion:

• Could you direct me to the prior consensus for this page? If prior to the latest report, would it be prudent to reconsider that consensus (as we did with COVID-19 when the WHO deprecated the coronavirus disease 2019 name)?
• My intent was not to suggest a plurality of adherants gives weight. I was instead taking WP:DUE as my guide: If a viewpoint is held by a significant minority, then it should be easy to name prominent adherents. I can appreciate that ability to name prominent adherents does not necessarily mean they must be listed by name in the article.
• I wanted to clarify if your primary concern was with the addition of Relman, or if you had concerns with the remainder of the above content (which is transcluded on other pages, namely Investigations into the origin of COVID-19). Per our other discussions, I expected you would have objected to the Redfield inclusion as well. So I wanted to either bring it to your attention if you missed it, or better understand your concern.

Appreciate your time. Bakkster Man (talk) 21:17, 29 April 2021 (UTC)

David Relman has no relevant expertise on coronaviruses, and therefore his opinion is undue. Redfield is probably due as he is actually a virologist and is former head of the CDC. Hemiauchenia (talk) 21:21, 29 April 2021 (UTC)

I agree with that interpretation, thank you. Bakkster Man (talk) 21:24, 29 April 2021 (UTC)

In this link there is a list of the "best experts" that can speak on "the origins of COVID and trying to understand the science underlying a lab leak hypothesis: https://twitter.com/Ayjchan/status/1381261347736981508?s=20, according to Dr. Alina Chan, a Vector and Genetic Engineering Specialist that has written about the debate on social media and journals. Forich (talk) 20:11, 30 April 2021 (UTC)

I would not trust anything coming from Alina Chan, who is just a postdoc (so, not an expert or authority on any topic) and moreover has been a prominent proponent of origin conspiracy theories. JoelleJay (talk) 03:55, 1 May 2021 (UTC)

JoelleJay The list from Chan that Forich linked to can also be found in an editorial she co-authored with Matt Ridley for The Telegraph [1] with citations here [2]. Your spurious claim that Chan is a proponent of conspiracy theories is undue in this discussion. CutePeach (talk) 16:48, 2 May 2021 (UTC)

That she has published the same list elsewhere doesn't make her more reliable. And her twitter feed more than establishes her pro-conspiracy stance. JoelleJay (talk) 01:14, 3 May 2021 (UTC)

If you can demonstrate your acussations on Chan I would agree on not considering her as a source for a list of experts. If you @JoelleJay: are not a top coronavirologist yourself, I suggest we ask in Wikiproject Virology both Chan's status and whether there are any top scientists we should use as the prominent voice of the minority position discussed.Forich (talk) 08:09, 3 May 2021 (UTC)

Well for one she is a post-doc with, apparently, 4 total papers (and only 2 in virology) so she is not an authority in virology whatsoever. For another, she has promoted the anti-natural-origin/lab-engineering conspiracies pushed by DRASTIC/Mr. Deigin (which is apparent by her uncritically citing the Segreto/Deigin BioEssays paper and Rahalkar's Frontiers in paper in her still-unpublished SARS-CoV-2 article). She is one of the more balanced and scientifically-literate natural-origin "skeptics", for sure, but her role is very clearly on the "Twitterverse speculation" side of things rather than the "backed by decades of highly-relevant research experience" side. JoelleJay (talk) 19:03, 3 May 2021 (UTC)

Well, point taken that she has not published extensively, but she is young, and I've read her recent paper on pangolin samples, and it looks like a very good piece of research. She is also good at communicating research in social media, in my opinion. I agree that some of the guys in that DRASTIC troupe seem unreliable, I hope she is not officialy part of them, I tend to read her tweets to stay informed on SARS-CoV-2. I will still ask in Wikiproject Virology, though. Forich (talk) 22:11, 7 May 2021 (UTC)

@Bakkster Man: I have to disagree with Hemiauchenia on this. David Relman is a Microbiologist and Microbiology is a superset of virology and coronavirology. He is especially due as he foretold of a crisis where a SARS coronavirus escapes from a lab to cause a pandemic [3] [4]. Coronavirologist Ralph Baric could also be due, as per [5], [6] and [7], but he hasn’t said much since that last interview.

I think Ebright is the most due, as he is leading on this issue from the front with open letters, while Relman and Lipsitch support more from the rear with commentary in the press. Ebright, Relman and Lipsitch were all founding members of The Cambridge Working Group and they have been advocating for increased regulation of gain of function research for years, due to the inevitability of occupational and laboratory acquired infections. CutePeach (talk) 16:50, 2 May 2021 (UTC)

@CutePeach:I appreciate the list and context of The Cambridge Working Group, very useful. Though I disagree that this make them more due. If anything, I think it would make them less reliable on the topic, since they're potentially more apt to be biased towards seeing the issue they've been advocating against? Which isn't to call their professional credentials into doubt, just a natural challenge for humans (if all you have is a hammer, every problem looks like a nail and all that). Bakkster Man (talk) 12:37, 3 May 2021 (UTC)

@Bakkster Man: I agree that scientists can be biased, but these scientists are not making biased statements. They state only that the theory should not be dismissed and advocate for a transparent and open investigation. I don’t think it's fair to characterize them as biased for advocating for an investigation into the lab leak hypothesis when the prevailing view is that it's "extremely unlikely". Relman declined to be interviewed on this by Fox News in order not to politicize the issue [8], Lipsitch took a lot of criticism for remaining silent for so long [9], and even Ebright, who is the most vocal, does not mention Wuhan Institute of Virology without pointing to the two other labs in the city as the possible sites of origin [10]. These scientists are concerned with the inherent bias that exists within the scientific community and they have always advocated for independent oversight from non scientists, such as bioethics experts. Their advocacy succeeded in pausing funding for certain kinds of GoFR in 2014 and their more recent calls pressured the WHO into widening the scope of its investigations into the origins of COVID-19. I think they are worth including. CutePeach (talk) 07:37, 26 May 2021 (UTC)

@CutePeach: I agree that scientists can be biased, but these scientists are not making biased statements. For clarity, I'm not suggesting these scientists are doing anything wrong. More the 'if all you have is a hammer, every problem looks like a nail' kind of thing. Because of their important work, they may be more likely to lean towards this as the source. It doesn't mean they're wrong, just that they might be more prone to lean this direction. That they advocate for a transparent and open investigation is exactly what I want as well, and once that new investigation has results we'll cover what it says. Per [[WP:CRYSTALBALL}}: "Although currently accepted scientific paradigms may later be rejected, and hypotheses previously held to be controversial or incorrect sometimes become accepted by the scientific community, it is not the place of Wikipedia to venture such projections." Bakkster Man (talk) 13:18, 26 May 2021 (UTC)

They state only that the theory should not be dismissed, which I agree with 100%, and have worked to make sure the articles do not do.

I also wanted to point out the Baric/Graham article (the only journal link above) had this to say the lab theory: In light of social media speculation about possible laboratory manipulation and deliberate and/or accidental release of SARS-CoV-2, Andersen et al. theorize about the virus’ probable origins, emphasizing that the available data argue overwhelmingly against any scientific misconduct or negligence. Bakkster Man (talk) 13:01, 3 May 2021 (UTC)

@Bakkster Man: Thanks for reading the Baric/Graham article. Let's not leave out the part that says Transparency and open scientific investigation will be essential to resolve this issue, noting that forensic evidence of natural escape is currently lacking, and other explanations remain reasonable.. That quote can be paired with what said in his RAI interview: if you're asking about intent, or whether the virus existed beforehand, it would only be in the records of the Institute of Virology in Wuhan [11], and the more recent open letter which confirms his position [12]. Baric has more papers on coronaviruses published in top-tier journals than any other coronavirolagist, so his expert opinion is very much WP:DUE in this article and related articles. CutePeach (talk) 00:11, 24 May 2021 (UTC)

So what change do you think should be made to the article? Bakkster Man (talk) 13:39, 24 May 2021 (UTC)

The change I would suggest, as I explained in our exchange above, is to include the varied number of scientists who signed the Science letter. They are not all Cambridge Working Group members, and I think we can agree either that they can be presented as an opposing POV to the Andersen et al letter, or even as a neutral point of view from a group of scientists of widely backgrounds and positions. Either way is fine for me. CutePeach (talk) 15:34, 26 May 2021 (UTC)

Have a specific suggestion? Because the way I'm interpreting going about this would likely be WP:UNDUE amount of text, for information we already have on the article by way of citing the letter itself. Bakkster Man (talk) 15:39, 26 May 2021 (UTC)

Specific suggestion: create a section on the etiology of the virus, documenting everything that has transpired so far, including the WHO Convened Global Study with China and the report they put out, and the responses it got from the WHO DG and WHO member states, saying "Echoing the WHO Director-General and WHO member states, several scientists, including David Relman of Stanford, Marc Lipsitch of Harvard and Ralph Baric of UNC penned a letter in Science Magazine saying that the WHO's report consideration of evidence supporting a laboratory accident was insufficient and that the two leading theories it assessed were not given balanced consideration". I’m sure you would agree to creating an etiology/origins section in this article, as we have in HIV and other articles on viruses. CutePeach (talk) 09:56, 31 May 2021 (UTC)

I liked the original paragraph posted by Bakkster. An observation to consider is that the premise "some scientists, including David Relman and former CDC director Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute" is not negated (not even weakly) by the follow up: "the March 2021 WHO report on the joint WHO-China study stated that such an explanation is extremely unlikely ", because, statistically, having a likely event by expert opinion can coexist with having the same event be extremely unlikely by some other expert opinion. If we wish to illustrate the strength of authority of the experts, then we may like to put less emphasis on the arrived statement of likelihood, and more emphasis on the authority of the source. Or better yet, we could cite a MEDRS that explicitely summarizes the evidence that allowed the WHO to conclude that it was extremely unlikely, so that we are totally transparent. Forich (talk) 19:56, 30 April 2021 (UTC)

To be more clear, according to a popular scale of likelihood statements (the one used for climate change by the IPCC) a likely statement belong to a range between 66%-90%, and an "extremely likely" statement correspond to a 1% - 5% chance. Divergence of opinions on the scale can not cancel each other unless one is based on better methods or has acces to better evidence. The current phrase puts a "While" conditional prefacing the likely claim followed by the extremely likely claim, which fails to comment on whether the original claim was weak, it only comments on there being several opinions. Forich (talk) 20:04, 30 April 2021 (UTC)

I'm a bit uncertain what you're suggesting, or at least how to accomplish it. I read the current wording (though it could be more clear) as intended to be While *minority opinion*, *majority opinion per MEDRS sources*. Bakkster Man (talk) 20:50, 30 April 2021 (UTC)

Ok, let me propose two versions that address the issue:

• Option 1: "While some individual voices from scientists, including former CDC director Robert R. Redfield, believe it is likely that the virus may have been studied by and escaped from the Institute, sources officially representing International Health Organizations, such as the March 2021 WHO report on the joint WHO-China study stated that such an explanation is extremely unlikely.
• Option 2: "While some scientists, including former CDC director Robert R. Redfield, interpret some circumstantial coincidence as suggestion that it is likely that the virus may have been studied by and escaped from the Institute, the March 2021 WHO report on the joint WHO-China study stated that such an explanation is extremely unlikely, based on insert evidence that supports WHO's conclusion here.

I prefer Option 2, but after reading the WHO report could not find the evidence that dismisses the lab leak hypothesis, perhaps you can help me find it. Forich (talk) 03:01, 1 May 2021 (UTC)

Full arguments against from the WHO report:

Extended content

The closest relatives of SARS-CoV-2 from bats and pangolin are evolutionarily distant from SARSCoV-2. There has been speculation regarding the presence of human ACE2 receptor binding and a furin-cleavage site in SARS-CoV-2, but both have been found in animal viruses as well, and elements of the furin-cleavage site are present in RmYN02 and the new Thailand bat SARSr-CoV. There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019, or genomes that in combination could provide a SARS-CoV-2 genome. Regarding accidental culture, prior to December 2019, there is no evidence of circulation of SARS-CoV-2 among people globally and the surveillance programme in place was limited regarding the number of samples processed and therefore the risk of accidental culturing SARS-CoV-2 in the laboratory is extremely low. The three laboratories in Wuhan working with either CoVs diagnostics and/or CoVs isolation and vaccine development all had high quality biosafety level (BSL3 or 4) facilities that were well-managed, with a staff health monitoring programme with no reporting of COVID-19 compatible respiratory illness during the weeks/months prior to December 2019, and no serological evidence of infection in workers through SARS-CoV-2-specific serology-screening. The Wuhan CDC lab which moved on 2nd December 2019 reported no disruptions or incidents caused by the move. They also reported no storage nor laboratory activities on CoVs or other bat viruses preceding the outbreak.

The difficulty here is the simplest arguments to summarize quickly are the ones based on a lack of relevant data, which is the primary critique of the report. Perhaps I'm just being overly cautious here, but I'd lean towards not trying to summarize. Bakkster Man (talk) 14:33, 1 May 2021 (UTC)

Thanks for bringing the arguments cited in the report against 4th origin. The WHO mission reported that "There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019", which is the main argument, supplemented by their assesment of the lab security standards and the absence of sick staff around the time of the outbreak. I agree that it can be tricky to summarize these arguments. My best effort is this: "While some scientists, including former CDC director Robert R. Redfield, speculate that it is 'likely' that the virus may have been studied by and escaped from the Institute, the March 2021 WHO report on the joint WHO-China study stated that such an explanation is 'extremely unlikely', because their examination of the labs revealed no virus before December 2019 that could have triggered the outbreak, and no signs of any of the concomitant circumstances that are known to accompany accidental leakages". Forich (talk) 22:47, 2 May 2021 (UTC)

References

• There is a piece in the New York Times titled The C.D.C.’s ex-director offers no evidence in favoring speculation that the coronavirus originated in a lab.. If we're adding the opinions of the ex-director as somehow DUE, can we first establish if he's offered any evidence for his speculation, and second decide if we need to name each scientist rebutting this statement? ProcrastinatingReader (talk) 17:21, 2 May 2021 (UTC)

I agree on keeping the mention as brief as possible (do not mention every pro lab leak guy), which leaves us with either: citing one prominent person (either Redford or Ebright), or perhaps citing the most recent open letter co-signed by Ebright, as it represents their collective position. Responding to ProcastinatingReader question, Redford did not disclose any new evidence, but we certainly can not dismiss him as unfamiliar with the circumstances of the pandemic. In fact, he is the one person we can be sure that was shown lots of data and pertinent questions about the pandemic origin in all the meetings he had during the early stages of the pandemic with the White House and the intelligence units. If you have evidence that Redford is not being honest with his assesment, it needs to be backed by RS. Forich (talk) 23:03, 2 May 2021 (UTC)

While Redfield is easily the more prominent, my read of his statement could essentially be boiled down to putting more weight on the open letter's conclusions, which makes it the more meaningful inclusion IMO. Redfield only makes sense for 'identifying prominent adherents' for proving it's a notable minority opinion per WP:DUE Bakkster Man (talk) 12:37, 3 May 2021 (UTC)

I question why there's so much emphasis on one opinion v. the other—as opposed to being clear that it's really not known, and that there may not be an actual consensus at this point. In other words—why focus on which explanation has "more evidence" rather than remain a bit agnostic and clarify that no one at this point really knows? A new article reveals that a report by scientists at Lawrence Livermore undermines the "consensus" argument and our article's assertion that entertaining a possible laboratory origin is a "conspiracy theory":

"A classified study of the origin of SARS-CoV-2 conducted a year ago by scientists at the Lawrence Livermore National Laboratory, the Department of Energy’s premier biodefense research institution, concluded the novel coronavirus at the heart of the current pandemic may have originated in a laboratory in China… the U.S. intelligence community has not been able to discount either theory, nor have the medical or scientific communities produced any consensus as to which theory is correct.

There's also clear evidence that US intelligence agencies believe there is a real possibility the virus escaped from a lab:

"US intelligence agencies still do not know "exactly where, when or how Covid-19 virus was transmitted initially" in China but remain focused on two primary theories, that "it emerged naturally from human contact with infected animals or it was a laboratory accident," the nation's top spy told Senate lawmakers on Wednesday."

This all seems worthy of inclusion, no? The information is newer than the NYT article claiming some sort of "consensus" by both scientists and intelligence agencies. As for the latter, the NYT quotes unnamed officials—as opposed to the DNI quoted by CNN. The above are more recent and are reliable secondary sources, which the WHO report is not. Thanks! Elle Kpyros (talk) 19:22, 4 May 2021 (UTC)

See WP:NOLABLEAK for a sensible round-up of the current state of sourcing. Alexbrn (talk) 19:31, 4 May 2021 (UTC)

One of the reasons why WP:MEDRS says to avoid news reports like those is because there is a long history of news media both making good-faith errors, but more importantly because they tend to create a false balance, making an issue out to be one expert says X vs another expert says Y. That's not generally how science is done. The ABCNews report that you link to is really an excellent (in a bad way) example of this problem. The editors and authors are fundamentally not qualified to assess the sources they are interviewing, and the end result is really worse than nothing at all. I'm not even sure whether intelligence agencies' evaluations are relevant or useful, except to the extent that they might be in a position to confirm a lab leak and have not done so. In the absence of direct intelligence evidence (and even then, consider that intelligence products usually omit their sources for obvious reasons), virologists and epidemiologists would be the people best positioned to determine the origin of the virus. Hyperion35 (talk) 22:19, 5 May 2021 (UTC)

Just to add, for a more specific explanation for why WP:MEDRS frowns upon media sources like these, see the MEDRS section WP:MEDPOP Hyperion35 (talk) 22:21, 5 May 2021 (UTC)

I agree with this assessment. Forich (talk) 22:34, 7 May 2021 (UTC)

David Baltimore

David Baltimore does not have an MD so it is doubtful that he would be an MD reliable source; however, he could perhaps be used as another proponent, like former CDC director Robert R. Redfield, that SARS-CoV-2 might have a lab origin. Baltimore states:[13]

“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

It is David Baltimore, so I will allow the virology experts on this page to hash out what to make of the article and his quote. --Guest2625 (talk) 08:48, 7 May 2021 (UTC)

Given that Baltimore classification is named after him, I think it's going to be a stretch to suggest he's not a notable and qualified individual. I think it's worth pointing out that MEDRS is about WP:BMI, which is broader than pure medicine, and as a biologist/virologist I'd say his credentials are applicable. Doesn't change my view that the theory is fringe, but I definitely think if we're going to mention one proponent Baltimore would be better than Redfield.

My one question is whether the Baltimore quote came from another source, or if he provided the quote directly to Bulletin of the Atomic Scientists, or if they sourced it elsewhere. If we link to a Baltimore quote, we should use the original source. Bakkster Man (talk) 12:31, 7 May 2021 (UTC)

A quick (not really reliable) search suggests the quote comes only from that article. It was first published on medium and the note that it was added after first publication and involvement of Baltimore in the Bulletin suggests a direct provision of the quote (guess it was added later to medium too?). Personuser (talk) 16:25, 7 May 2021 (UTC)

That's my impression, which makes me somewhat hesitant. It's likely a WP:RS, but it's definitely one of the weirder ones. Here's hoping that this gets picked up by a more traditional source to remove that concern. Bakkster Man (talk) 16:49, 7 May 2021 (UTC)

• Any biomedical claims need WP:MEDRS. Weirdo self-published crap, not so much. Alexbrn (talk) 19:31, 7 May 2021 (UTC)
• Whether Baltimore is an expert or not, this is a non-peer-reviewed primary claim. One expert looking at viral genome sequence does not constitute a MEDRS source, and it is impossible to claim that a statement about a viral genome is not biomedical. The ultimate problem is that you can find one expert, somewhere, who will advocate in favor of any fringe or even patently nonsense idea. There are a few biologists who have endorsed Biblical Creationism, for example. Another problem with sourcing a quote from a non-scientific media report is that these sorts of statements aren't qualitative or quantitative. To what extent is Baltimore certain that furine cleavage sites could not have evolved naturally? A real scientist would have to qualify that remark, especially given that the statement "X could not evolve naturally" is one of the most consistently disproven statements in biology.

  Remember, ideally we want peer-reciewed published reviews, or certsin types of reports from major medical organizations. Secondary, not primary. Hyperion35 (talk) 18:55, 8 May 2021 (UTC)

For Redfield we use the NY Times, which probably isn't a MEDRS either. He also stressed that this is nothing more than his opinion. The quote from Baltimore is even less strong, since it's about his first impression. I believe the sentence is worth keeping in some form, but doesn't need any more prominence than it already has. If we really need to make some names, using just Redfield seems the most apropriate soluton, but since we are reporting an opinion an contrapposing it to RSMEDs and general consensus this doesn't seem to require the same reliability as medical claims, rather more careful phrasing. Personuser (talk) 23:14, 8 May 2021 (UTC)

I'm not all that comfortable with the Redfield quote either. I can see an argument that his position probably means that we'll have to mention it, although I do have to say that I cannot imagine any circumstances where the director of my agency would publicly contradict a major report, especially to news media. Part of the problem here is that we have these non-qualified opinions from individuals vs heavily-reviewed secondary reports from groups that are full of qualified statements like "highly unlikely". To a non-expert, the certainty of quotes from experts like Redfield and Baltimore seem more powerful than uncertain statements from a group. To experts, it's the other way around. I mention this because I do understand why some people prefer Redfield and Baltimore, it's the whole "I know/trust this guy, and he's saying it straight, no weasel words". And I know that we'll need to be able to help other editors understand how to think like an expert. Hyperion35 (talk) 12:01, 9 May 2021 (UTC)

• The existing wording was a prime example of WP:FALSEBALANCE ("Some think X, most think Y"). I have rewritten it and added additional sources to make clear where things stand outside of politics and Twitter echo-chambers. RandomCanadian (talk / contribs) 16:02, 9 May 2021 (UTC)

We're definitely getting into tricky territory here. On the one hand, we need to word it carefully not to give false balance. On the other, it's becoming impossible to ignore that this is a significant minority opinion which merits some level of WP:DUE inclusion. But we also can't go so far at to write it off entirely as conspiracy, misinformation, or politics (unless we can cite a WP:RS determining which basket all these prominent adherents fall into, particularly claims of partisan politics). It's extra tricky because the first way I'd think to address it (describe the rationales for the minority proponents, countered by why they're rejected by the mainstream) increases the word count and gets us back into false balance territory. But we need to figure something out, complete abolition outside the Misinformation article isn't going to fly any longer. Bakkster Man (talk) 19:26, 9 May 2021 (UTC)

I mean, it's an opinion, perhaps, but it's an unpublished, unreviewed opinion, stated without any qualifiers. It's being reported only in the popular press. Bear in mind that it doesn't actually need to be written off at all, it doesn't need rebuttal, and it doesn't necessarily have to be "conspiracy, misinformation, or politics". The simple fact is that it's basically unverified speculation, sure it may be speculation by experts, but it's still speculation. Redfield and Baltimore don't need to have any sort of bad intentions to simply be wrong, to fall victim to various logical fallacies, especially in off-the-cuff first take opinions. What matters is that when larger groups of people examine this evidence, they determine that the ides of a lab leak is highly unlikely. We should concentrate on the published secondary sources and not unpublished (in the scientific sense) primary opinions and speculation. Hyperion35 (talk)

My thoughts come primarily from WP:DUE, that this opinion has enough prominent adherents to be worth discussing somewhere on the encyclopedia as a legitimate hypothesis. Certainly not on every page, and definitely with the proper context of the current consensus opinion, but it is DUE a mention. I completely agree, it's probably just a group of people who are used to looking for certain things getting spun up because they found something that can be explained with something that suits their specialty or whatever reason, just the human nature that sees patterns where there are none. But I can't shake that it remains notable that so many are seeing this pattern, and we can't just sweep it under the rug or qualify it all as misinformation or conspiracy (at least not yet). Which is why I'm struggling, the guidelines are at odds, it requires a careful balance between the two, and walking it while hardliners tug in each direction doesn't make for an easy answer. Bakkster Man (talk) 22:55, 9 May 2021 (UTC)

My position is that it is unambiguously WP:FRINGE, and given what most sources tell us, we shouldn't present it as an accepted scientific hypothesis (because that is not how scientific sources describe it). That doesn't preclude us adding DUE statements about the generic topic of conspiracy theories about the origins, which are not limited to just the lab leak. How generic or how precise remains open to some discussion, so long we don't fall into the trap of false balance that I identified. Cheers, RandomCanadian (talk / contribs) 00:30, 10 May 2021 (UTC)

I think this continues to be our point of disagreement, that being FRINGE means it's not an acceptable scientific hypothesis. Not widely accepted, otherwise it would be the mainstream view, but I keep going back to the idea that the WHO wouldn't have evaluated a lab accident as their fourth hypothesis if it weren't a valid - but extremely unlikely - science (which is why they didn't consider "deliberate release or deliberate bioengineering"). And this is why I can't support treating all suggestions of accidental release as conspiracy, that would mean that the WHO published a study regarding a conspiracy theory. To put it another way, we have a MEDRS source stating that "a laboratory incident, reflecting an accidental infection of staff from laboratory activities involving the relevant viruses" is a legitimate scientific hypothesis (falsifiable, etc) and need to treat it as such.

I'd prefer if we kept the discussion to how much of a minority opinion it is, and thus how much weight is due on a given article. I don't think it should be much weight, or on more than one of our articles, but I can't agree with never once mentioning that serious scientists have legitimate reasons they believe this scenario that others believe is 'highly unlikely'. Bakkster Man (talk) 13:27, 10 May 2021 (UTC)

So we need to determine how we judge what is DUE and what is UNDUE. Various papers either mention it in passing, sometimes obtusely ("Andersen et al. theorize about the virus’ probable origins, emphasizing that the available data argue overwhelmingly against any scientific misconduct or negligence"), sometimes more directly ("Conspiracy theories about a possible accidental leak from either of these laboratories known to be experimenting with bats and bat CoVs that has shown some structural similarity to human SARS-CoV-2 has been suggested, but largely dismissed by most authorities." or "Despite these massive online speculations, scientific evidence does not support this accusation of laboratory release theory."). Sometimes it isn't even mentioned (Hu et al. Nat Rev Microbiol, for example). And of course the popular press does mention it, but that shouldn't bear influence on the scientific aspect. The article currently has 2 sentences on it, which seems fine by me: "A few individuals, including former CDC director Robert R. Redfield, have claimed, without evidence, that the virus may have been studied by and escaped from the Institute.[103] Most virologists who have studied coronaviruses consider the possibility very remote,[104][105] and the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".[103][88]" RandomCanadian (talk / contribs) 13:51, 10 May 2021 (UTC)

In general I agree, that our current wording is probably about the right amount of weight on this article. The following MEDRS paper from early this month was posted on the Investigations talk page, and might provide a much cleaner citation than Baltimore, Redfield, or other stated opinions.[14] Though it also prompts a rewording, as it's no longer appropriately described as "a few individuals without evidence". Bakkster Man (talk) 15:04, 10 May 2021 (UTC)

As was mentioned above on the talk page, that paper appears to have been published in an oncology journal. It is unclear as to why the authors chose to publish in an oncology journal, but it does raise some questions as ti whether the journal was able to perform proper peer review. And additionally, it is still a primary source. Hyperion35 (talk) 15:32, 10 May 2021 (UTC)

I share your concerns on the author and chosen journal, similar to my concerns about the Baltimore quote published by the Atomic Scientists. Is it a primary source, though? I thought reviews attempting to sum up the state of research were generally considered secondary. It might be wrong, weak, or a number of other things that mean we don't use it, but it does appear to be secondary to me. Personally, I wouldn't want to use it for suggesting the hypothesis is any more likely than the WHO's conclusion, but for use as a descriptor of the reasons why the scientists who ascribe to the hypothesis would decide to do so, and even then we should replace it if a less problematic source can be found. Bakkster Man (talk) 16:03, 10 May 2021 (UTC)

Hadn't seen it that way. If you can suggest a one sentence addition about said "reasons" it could maybe work, but again it's walking the fine line between DUE/UNDUE as far as the science is concerned. RandomCanadian (talk / contribs) 16:06, 10 May 2021 (UTC)

I agree, it's a fine line. I'll take a pass at this page and see if there's anywhere that makes sense (the Neuropilin-1 + ACE2 + Furin genetics might be the only bit specifically notable to this page), but mostly I'd consider it for the brief description on the Origins page. Bakkster Man (talk) 13:17, 11 May 2021 (UTC)

This could possibly work for some of the arguments, but it's not even in a journal (only a page on the publisher's website) so I'm dubious about its suitability. RandomCanadian (talk / contribs) 16:31, 11 May 2021 (UTC)

Choosing a sentence

To move the editing along, let's have a straw poll. Which version of the sentence should be included in the article? Either:

Option 1. A few individuals, including former CDC director Robert R. Redfield, have claimed, without evidence, that the virus may have been studied by and escaped from the Institute. Or,

Option 2. A few individuals, including virologist and former Caltech president David Baltimore, have claimed, without evidence, that the virus may have been studied by and escaped from the Institute.

Preferences:

• Option 2 is my preference since like other editors have said David Baltimore is the most prominent virologist (given his Nobel prize, virus classification system, and extensive virology lab work) who supports the possibility of a lab origin. He is more prominent than Redfield. He is a good example that there are some individuals in the virology community who support the possible lab origin fringe viewpoint. --Guest2625 (talk) 09:35, 11 May 2021 (UTC)

  Could you add which citations you'd use for each? I feel like that's as much an element of the decision as anything. I'd also like to propose a slight tweak to the 'without evidence'. While it's true there's no direct evidence, the current wording could also give the impression they have no rationale behind their belief. Suggested rewordings: "...believe the genetic adaptations of the virus are most easily explained by study of the virus in culture at the Institute, though there is no evidence of this." Or: "...have claimed the genetic adaptations of the virus could have arisen through study of the virus ex vivo at the Institute, though there is no direct evidence of this." Bakkster Man (talk) 13:11, 11 May 2021 (UTC)

  Why not use "speculate" since it is shorter than "believe without evidence" Forich (talk) 15:45, 11 May 2021 (UTC)

  "Without evidence" is a stronger and more accurate wording. Amongst other, the paper I cite in the section below (Frutos et al.) has, explicitly, "Therefore, although a laboratory accident can never be definitively excluded, there is currently no evidence to support it." RandomCanadian (talk / contribs) 15:50, 11 May 2021 (UTC)

I'd like to make sure we don't give undesired implications with how we use the word 'evidence'. Is their statement truly without any evidence at all (even circumstantial), or just lacking direct evidence? Do we say the same about the cold/food chain which lacks direct evidence? There's no conclusive evidence or direct or intermediary spillover either. I think we can be clear about the weight given these minority/fringe hypotheses, without being overly definitive until we have that definitive conclusion. This is part of why I gave one wording with 'direct evidence'. Bakkster Man (talk) 20:43, 11 May 2021 (UTC)

Alternatives to consider in order of strength of evidence: "speculate" -> "suspect" -> "believe" -> "suggest". You hit a nail in the head with your point about the circumstantial evidence: it is often disregarded as scientifically invalid, as in Andersen's tweets about the lab leak. In his view, you either have direct evidence or no evidence. I hope we can find a middle ground that reflects that circumstantial evidence is one tiny step better than no evidence. Forich (talk) 23:06, 13 May 2021 (UTC)

No good evidence? No convincing evidence? No usable evidence? No definitive evidence? No valid evidence? No high-quality evidence? Not enough evidence? Just throwing words around.

After all, if I take a homeopathic remedy and I get better after that, that is a sort of evidence, but not one that would count in any scientific sense. --Hob Gadling (talk) 14:16, 14 May 2021 (UTC)

Yeah, my point above was mostly that there's not "definitive evidence" for any of the four WHO-evaluated hypotheses, which is why it's such a topic of debate around here. The only thing the WHO stated conclusively was that the virus probably has an animal reservoir, but even then only seemed to say it was likely bats, hedging that it might just be because of increased bat CoV surveillance post-SARS. Evidence still missing that would be considered definitive include: the human index case, the last pre-human transmission viral strain, and a 'chain of custody' showing the path of transmission from point A in reservoir species to point B in the index case (infection via outdoor contact, food chain, or lab contamination).

What evidence is "convincing" and "enough" are the points of opinion on which the mainstream and fringe differ. How we explain this is really the question at hand. Mainstream interprets the evidence one way, a minority come to different conclusions. Bakkster Man (talk) 15:03, 14 May 2021 (UTC)

• Given a choice of the two, I'd rather mention Redfield than Baltimore. Redfield's position at the CDC is really the only reason this is worth mentioning. If it were just Baltimore I'd think it would be ignorable, there's always at least one scientist who will go against scientific consensus, and Nobel laureates are often the ones doing that later in their careers, like Pauling or Margulies. Hyperion35 (talk) 16:51, 11 May 2021 (UTC)

  Didn't express myself on the question, but yeah, CDC position is what makes Redfield mentionable. RandomCanadian (talk / contribs) 17:01, 11 May 2021 (UTC)

• My preference is to not mention any individuals supporting the lab leak theory in this article; that material is better suited for Investigations into the origin of COVID-19. (There are transclusions, so the content is unfortunately linked right now). If I had to pick one name, I would go with the CDC director. User:力 (power~enwiki, π, ν) 18:05, 12 May 2021 (UTC)
• Thinking things over, I might also prefer Redfield, because he is the former CDC director, and the reader is more familiar with the word former director of CDC than either Baltimore or Redfield. The bigger question, which Forich and Bakkster Man raise, is all the qualifiers that are currently hanging around and on the sentence. Such as the sentence before about right-wing echo chambers, and the sentence having the qualifier "without evidence". What would be good if the two letters "The proximal origin of SARS-CoV-2" (March 2020) and "Investigate the origins of COVID-19" (May 2021) were used for the two opposing camps. Ironically, the papers are in the opposing journals Nature and Science. The Anderson paper is the majority position (although dated), since it's been cited a couple thousands times, but clearly the fringe lab possibility is represented by the more recent Science paper. --Guest2625 (talk) 08:32, 14 May 2021 (UTC)

I think with some careful wording, we can better separate the fringe scientific views of the Science letter (indicative of a larger community of adherents), from the literal conspiracy theories. The conspiracies are rightly identified as amplified by right-wing media for political purposes. We just need to phrase that in relation to the scientific views so it doesn't give the impression that the WHO-investigated hypothesis was the conspiracy theory. Perhaps moving the conspiracy line to the end of that paragraph? It moves us out of chronological, but makes the conceptual separation more clear, and reduces the weight we place on the conspiracies (we can just say the possibility has been ruled out). Bakkster Man (talk) 12:51, 14 May 2021 (UTC)

I agree. This is a science article, so the political content and controversy should be minimized or removed. The removal and rewording of the political coat racking (in the form of a sentence or two) from the article will greatly improve the article. --Guest2625 (talk) 09:58, 15 May 2021 (UTC)

• Now that we have the Nature open letter, is that a better source to use? Gets us away from naming anyone on the page (list of authors available in the citation), gets us a worthwhile journal citation instead of a MEDPOP one, and avoids the potential UNDUE implications of saying 'this important person believes this'. Their assertion is also less strong than the Baltimore/Redfield one, suggesting it deserves more thorough study, rather than that it's necessarily more likely than not. This might make for a more easily balanced sentence. Bakkster Man (talk) 12:51, 14 May 2021 (UTC)

I support replacing Redfield with the Science letter (is it Science or Nature, I believe you refer to Science). The authors "call for further inquiry into origins of the coronavirus" which echoes previous calls from US and WHO, as User: RandomCanadian also suggests here. Forich (talk) 22:46, 14 May 2021 (UTC)

I also support the substitution of Redfield with the Science article. The current paragraph is:

Available evidence suggests that SARS‑CoV‑2 has a natural animal origin.[101] Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated.[102] Early in the pandemic, conspiracy theories spread on social media claiming that the virus was bio-engineered by China at the Wuhan Institute of Virology,[103] amplified by echo chambers in the American far-right.[104] A few individuals, including former CDC director Robert R. Redfield, have claimed, without evidence, that the virus may have been studied by and escaped from the Institute.[105] Most virologists who have studied coronaviruses consider the possibility very remote,[106][107] and the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".[105][88]

Proposed new paragraph:

Available evidence suggests that SARS‑CoV‑2 has a natural animal origin.[101] Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated.[102] A few individuals, including a small minority of virologists, have proposed that both an animal origin and an accidental escape of a virus from a lab are feasible hypotheses and should both be investigated.[15] Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote,[106][107] and the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".[105][88]

This form of the paragraph is neutral and limits the politics of the paragraph. --Guest2625 (talk) 09:58, 15 May 2021 (UTC)

It's worth remembering that the lab-leak origin being discussed as a 'feasible hypothesis' remains (in a way) an animal origin. As the WHO report makes clear, intentional engineering of the virus has been ruled out. So I think we need to be more clear on that.

I think we should step back and ask: 1) What do the citable sources say? 2) What do we think is worthwhile and DUE for this article? My take:

• Original reservoir from animals, likely bats.
• Precise origin and pathway uncertain, investigations continue.
• Origin is politically contentious.
• Mainstream considers laboratory-leak origin "extremely unlikely".

From there, it's what to do with the fringe. Do we even mention it here beyond the above points? Do we dismiss it entirely as politically motivated or not evidence-based (IMO, inaccurate), say they weight the available evidence differently (UNDUE weight potential here), or simply leave the rationale for another article? Bakkster Man (talk) 13:59, 17 May 2021 (UTC)

I join Forich and Guest2625 in supporting Bakkster Man's proposal to replace the Redfield quote with the Science letter. I agree also to Bakkster Man's four point breakout of the Science letter, but I would add the author's concern that the two predominant theories were not given balanced consideration.Mysticriver1 (talk) 18:15, 20 May 2021 (UTC)

I think the 'deserves more consideration' is probably the right way to phrase the letter, and is probably language that most will agree is WP:DUE. Bakkster Man (talk) 18:32, 20 May 2021 (UTC)

I think we should mention it the way the letter says it.Mysticriver1 (talk) 18:38, 20 May 2021 (UTC)

Agreed, for reference that was "the two theories were not given balanced consideration". Bakkster Man (talk) 18:54, 20 May 2021 (UTC)

Yes, thanks.Mysticriver1 (talk) 19:00, 20 May 2021 (UTC)

A practical solution to the Undue issue can be this: allocate 1 sentence to lab leak, 1 sentence to frozen food, 2 paragraphs to intermediate jump, 3 paragraphs to direct zoonosis fron bats. The 1 sentence allocated to lab leak requires surgical writing prowess, though. Forich (talk) 20:44, 20 May 2021 (UTC)

I propose the following new revised paragraph:

A. Available evidence suggests that SARS‑CoV‑2 has a natural animal origin.[101] Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated.[102] A few individuals, including some virologists, have proposed that both an animal origin and an accidental escape of a virus from a lab are viable hypotheses and should both be investigated.[16] The lab origin hypothesis assumes the escape of an unpublished natural virus studied at a lab or a strain evolved further in a lab environment of imposed evolutionary pressure.[17][18][19] Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote,[106][107] and the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".[105][88]

This version of the paragraph adds an extra sentence on the lab thing which is about the right amount of material to include in this article on a non-majority hypothesis. --Guest2625 (talk) 08:05, 22 May 2021 (UTC)

Why remove the mentions about actual bollocks? I say one sentence for conspiracy theories in general (to note their existence) and one sentence about the lab leak (as a "possibility about which some have called for more investigation", sourced to the Science letter and newspaper reports of it; not with any of the NON-MEDRS sources [already discussed multiple times over] you present). RandomCanadian (talk / contribs) 14:25, 22 May 2021 (UTC)

Here's another version of the paragraph:

B. Available evidence suggests that SARS‑CoV‑2 has a natural animal origin.[101] Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated.[102] A few individuals, including some virologists, have proposed that both an animal origin and an accidental escape of a virus from a lab are viable hypotheses and should both be investigated.[20] There is no available evidence for the the lab origin hypothesis, which assumes the escape of an unpublished natural virus studied at a lab or a strain evolved further in a lab environment of imposed evolutionary pressure.[21][22][23] Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote,[106][107] and the March 2021 WHO report on the joint WHO-China study stated that such an explanation is "extremely unlikely".[105][88]

This version includes the statement about the lack of available evidence. With this clause the sentence does have a better transition so perhaps is better. --Guest2625 (talk) 09:28, 23 May 2021 (UTC)

• Perhaps there's room to distinguish further? Nearly everyone agrees that further study is required. Whether phrased as finding the definitive origin or ruling out the theory, it's the broadest agreement we have. Should we split that from the minority opinion(s)? Specifically: 1) the lab hypothesis is more likely than others, contrary to the WHO's conclusion, or 2) existing investigations have been performed in an unacceptable manner. Bakkster Man (talk) 14:38, 24 May 2021 (UTC)

Paragraph on lab accident

The wording of the following paragraph is in dispute:

Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated, and, early in the pandemic, conspiracy theories spread on social media claiming that the virus was bio-engineered by China at the Wuhan Institute of Virology, amplified by echo chambers in the American far-right. Others, including politicians and some scientists made unsubstantiated claims that the virus may have accidentally escaped from the Institute. This has led to calls in the media for further investigations into the matter. Most virologists who have studied coronaviruses consider the possibility very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

I think it is fine to live edit the paragraph; however, it might also be beneficial to have a simultaneous conversation here on the talk page. At the moment the paragraph has problems with non-neutral wording, editorializing, and straying from discussing science which is the main theme of this article. Maybe a good way to improve the paragraph is for everyone to provide their ideal version of the paragraph.

I would suggest the following version of the paragraph:

Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated. Some scientists have stated that the virus may have accidentally escaped from the Wuhan Institute of Virology. This has led to calls in the media for further investigations into the matter. Most virologists who have studied coronaviruses consider the possibility very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

The benefit of this version is that it cuts out most of the politics, the wordiness, and keeps the statement about the lab accident to one sentence and the paragraph very brief. --Guest2625 (talk) 09:30, 31 May 2021 (UTC)

The problem is this makes it seem likes it's a WP:GEVAL on-the-one-hand-on-the-other kind of situation where the sourced reality is that in an uncertain situation sensible people embrace that uncertainty (while noting that we have likely scenarios, and unlikely ones) – while meanwhile a vocal mass of wingnuts and conspiracy theorists have embraced the lab leak conspiracy theory based on false evidence and/or no-evidence, while blending their beliefs with political/antivax/racist views. We need to make plain this is how the "balance" is. Alexbrn (talk) 09:40, 31 May 2021 (UTC)

Thank you for the feed back. This new version should address the above concerns:

Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, in the context of global geopolitical tensions, the origin is still hotly debated. Some scientists have said that the virus may have accidentally escaped from the Wuhan Institute of Virology and have asked for an investigation of both possibilities. Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

The benefit of this version is that it trims out some more non-science clutter, and then allows the rebuttal sentence of the majority to directly follow. At the moment there is no false equivalence, since the first sentence in the paragraph clearly states that the available evidence indicates a natural origin. And also, the last sentence minimizes the possibility with both the view of the majority of the scientists and the report of the WHO. --Guest2625 (talk) 11:34, 31 May 2021 (UTC)

We can't use an old source to say a matter is "still hotly debated", per WP:RELTIME. And we need to be clear that it's a debate not within science, but within the domain of politics and conspiracism. We should also include the new Science-Based Medicine source for an expert overview on this question of fringe science.[24] Alexbrn (talk) 11:41, 31 May 2021 (UTC)

Good point about the statement about geopolitical debate causing confusion. The best thing to do is eliminate it an all non-science commentary and keep that material for the non-science articles on the topic. Here are three new versions. The first with no qualifier as concerns the evidence and the two others making mention:

A. Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, some scientists have said that the virus may have accidentally escaped from the Wuhan Institute of Virology and have asked for an investigation of both possibilities. Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

And

B. Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, some scientists have said without direct evidence that the virus may have accidentally escaped from the Wuhan Institute of Virology and have asked for an investigation of both possibilities. Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

And:

C. Available evidence suggests that SARS‑CoV‑2 has a natural animal origin. Nonetheless, some scientists have said with only circumstantial evidence that the virus may have accidentally escaped from the Wuhan Institute of Virology and have asked for an investigation of both possibilities. Most virologists who have studied coronaviruses consider the possibility of a lab origin very remote, and the March 2021 WHO report on the joint WHO–China study stated that such an explanation is "extremely unlikely".

Not quite clear which version is the best. Look forward to hearing other people's feedback and their suggested version of the contested paragraph. --Guest2625 (talk) 11:59, 31 May 2021 (UTC)

These all lose the pertinent point that this is a torch the American far right are carrying. Per WP:GEVAL we need to make clear the "lab leak" is (or is a central pillar of) conspiracy theories, otherwise we risk giving undue prominence to a WP:FRINGE notion. Alexbrn (talk) 12:19, 31 May 2021 (UTC)

Agreed. All of the suggested variants remove, without reason, any and all mentions of politics (whether related to ruled out bollocks or to the lab leak), and thus paint an inaccurate picture of a "scientific controversy" when in fact the lab leak is still considered by best sources to be extremely unlikely, without evidence to support it, and is more political noise than anything else. RandomCanadian (talk / contribs) 18:04, 31 May 2021 (UTC)

While the political side is clearly due on COVID-19 misinformation, I think we need to be careful here. Most notably, to not treat the "unlikely" WP:FRINGE/ALT theory and the politics/conspiracy surrounding and using it as synonymous. Lumping the scientific theory with the conspiracy doesn't necessarily give it WP:DUE weight, it might give it WP:UNDUE dismissal. Perhaps a simple paragraph break between the scientific dismissal of the minority science, and the political (mis-)usage of it, would make this distinction clear. Bakkster Man (talk) 22:43, 31 May 2021 (UTC)

References
References

Extended-confirmed-protected edit request on 4 June 2021

There are currently five list-defined references unused in the article, which is creating an error. 92.24.246.11 (talk) 12:44, 4 June 2021 (UTC)

 Done in revision 1026837835 by Boghog (talk). Rotideypoc41352 (talk · contribs) 15:33, 4 June 2021 (UTC)

Science opinion letter

The current article strongly supports the zoonotic origin theory, relying on the WHO report to call the lab accident hypothesis "extremely unlikely." Today a new letter came out from 18 scientists published as a letter to the journal of Science calls this evaluation not a "balanced consideration" and that both zoonotic and lab leak remain viable: https://www.reuters.com/business/healthcare-pharmaceuticals/origins-covid-19-need-be-investigated-further-leading-scientists-say-2021-05-14/

Not mentioned in this article, but found elsewhere in places like the Wades article, are serious critiques that the WHO report was tainted by serious conflict of interest.

The article should be updated to reflect a more balanced take and not just rely on the WHO report to call the lab leak "extremely unlikely." When I look at the evidence currently, the lab leak explanation is becoming the more parsimonious explanation. Spudst3r (talk) 19:42, 14 May 2021 (UTC)

• This is a non-peer-reviewed letter from several scientists. It is nowhere near the same, jn terms of sourcing, as the WHO report. See MEDRS, please. Also, the letter does not even support a "lab leak" hypothesis, it simply asks for more investigation. But again, it is not peer-reviewed. It is the opinion of a couple of scientists, but they do not show ther work. As for potential COI, please make sure that you fully understand what constitutes COI. And in terms of what yiu see when you look at the evidence, see WP:OR. Also, please consider that if you are not an expert in the field, you should probably take a step back and take some time to familiarize yourself with the research and understand why the current scientific consensus for a wild zoonotic episode exists. Hyperion35 (talk) 21:33, 14 May 2021 (UTC)

  The opinion letter is a WP:PRIMARY piece for the opinion of its authors. They are, at the very best, a very small scientific minority (the other end of the scale is them being nothing more than a routine conspiracy theory grounded in geopolitics and blame-shifting). If you're not happy with the WHO report, we can cite about half a dozen other high-quality sources (some of which do cite the WHO report, showing it is an acceptable source) which say the same thing - see WP:NOLABLEAK. RandomCanadian (talk / contribs) 22:07, 14 May 2021 (UTC)

  Yeah, not a useful source when we have decent WP:MEDRS ones. The fact that some people have tried an end run around the normal scientific process to do a letter if anything sets the seal on the very fringe-iness of it - similar "open letter" sources are available (and of course have been pushed here on en.wiki) for climate change denial, cryonics, etc. So in short, let's continue to follow the best sources and keep it simple! Alexbrn (talk) 12:25, 15 May 2021 (UTC)

There are several secondary sources, namely a NYT and Wall Street journal pieces and countless more. The inclusion is important because it provides more context and the debate in the field. Currently, the page makes it seem like no one supports the idea of a zoonotic origin followed by a lab spillover, but there is support for its validity. WP:FRINGE itself states that The neutral point of view policy requires that all majority and significant-minority positions be included in an article. No MEDRS source rules out this possibility or considered it impossible, and several authorities in the field consider it viable.

Currently, the article accept as gospel the word of the WHO, but a neutral point of view must include also those scientists who disagree or are skeptical of the WHO. The fact that there are such opinions in the field cannot be left out. Eccekevin (talk) 03:43, 16 May 2021 (UTC)

It's clear it's "supported" (odd concept) by conspiracy theorists and politically-motivated amateurs online, per the cited sources. As a possibility, it's "valid" in the sense it's possible but extremely unlikely. The sources say these things so Wikipedia does too. If you want to undercut the WHO, you need a decent source, not journalism. Alexbrn (talk) 03:51, 16 May 2021 (UTC)

But that is the issue. Currently, this Wikipedia page does not include any information on the Science letter or any of the other high-profile scientists who disagree with the WHO. Eccekevin (talk) 04:06, 16 May 2021 (UTC)

If there are scholarly secondary sources showing this is due (i.e. that discuss "the letter"), then that may be possible. But if such sources are ignoring it and it's only getting traction in lay press - then no. There will always be rogue scientists. Alexbrn (talk) 04:12, 16 May 2021 (UTC)

Is Alina Chan really a prominent scientist? This article is not for a blow-by-blow account of leak claims and calls for investigation, that should be in Investigations into the origins of COVID-19. This is a brief summary paragraph that the lab leak claims are considered unlikely by the majority of scientists, including the letter is getting into the weeds. There are thousands of researchers who have worked on COVID-19, why do these 16 matter in particular? Hemiauchenia (talk) 04:14, 16 May 2021 (UTC)

In any case since "the letter" says "we agree with the WHO director-general", I'm not even sure how it's being seen as some kind of challenge to the prevailing opinion. Alexbrn (talk) 04:19, 16 May 2021 (UTC)

They agree with the WHO insofar as both possibilities "are viable" and must be "taken seriously". The issue is that this is not reflected by the page. Eccekevin (talk) 04:27, 16 May 2021 (UTC)

We say it's extremely unlikely per the best sources. Come back when/if similar weighty sources pick this letter up. Per the general sanctions for this topic (which you are now are of) we should not be using non-MEDRS/non-peer-reviewed scientific content. Meanwhile, I see there a discussion about whether it might be due in the Investigations into the origins of COVID-19 article. Alexbrn (talk) 04:32, 16 May 2021 (UTC)

The problem is that you do so by using an article like this one, which is from a single scientist from Indonesia in Reviews in Medical Virology (a journal so unknown it does not even have a Wiki page) and a bunch of 2020 papers who are severely outdated, while a letter on Science (which is edited by the editors of Science which are no fools) by many famous scientists is completely disregarded. I don't argue against the fact that it is a minority viewpoint, but indeed it has to be treated as such, instead of treating it like a conspiracy theory as it is now, without even mentioning the support it has. You say on the page that most scientists dismiss it, but then you refuse to aknowledge those who support it. Eccekevin (talk) 04:59, 16 May 2021 (UTC)

Here's the problem. Saying pmid:33586302 is "from a single scientist from Indonesia" (why does the country matter, hmmm? Does it in some way nullify Hakim's virology expertise?[25]) rather swerves round the facts that:

1. This is a review article surveying the work of others rather than advancing novel research
2. Is peer-reviewed
3. Is from a virology journal, so is completely on-point
4. The journal, far, from being "obscure" is well-established with a solid impact factor
5. And is of course MEDLINE-indexed[26]

In short, one of our WP:BESTSOURCES. So implying this is a poor source seems like trying to warp reality to fit an agenda (rather in keeping with the whole lab leak thing). So long as we properly reflect golden sources like this, we are being good editors. Alexbrn (talk) 12:09, 16 May 2021 (UTC)

• That review article dedicates only one paragraph to the accidental lab leak, and does not really even address is properly. The only data is brings forth is this study (cited as 87) SARS-CoV-2, Covid-19, and the debunking of conspiracy theories that says it has a natural origin, but that is not being contested nor is in opposition with the accidental lab leak hypothesis. AS the Science letter says, it is perfectly possible to have a natural origin, been studied in a lab, and then been accidentally released from that lab. The review that you say is your "best source" talks about it and say that there have been accidental releases in the past but now there are stringent measures. That's it. It doesn't really provide anymore evidence against it, other than that the Chinese say that none of the lab workers have contracted the virus. This review surely isn't your best source, because if it is it is quite a poor one. Eccekevin (talk) 18:31, 17 May 2021 (UTC)

  I set out the reasons why it's a good source, the fact that it doesn't align with the POV a random Wikipedia editor wants to push doesn't figure in that evaluation. Alexbrn (talk) 19:32, 17 May 2021 (UTC)

  You're always free to take a stroll at WP:NOLABLEAK and look at the sources there. We don't criticise reliable sources, we report what they say. If the vast majority of MEDRS say "the lab leak is extremely unlikely" or "the virus almost certainly has a zoonotic origin", then that's what we write, without unduly legitimising FRINGE positions. RandomCanadian (talk / contribs) 18:41, 17 May 2021 (UTC)

Of course, that isn't the only source. Just a second strong MEDRS source on top of the WHO study. A study, it should be pointed out, said that continued investigations would be required, which the WHO DG agreed with and reinforced, and the the Science letter says they agree with him. But that doesn't change the current mainstream view. Bakkster Man (talk) 18:49, 17 May 2021 (UTC)

But that's exactly the problem. I never questioned that it's the majority viewpoint. I question the deliberate exclusion of any other viewpoint. Scientific analysis of the genome of the virus can only determine a zoonotic origin, but cannot determine whether it jumped from bats to humans in the nature of because of a lab spillover. Your own BESTSOURCE says as much and concludes that However, an independent forensic investigation is probably the only course of action to prove or disprove this speculation. Hence, this is more an investigation/political question than a scientific/genomic one. And given the many calls of skepticism for the past joint WHO-China investigation and the many scientistic speaking out (particularly in the Science letter but in many other places too), Wikiepdia should reflect the fact that many experts in the field consider both options viable and do not dismiss them as strongly as the current wording of the page suggests. Eccekevin (talk) 20:55, 17 May 2021 (UTC)

And now we're back to the topic regarding how much discussion of the minority possibilities are WP:DUE for this article, versus how much is WP:DUE on Investigations into the origin of COVID-19, including a sandboxed update attempting to better describe the fours hypotheses including this alternative. Bakkster Man (talk) 21:26, 17 May 2021 (UTC)

I think the sandboxed update is excellent. Most importantly, I think it importantly lays out the distinction between the "Deliberate bioengineering of the virus" and "the possibility of a collected and studied virus inadvertently spilling out". This is a fundamental distinction since they are two completely different hypotheses (the former has no scientitic support and does not include a zoonotic origin, the latter has those scientists who consider it viable and does invlude a zoonotic origin). Eccekevin (talk) 23:38, 17 May 2021 (UTC)

I get the distinction. But the problem remains that there isn't really any evidence for even that version of the "lab leak" hypothesis beyond "there is a laboratory in Wuhan". While the lab does research on bat coronaviruses, there is no evidence that they were studying SARS-COV-2. The initial outbreak was not centered on the laboratory. SARS-COV-2 has many differences from the SARS coronaviruses that were being studied. Even the lack of cooperation from China and their government's insistence on controlling information isn't actually evidence in favor of this hypothesis, because the PRC is governed by a single authoritarian political party with zero traditions of openness and transparency. The best that our sources can say is that more research is needed, and if you can find me a single medical paper, any medical paper, punlished any time in the past half-century, on any topic, that does not say "more research is needed", then I might grrant that phrase a level of valid consideration. Meanwhile the zoonotic spillover hypothesis basically says that SARS-COV-2 emerged in a manner similar to SARS-COV-1 and MERS. This explanation requires the fewest unsupported assumptions. Hyperion35 (talk) 12:40, 18 May 2021 (UTC)

I'm a bit less absolute on the level of evidence. I tend to see it less as a lack of evidence (broadly speaking, including 'reasons to look more closely'), and more as a lack of strong and reliable sourcing describing why one camp sees the virus genome as more likely to be a result of growth in culture. With the closest being the In Vivo review, not a virology journal but hypothetically explaining the circumstantial evidence these scientists coming to the alternate conclusion are basing that call on. And again, it doesn't change my read on the likelihood or fringe status of the lab hypothesis, just whether we claim there's "no evidence" or "circumstantial evidence". Bakkster Man (talk) 13:30, 18 May 2021 (UTC)

The lack of definitive evidence is somehow already covered by expressions like "extremely unlikely". Considerations about the genome are surely the most relevant to this article and aren't on the same plane as twitter conspiracy theories or probably inappropriate statements by prominent figures on the popular press, but require good sources. In the sandbox addressing every hypotesis helps to avoid giving too much stress on the lab leak, but it may be too lenghty for this article. On a side note: wouldn't it make more sense to transclude from Investigations into the origin of COVID-19 here, rather than the other way around? Personuser (talk) 18:24, 18 May 2021 (UTC)

The sandbox is intended for the origin investigation article, I agree it wouldn't fit here. As for which direction we transclude, maybe but this article existed before that one, so probably just path dependency. Bakkster Man (talk) 18:57, 18 May 2021 (UTC)

• I want to add a bit more explanation to Alexbrn's excellent answer. This is one situation where Wikipedia's policies reflect how these questions are answered in the real world as well. While MEDRS and BESTSOURCES tell us what to do, I am concerned that some of the disagreement here may reflect a lack of understanding why we do it this way. To be clear, Wikipedia policies and guidelines are the what matters in terms of what we put into the article, but I can also see how these standards might seem arbitrary to non-professionals, and so I want illustrate how healthcare professionals approach this. It's a bit long, so I'll make it collapsible to save space.

long explanation

A few years back, my agency decided to make some changes to regulations surrounding opioid (and other substances of abuse) treatment. Now, there is no lack of popular news coverage of the opioid epidemic, but we did not consult that. While it was of great public interest, it simply lacked serious depth, preferring to interview individuals rather than presenting any sort of serious statistical or cost-benefit analyses. What few interviews they had with professionals didn't require them to qualify or quantify their comments or show their work, and they rarely gave any information about whether a given professional's opinions represented a majority view or if they were a lone crank. Individual papers on opioids are a dime a dozen. They range all over the place in quality and findings. I even came across a (non-peer-reviewed) study that purported to show that laws expanding the distribution, possession, and use of naloxone correlated to an increase in opioid deaths (spoiler: it was horribly flawed). You could easily come up with dozens of different and mutually-exclusive proposals based on which individual primary-source paper that you could find. Suboxone? Buprenorphine-only? Methadone? Cold turkey? Do you want to play paper roulette with thousands of lives on the line? We instead looked at reviews published in the relevant journals in the field (ie secondary sources), and had our CMO look over them (which might make it a tertiary source), and this narrowed our approach dramatically, giving us a better idea of what treatment options would lead to the best outcomes, which were first line, second line, contraindications, etc. But that wasn't quite enough, because in a field this complicated you need a better idea of how to translate those findings into clinical practice, and so we consulted with the American Society for Addiction Medicine (ASAM), and consulted with them about their treatment guidelines. They had an excellent scale to allow physicians to classify a patient's addiction level, and recommendations for treatment based on those levels (ie outpatient medication management, short inpatient treatment, intensive inpatient treatment, etc).

My point is that this decision tree is a good example of how MEDRS is based on real-world usage, and why experts generally prefer expert evidence-based guidelines from relevant organizations (such as the WHO report in this article) as the best source of information, and peer-reviewed secondary reviews from specialty journals (like the study Alexbrn mentions) as the next-best thing. When professionals like Alexbrn or myself are saying that some sources are better than others, and some sources are all but useless, it is not because we like or dislike what they are saying. We are not just playing around to put a specific spin on the article or to dismiss your views. It is because in the real world, when you are making serious decisions, this is how you evaluate the available evidence. Hyperion35 (talk) 21:14, 16 May 2021 (UTC)

An even more thorough explanation can be found here: WP:WHYMEDRS. And I want to add, regarding the opinion letter, that pretty much all scientific methodology, from double blinding to peer review, is designed to prevent the opinions of the scientists doing the studies from colouring their results. Opinions of scientists are not a source of truth, they are a source of bias. --Hob Gadling (talk) 05:42, 17 May 2021 (UTC)

By requiring WP:MEDRS for evidence of the lab leak theory the prevailing wiki editors are using a sleight of hand. Whether the virus was leaked or not from the lab is an orthogonal question to the one of whether it has a zoonotic evolutionary origin. Promoters of the lab leak theory don't doubt the virus has a zoonotic origin, they just suggest that the intermediate host was humanized mice in the Wuhan Institute. The actual question of a lab leak is not even scientific in nature about the structure/biology of the virus itself, but an operational one. Spudst3r (talk) 19:55, 24 May 2021 (UTC)

Two thoughts on this. First is that, in general, we do treat this orthogonal point of commonality that way. Almost everyone agrees, the ancestor of SARS-CoV-2 is a virus with an animal reservoir. The pathway from there to humans is debated, but not that it's zoonotic.

Second, I'm curious that you say The actual question of a lab leak is not even scientific in nature about the structure/biology of the virus itself, since lab theory proponents primarily point to structural elements of the virus as evidence that its evolution was due to growth in lab culture. And those kinds of claims (for instance, that ACE2 most likely came from culture) absolutely need MEDRS. Bakkster Man (talk) 20:06, 24 May 2021 (UTC)

I agree there, claims around the furin cleavage require MEDRS. But other areas of the circumstantial evidence, like the lab's weak BSL-2 lab security are certainly operational points. Wuhan's lack of proximity to the local bat population or evidence of local infection nearby, the lack of hospital surveillance logs for the virus before Nov 2019, the timelines for MERS/SARS finding intermediate hosts vs COVID, and not being able to find the virus after testing 80,000 animals are not complex biology/health claims that require MEDRS. They are investigatory facts of the present situation. As there is no smoking gun yet for either the lab leak or natural origin claim, the article should reflect the fact that the evidence supporting both hypothesis still remain circumstantial -- and let the reader decide by giving an appropriate discussion of the available evidence for the different hypothesis.Spudst3r (talk) 23:56, 24 May 2021 (UTC)

Nearly there. It's not for us to analyse the evidence and decide what the article needs to say. We need to follow the best sources on the matter. Given that the origin of a human infection is a complex issue, I would agree that it's something best left to the experts who have spent their life studying the topic, and not the journalists. WP:RS seems to head in this direction to: whether you think MEDRS applies or not, that should still be the standard we use. See WP:SOURCETYPES: "Many Wikipedia articles rely on scholarly material. When available, academic and peer-reviewed publications, scholarly monographs, and textbooks are usually the most reliable sources." and WP:NEWSORG: "Scholarly sources and high-quality non-scholarly sources are generally better than news reports for academic topics." - whether the origin of the virus is a biomedical claim or not, it's still an academic topic. And the best sources, as documented at WP:NOLABLEAK, don't give equal validity to both theories. We can note the minimal dissent about this, without unduly legitimising it. RandomCanadian (talk / contribs) 00:08, 25 May 2021 (UTC)

BSL-2 lab security sounds biomedical to me. Wuhan's lack of proximity to the local bat population or evidence of local infection nearby both are biomedical issues. lack of hospital surveillance logs for the virus This is literally a claim about a medical facility and medical records. the timelines for MERS/SARS finding intermediate hosts vs COVID You mean virology? not being able to find the virus after testing 80,000 animals I mean maybe you could count this as zoology, but seriously now how is viral testing not biomedical? the article should reflect the fact that the evidence supporting both hypothesis still remain circumstantial -- and let the reader decide by giving an appropriate discussion of the available evidence for the different hypothesis Except that's not what the sources say. The best sources that we have explicitly say that a lab leak is extremely unlikely, they are clear about a zoonotic spillover event. This is the same special pleading I'd expect to hear from Creationists, the same "teach the controversy" and "let people decide on their own" canards. Hyperion35 (talk) 01:33, 25 May 2021 (UTC)

In addition to broadly agreeing with the above comments that these items are more accurately described biomedical in nature (and even if not, scholarly secondary sources remain best to prioritize with information so contentious), I'd like to note that these suggestions seem to support putting WP:UNDUE weight on (as you said) circumstantial evidence. While I am in favor of making clear that advocates for the minority position (and it is a minority position) have rational reasons for believing it is a likely explanation, I don't think we should spend more time explaining these pieces of circumstantial evidence than the mainstream perspective. And if we do explain specific details, I'd suggest it go in Investigations into the origin of COVID-19#Investigations where some of these pieces of evidence are already discussed, instead of this page (again, being careful not to unbalance the text and be UNDUE). Bakkster Man (talk) 13:26, 25 May 2021 (UTC)

The paper by Wade, again

The evidence for natural emergence is currently just as circumstantial as the lab leak, if not more. If it isn't, cite the evidence, not a WHO report that doesn't engage with the evidence written under serious conflict of interest. As the Wades article argues:

"It’s documented that researchers at the Wuhan Institute of Virology were doing gain-of-function experiments designed to make coronaviruses infect human cells and humanized mice. This is exactly the kind of experiment from which a SARS2-like virus could have emerged. The researchers were not vaccinated against the viruses under study, and they were working in the minimal safety conditions of a BSL2 laboratory. So escape of a virus would not be at all surprising. In all of China, the pandemic broke out on the doorstep of the Wuhan institute. The virus was already well adapted to humans, as expected for a virus grown in humanized mice. It possessed an unusual enhancement, a furin cleavage site, which is not possessed by any other known SARS-related beta-coronavirus, and this site included a double arginine codon also unknown among beta-coronaviruses. What more evidence could you want, aside from the presently unobtainable lab records documenting SARS2’s creation?

Proponents of natural emergence have a rather harder story to tell. The plausibility of their case rests on a single surmise, the expected parallel between the emergence of SARS2 and that of SARS1 and MERS. But none of the evidence expected in support of such a parallel history has yet emerged. No one has found the bat population that was the source of SARS2, if indeed it ever infected bats. No intermediate host has presented itself, despite an intensive search by Chinese authorities that included the testing of 80,000 animals. There is no evidence of the virus making multiple independent jumps from its intermediate host to people, as both the SARS1 and MERS viruses did. There is no evidence from hospital surveillance records of the epidemic gathering strength in the population as the virus evolved. There is no explanation of why a natural epidemic should break out in Wuhan and nowhere else. There is no good explanation of how the virus acquired its furin cleavage site, which no other SARS-related beta-coronavirus possesses, nor why the site is composed of human-preferred codons. The natural emergence theory battles a bristling array of implausibilities." Spudst3r (talk) 20:15, 7 June 2021 (UTC)

If you're going to keep citing self-published (or re-published) opinion pieces by non-scientists, might as well present recent pieces in newspapers, such as this, which has a decent overview (also citing Nature and Gorski in SBM). In either case, we shouldn't use either of these sources for anything scientific if we have better sources available. And we do: going on PubMed or Google Scholar and making a targeted query for review papers about the subject will leave you with plenty of relevant results. RandomCanadian (talk / contribs) 21:41, 7 June 2021 (UTC)

As for an example of an actual scientific paper which deals with the subject, see this. RandomCanadian (talk / contribs) 21:48, 7 June 2021 (UTC)

Yeah, I keep going back to, if these are such smoking guns, why don't we have journal sources for them? Either there's an actual push from mainstream journals not to touch it, or it's actual unsubstantiated quackery. In either case, zoonosis is the mainstream view we have to cite as such.

Honestly, I'd love to put credible info on the codon usage and stuff (here or the Origins article) if there's credible reason to say it's a view of the proponents. But the last thing I (and I suspect the proponents want) is citing only mediocre papers that make it clear how non-mainstream the actual science on the topic is. Provide the peer-reviewed source making these claims, then we can talk about them as science instead of hunches and (to be blunt) conspiracy theories. Bakkster Man (talk) 21:54, 7 June 2021 (UTC)

@Bakkster Man: I was looking at other pages trying to figure out what the above was a duplicate of before realising it was right here all along - right below, at #Wade_article_and_others._Extremely_POV_origin_section. Should we merge this with that or just close it as unhelpful dead-horse beating? RandomCanadian (talk / contribs) 21:58, 7 June 2021 (UTC)

@RandomCanadian: I dunno, I've kinda given up on having any expectation of consistent, unified discussion. Different people have their own entirely unique (or at least, perceived to be so) grievances, so nobody wants to combine them. Bakkster Man (talk) 22:59, 7 June 2021 (UTC)

Wade article and others. Extremely POV origin section.

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

---

There is now considerable evidence beyond right wing bullshit. I would encourage people to read https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/ (There are other sources)

The WHO team that investigated had Peter Daszak on it, who was the person that oversaw the US grant that funded the lab. It is the international virology community that is being accused here, not just Wuhan.

The section in this article is extremely POV, saying about five times that they think it had a natural origin. It needs balance.

No natural precursor has been found. The lab was studying gain-of-function Corono viruses. And China has censored the data. This needs to be said.

Look beyond your political biases. Just because Trump is an idiot does not mean he is always wrong -- even a stopped clock is correct twice a day. Tuntable (talk) 06:39, 2 June 2021 (UTC)

aaaand you've been reverted because your edits baselessly suggest that gain of function research was performed on the virus, which there is exactly zero evidence for, based on unreliable sources. It's your perspective that's extremely POV, not the articles. I think your opinion can safely be ignored. Hemiauchenia (talk) 08:12, 2 June 2021 (UTC)

...I'll be charitable to OP: No natural precursor *inhales* Bruh. brUH?? The bat coronaviruses? SARS-CoV-1? Literally the many coronaviruses out there we haven't even found yet? This is not the first time a virus has jumped species, nor will this be the last. It happens all the time! Friend. Friend. A virus does not need a GoF lab to be dangerous. Rotideypoc41352 (talk · contribs) 12:32, 2 June 2021 (UTC)

I'll be nice and also point them to the just preceding section for a thorough refutation of one of the bullshit claims made by Wade. See also this (recent) paper, which elegantly puts it: "Other strategies, more speculative than those listed above, have been used to suggest that SARS-CoV-2 came from a laboratory accident at the Wuhan Institute of Virology (Rogin, 2020). The evidence indicates that SARS-CoV-2 was not purposefully manipulated (Andersen et al., 2020). Moreover, the notion that the SARS-CoV-2 pandemic resulted from a laboratory accident at the Wuhan Institute of Virology (Rogin, 2020) is not necessary to explain the pandemic."" Also, top virologist quoted indirectly here saying that "The suggestion that it would have taken some Chinese science experiments to get the virus from bats in Yunnan to human beings in Wuhan seemed to leave him slightly affronted, on behalf of the natural world."... And yes, it happens, all the bloody time - recent example...RandomCanadian (talk / contribs) 12:58, 2 June 2021 (UTC)

There is nothing in these statements that refutes Wade. Sure, it might have been natural, but that does not mean it might not also have been GoFed. There is no strong evidence either way at this point, as Wade points out.

• Wade asserts that the virology lab was doing gain-of-function research on Coronoviruses. Does anybody dispute this? Was he lying?

• Wade asserts that there are no known precursors in humans or animals despite a large search, and that the precursors for SARS etc. were found within months. Again, is that disputed?

• Wade asserts that the Chinese government has sealed all records, and has banned all Chinese researchers from publishing on this. Again, is he lying?

• Wade asserts that Daszak was overseeing the funding of the lab, therefor was not impartial. Yet he was on the WHO team and organized the initial Nature article. Was that also a lie?

That above would certainly lead to strong suspicion about the lab. There are technical bits a well, but that is enough for now.

Maybe Wade is full of shit. But he is widely read and quoted. He deserves to be heard even if only to have his arguments properly debunked.

There are certainly other very credible authors that have doubts https://science.sciencemag.org/content/372/6543/694.1

The anger and censorship above only adds wait to the idea that Wade is correct. The section in the article reads like propaganda, vs Wade's sober writing. I also presume that some (not all) of the editors of this article are Chinese government employees. Tuntable (talk) 03:18, 3 June 2021 (UTC)

Wade is a non-scientist, publishing in a non-topic related journal, for which we have no evidence of peer-review (since the piece in question is a copy of a previous self-published Medium post). His opinion (since that is what the paper sums up to) cannot be taken seriously (he's not helped by his previous record of publishing a book about genetics widely rejected by experts in that field) since he is not a relevant expert, and since WP:ARSEHOLES applies. Yes, of course, some of what he says is true. The conclusions he makes from it are patently incorrect, and significantly at odds with what actual experts are saying (see this from a reputed skeptic source for rebuttals of his claims). Per WP:FRINGE, he doesn't deserve mention here, since this isn't an article about fringe theories, and putting him here would be the epitome of undue legitimisation (WP:FALSEBALANCE). The letter in Science is being misinterpreted (it does not argue for Wade's scenario of a deliberately engineered virus). Anyway, I've made my point. Unless you have better sources than Wade, Segretto, Deigin, or the like, this cannot go in except as a very minor, generic mention about conspiracy theories and misinformation. RandomCanadian (talk / contribs) 04:27, 3 June 2021 (UTC)

We can go at the facts all day, unless you'd like to retrieve Russell's teapot. Three too many of us have laid out the research from others who have put in the blood, sweat, tears, and toil for their skills and knowledge. Plus, saying some (not all) of the editors of this article are Chinese government employees makes people less likely to believe you are here to build consensus and more likely to just let WP:GS/COVID19 run its course. Not anger (ran out long ago), not "censorship" (this is a private website), just sober writing. Rotideypoc41352 (talk · contribs) 18:28, 3 June 2021 (UTC)

"My citation is better than your citation" does not cut it. Wade is a respected journalist and he certainly does not read like he is blatantly lying. If he was then that would be of interest. Neither you nor the article have addressed even one of the points Wade made. Maybe Wade is wrong, I came to this article to find out. But there is no real content other than that the some people (including virologists) are passionate about not discussing the Wuhan case, and quick to censor any mention of it, or even to include a citation. That strongly suggests that Wade is correct, and I suspect that this will come out over the next few months. Tuntable (talk) 03:32, 5 June 2021 (UTC)

I suspect that this will come out over the next few months. Entirely possible, but also not our job to try and predict. WP:CRYSTAL Bakkster Man (talk) 13:49, 5 June 2021 (UTC)

And thank you for the Gorski paper. However, it does not address Wade's points directly. And it reads like an angry rant while Wade reads like a considered analysis of the facts. I think it is patently obvious that just given the points that I pulled from Wade above that the WIV is definitely a possible source, and it would be very difficult to disprove that given the records are sealed. But I would like more information on the technical arguments, the closeness to RaTG13, the codons used in the Furin cleavage site. But I don't see anything in either this article. The fact that it might have arisen naturally certainly does not prove that the WIV is innocent.Tuntable (talk) 03:41, 5 June 2021 (UTC)

I might add that the Gorski paper mischaracterizes the Furin argument, which was that it uses human codons. It also mischaracterizes the RaTG13 argument, which is that the SARS-CoV-19 virus is almost identical to RaTG13 for most of it, except for the spike protein, suggesting that that RaTG13 was used as a backbone, and the spike stuff added. If there is a good paper that realistically refutes Wade, I have not seen it.

• Wade: https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/
• Deigen on RaTG13: https://yurideigin.medium.com/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748
• Yan https://zenodo.org/record/4028830#.YK7UoqERWp3

Tuntable (talk) 04:14, 5 June 2021 (UTC)

You obviously do not understand why we have restrictions on sourcing. It is not because the not-so-good-sources are lying. (Well, some of them do.) It is because Wade, as a non-scientist, does not understand scientific subjects as well as a scientist does, and because the editors of "Bulletin of the Atomic Scientists" are specialists in something else and not competent to recognize his rookie mistakes and remove them. Therefore, Wade's piece is worthless as long as we have texts which were written by actual experts and checked by other experts. "Check what the source sounds like to you" is not part of the Wikipedia sourcing quality criteria.

The only reason why any person would prefer Wade as a source is because Wade is saying what that person wants to hear. Trying to force Wade into articles is simply POV-pushing. --Hob Gadling (talk) 06:00, 5 June 2021 (UTC)

@Tuntable: If you can provide strong sources (WP:SCHOLARSHIP, not WP:SELFPUB) about the FCS codons and spike protein elements, then I'm in favor of adding them (more likely to the Investigations article, depending on the source's reliability). Shouldn't be too hard, if Wade and Deigen are citing meaningful science (which Yan is not). Bakkster Man (talk) 13:49, 5 June 2021 (UTC)

(edit conflict) OP, consensus is against you regarding the inclusion of your source, its claims, and non-WP:MEDRS in general. Consensus is also against you regarding the purpose of this article and even Wikipedia in general (rebutting fringe vs summarizing info from secondary sources with editorial oversight from experts independent of the subject). Rotideypoc41352 (talk · contribs) 14:18, 5 June 2021 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Wuhan source "conspiracy" should be addressed because it is widespread

Even Biden suggesting it is plausible enough to require an investigation. It does not matter whether it is true or not. It does not matter who are the most eminent references. It needs to be properly addressed because it is now widespread. People will come to Wikipedia to determine whether it is true.

Having read the article, and the the talk, I still do not have any clear idea why the lab leak hypothesis is considered to be complete nonsense. I understand that many eminent people have said so, and that some of the technical arguments for the lab leak may be dubious. But I have not seen anywhere any proof that it is not possible.

To address it requires summarizing the case for and against. Many people (including myself) are much more interested in rational arguments than authoritative ones. To address the "conspiracy" the arguments put forth by the conspirators need to be stated clearly and succinctly, and then facts provided by eminent sources used to debunk them. Rather than agonizing on about a generic paragraph that gives appropriate weight, provide the facts and let the reader decide.

Personally, it appears obvious that the labs are suspicious because of geography, the lack of animal or human precursors, the fact that the WIV was doing gain-of-function research on coronoviruses at the time, and the fact that the Chinese government has closed access to relevant records, and that nobody has ever said that such a chimera could not, in theory, be created. That seems more than enough to make the conspiracy very plausible.

As @SSSheridan: points out, this consensus has changed recently, although I think there have always been substantial doubts. As @Eccekevin: points out, the WHO is a important but not infallible source. As @Spudst3r: points out, the discussion is not just scientific, but operational, as humanized mice could be the animal intermediatory. Certainly the Ebright concerns raised by @CutePeach: should be mentioned. The technical details for and against would make a very interesting article, as @Elle Kpyros: has suggested.

BTW. Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know.

Incidentally, the WHO report said "There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019," -- What about RaTG13? Also, did the WHO team actually study the WIV in any detail? And did the team include people closely associated with the WIV (like Peter Daszak)? Tuntable (talk) 07:16, 6 June 2021 (UTC)

As @Eccekevin: points out, the WHO is a important but not infallible source. While I agree, you need to provide some kind of reliable, scholarly source making a contrary claim. If the WHO makes one claim, consistent with a bunch of other high quality papers, and the best we can find making a link to humanized mice is a non-MEDLINE article from a single non-virologist, then even if we cite such a paper it would indicate its WP:FRINGE/ALT status by being stuck in a less prestigious journal by a non-expert. If it's a clear issue, it's an easy fix. So provide the links. Though I'll warn, they probably would need to go in the Investigations article (where there's a good argument MEDRS doesn't apply) rather than here (where there's a good argument MEDRS does apply).

Do any of the eminent references provide evidence that the intermediatory could not be humanize mice? That would be interesting to know. To reiterate, unless we have a reliable source that suggests they could be the intermediary, why would we cite a source source saying a thing wasn't possible. We'd have a hella long article if we had to list and cite every possibility that was ruled out that nobody suggested should be considered in the first place. Sure, we ruled out a meteor, but did we rule out a comet? What about Martians? Titans? Alpha Centaurans?

Here's the thing about the whole debate. Even if you think the explanation is most likely to be true (it might be) and the scientific establishment is suppressing it (they might be) and that the truth will eventually come out, then until it does WP policy still says we should give the credibility to the credible sources, until the situation changes. And it's why we changed our writing on the topic after the WHO study was published, the mainstream view had changed and we reflected that. Bakkster Man (talk) 13:31, 6 June 2021 (UTC)

In Wikipedia, we do need sources in order to stop nonsense flat earth theories being presented as fact. But that does not mean that as editors we cannot apply common sense and make sensible deductions. The goal is to produce good articles, not just mindlessly follow some bureaucratic process.

While the scientific literature might be the major source for scientific truth, it is not the only source for what should be included in an article. One thing to consider is what people that consume the article might be wanting to find out. That is, ultimately, the goal of the exercise. And the Scientific literature has no bearing on that.

It is completely obvious that many people are concerned that the virus may have leaked from WIV. The reasons that I gave for plausibility are obviously solid, and none of the scientific literature disagrees with them. And it is equally obvious that humanized mice are used for gain-of-function research, which is why it is obviously important to know whether that is technically feasible.

I am not for a moment suggesting that the article should say that the conspiracy theories are correct. But the fact that readers (like myself) what to know is reason enough to deal with them.

In this case, we also know that some of the scientific opinions have been written by people that have a vested interest (E.g. Dazsag, and Shi).

I would add that the following paragraph reads like a rant rather than a sober, Wikipedian analysis.

Yet, its origin, which remains unknown, have become debated within the context of global geopolitical tensions. Early in the pandemic, conspiracy theories spread on social media claiming that the virus was a biological weapon developed by China, amplified by echo chambers in the American far-right. Other conspiracy theories promoted misinformation that the virus is not communicable or was created to profit from new vaccines.

This led me (and I suspect many other readers) to suspect that it was written by members of the Chinese government, a suspicion that I still hold.

Incidentally, I would not mind a section titled "Conspiracy Theories as to the Origins of the Virus". Then the context would be clear. Tuntable (talk) 00:49, 7 June 2021 (UTC)

1. We give credence to the hypothesis on Investigations into the origin of COVID-19. 2. We cover the conspiracy theories at COVID-19 misinformation#Virus origin theories. 3. If you can't cite a reliable source connected these dots, then we can't cite your original research. 4. Sounds like a WP:AGF violation. Bakkster Man (talk) 01:04, 7 June 2021 (UTC)

If you want to read about the different possible lab origin scenarios, here is a review article that discusses them "On the Origin of SARS-CoV-2: Did Cell Culture Experiments Lead to Increased Virulence of the Progenitor Virus for Humans?". This review article is MEDRS compliant (i.e. it's a review and in MEDLINE) and written by a well qualified geneticist Bernd Kaina. Here is his biography. If there is a problem with this review article, I would like to hear what the problems are. --Guest2625 (talk) 08:00, 7 June 2021 (UTC)

It's not MEDRS compliant - it's in an entirely off-topic journal (we wouldn't cite a journal about virology in an article about cancer - same thing here, we won't cite a journal about cancer in an article about virology and infectious diseases). If you want an actual overview of lab scenarios in a reasonable journal try "Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover model to the viral circulation model". RandomCanadian (talk / contribs) 12:18, 7 June 2021 (UTC)

Thank you for raising your concerns. It appears the problem is that your knowledge of the furin research field is limited. Here is a review article to get up to speed: "Furin‐mediated protein processing in infectious diseases and cancer". Furin derives its name from the upstream region of an oncogene known as Feline sarcoma oncogene (FES). The gene was known as FUR (FES Upstream Region), and therefore the protein was named furin. Furin is a very important protease in cancer research. Note this quote from the furin review article above:

"Furin has been termed a ‘master switch of tumor growth and progression’28, 29 as its aberrant expression or activation can promote the formation and progression of various malignancies including colon carcinoma, rhabdomyosarcoma, head and neck cancers, lung, skin and brain tumors."

Bernd Kaina is a trained geneticist and microbiologist who is qualified to discuss genetics and furin which is quite relevant to the field of oncogenes and oncology. This is a quote from his wikipedia article:

"He identified the repair enzyme O-6-methylguanine-DNA methyltransferase (MGMT) as a protection mechanism against the killing, clastogenic, recombinogenic and carcinogenic effects of alkylating carcinogens."

This microbiologist works with cell cultures all the time in his field and fully understands serial passaging in a cell culture. I'm sure he has used the HeLa cell line once or twice. And wow look at that the cell line was derived from the cervical cancer cells of Henrietta Lacks, a 31-year-old African-American mother of five, who died of cancer on October 4, 1951. That's just an interesting aside. Anyone who wants to use this review should go ahead and use it. If there is still some disagreement on this topic, the discussion can be taken to the reliable noticeboard where there will be qualified editors who can voice their opinion as to the merits of the concerns. --Guest2625 (talk) 10:23, 8 June 2021 (UTC)

The above contribution, a bit shorter: "First I pretend to be polite by saying thank you, but then I am actually extremely rude by ignoring what you said, then randomly accusing you of not knowing very basic stuff, and then I tell you other, partly very basic stuff (which has nothing to do with the article), implying you did not know that either."

I'll repeat what RandomCanadian said: It's not MEDRS compliant. Full stop, end of story. Bye. --Hob Gadling (talk) 11:50, 8 June 2021 (UTC)

@Guest2625: While I'd consider this a usable citation as an example for circumstantial evidence for a lab origin (CCG-CCG FCS, primarily) on Investigations into the origin of COVID-19, I wouldn't go so far as to say that this paper is a secondary source for those claims. While this is nominally a review article, it's closer to a well cited opinion piece. Most importantly, the specific claims about the CCG-CCG codons and FCS appear to be primary claims based on research coming to the opposite conclusion. For instance, he cites the Nature letter regarding the codons used, but appears to come to his own (vastly different) conclusion on what they mean. His claim that This supports the hypothesis that the PCS/furin cleavage site was gained by a recombination event(s) involving these virus sequences. This notion is important in considering possible zoonotic events, placing laboratory events in the realm of the highly possible is uncited, making it a primary claim rather than a review of the existing literature. Maybe I've missed it in the citations (if so, please point me to it, this source seems the closest to directly applicable), but the paper doesn't directly cite it.

So again, worthwhile to add to Investigations as a peer-reviewed paper explaining one of the pieces of evidence seen as circumstantially supporting that hypothesis, but not here for making wikivoice claims about the virus (because it's contradicted by stronger sources, WP:SCHOLARSHIP). Bakkster Man (talk) 14:49, 8 June 2021 (UTC)

It is not just "My" original research. It is quite widely quoted, and has prompted an inquiry by the US President. That does not make it correct, but it certainly makes it notable.

I believe that this should be covered here, but I will add a reference to the other article, of which I was unaware. I expect you to instantly revert it for some obscure reason. But the other article does not cover the issues either. So we can continue the discussion there. Tuntable (talk) 01:16, 7 June 2021 (UTC)

When Scientific papers describe the status of the lab leak using terms such as "Therefore, although a laboratory accident can never be definitively excluded, there is currently no evidence to support it." and "Despite these massive online speculations, scientific evidence does not support this accusation of laboratory release theory. Yet, it is difficult and time‐consuming to rule out the laboratories as the original source completely. It is highly unlikely that SARS‐CoV‐2 was accidentally released from a laboratory since no direct ancestral virus is identified in the current database."; then we don't need to address it simply because it would fit the Zeitgeist. Note that we correctly describe the lab leak as "possible but unlikely". As for the proper conspiracy theories (the ones that have been ruled out), well, yes, we describe them as such. If you wish to cast aspersions about other editors, you're free to do so, but freedom of speech does not imply freedom from consequences, especially not here on Wikipedia where civility and collaboration are required. RandomCanadian (talk / contribs) 03:16, 7 June 2021 (UTC)

Agreed it should be included. And FYI MEDRS doesnt apply to history. The history of how the virus might or might not have come about is not subject to MEDRS as it is Wikipedia:Biomedical_information#What_is_not_biomedical_information?. Thanks! Jtbobwaysf (talk) 15:54, 8 June 2021 (UTC)

Something happening now and that virologists and epidemiologists are actively researching is hardly history. Rotideypoc41352 (talk · contribs) 16:05, 8 June 2021 (UTC)

@Jtbobwaysf: See above for WP:SCHOLARSHIP reasons to place less weight on this source that stronger sources contradicting it (and why the claims it's suggested being cited for are WP:PRIMARY), MEDRS or not. For the record, I've cited the source at Investigations into the origin of COVID-19#Laboratory incident, where that concern doesn't apply. Bakkster Man (talk) 16:08, 8 June 2021 (UTC)

Is there a policy in place that states that scholar articles are due more weight over other high-quality RS? Or is this only going back to the "MEDRS-required" POV? Jtbobwaysf (talk) 16:30, 8 June 2021 (UTC)

WP:SOURCETYPES, a guideline: When available, academic and peer-reviewed publications, scholarly monographs, and textbooks are usually the most reliable sources. --Hob Gadling (talk) 17:00, 8 June 2021 (UTC)

I'll also add WP:FRINGELEVEL, making note that the above source has yet to be cited by another paper, while making claims contrary to papers with significantly more citations (including ones he cited).

To be more specific, I don't see the issue here as scholarly vs not-scholarly. The Kaina paper is a scholarly source, but a weaker one. So the stronger sources should be given priority, where the two disagree. Why? Per WP:FRINGELEVEL, because it indicates Kaina's opinion has a lower acceptance, and that significantly lower level of acceptance (as evidenced by a lack of peer-reviewed papers making the claim and being cited by peers) is why I refer to it as WP:FRINGE/ALT. This is also exactly why I supported adding it to the Investigations article, but not here: Ideas that are of borderline or minimal notability may be mentioned in Wikipedia, but should not be given undue weight... Wikipedia is not a place to right great wrongs. Fringe theories may be excluded from articles about scientific topics when the scientific community has ignored the ideas. However, ideas should not be excluded from the encyclopedia simply because they are widely held to be wrong. Bakkster Man (talk) 17:46, 8 June 2021 (UTC)

Tangentially, WP:RSCONTEXT was the other policy I used regarding the paper. Specifically, which parts of the paper were new primary claims, and which were a secondary review of the existing literature. In other words; treat the primary claims as primary, and the secondary claims as a review. This prevents the 'sneaking in' of an exceptional claim by this author, as if it were reliable because it was in a review paper and thus what the literature as a whole said (why we place so much weight on secondary review sources). Bakkster Man (talk) 17:55, 8 June 2021 (UTC)

Rarity of Furin Cleavage Site is inaccurately described here

The article says: SARS‑CoV‑2 is unique among known betacoronaviruses in its incorporation of a polybasic site cleaved by furin. Is this correct? I've read that FCS is common among coronaviruses and uncommon on Sarbecoviruses. I don't know how it stands among betacoronaviruses. Can we get this claim fact-checked? Forich (talk) 21:02, 31 May 2021 (UTC)

Per Hu et al., Nat Rev Microbiol. 2020 Oct 6 : 1–14.

Another specific genomic feature of SARS-CoV-2 is the insertion of four amino acid residues (PRRA) at the junction of subunits S1 and S2 of the S protein26 (Fig. 3a). This insertion generates a polybasic cleavage site (RRAR), which enables effective cleavage by furin and other proteases. Such an S1–S2 cleavage site is not observed in all related viruses belonging to the subgenus Sarbecovirus, except for a similar three amino acid insertion (PAA) in RmYN02, a bat-derived coronavirus newly reported from Rhinolophus malayanus in China.

And per Kai-Wang To et al., Emerg Microbes Infect. 2021; 10(1): 507–535., this is also an important factor in virulence:

It contains two subunits S1 and S2 with a polybasic site PRRA at the junction, which enables effective cleavage by furin and other proteases [5]. This multibasic cleavage site appears to be an important virulence factor which may enhance virus replication and multiple tissue tropism as in the case of avian influenza A(H5N1) virus [20, 21]. Mutations in this site can attenuate pathogenicity in animal models and may be an attractive option for designing live attenuated vaccines [21].

I also remember reading something about the furin cleavage site being under selective pressure, but I can't find the paper at the moment. Cheers, RandomCanadian (talk / contribs) 22:10, 31 May 2021 (UTC)

@Forich: And to clarify your confusion, Sarbecovirus is a subgenus of Betacoronavirus. See Betacoronavirus#Sarbecovirus (lineage B). RandomCanadian (talk / contribs) 22:49, 31 May 2021 (UTC)

In addition, (from Science-Based Medicine), refuting a conspiracy theory, but I'll quote for the scientific facts: "Basically, Wade’s argument seems to be that because a furin cleavage site of this sort hasn’t been seen in SARS-related beta coronaviruses before it must have been engineered. The problem is that such furin cleavage sites are common in a wide variety of viruses, including coronaviruses, and that scientists already had identified plausible mechanisms by which it could have ended up where it did in SARS-CoV2 last year: [...]" - this cites as a source the recent Wu and Zhao, Stem Cell Res. 2021 Jan; 50: 102115. for FCS occuring naturally in CoVs. RandomCanadian (talk / contribs) 01:47, 1 June 2021 (UTC)

@RandomCanadian:, thanks for your responses and for bringing good sources. They answered partially my question. Now we know this:

1. Subfamily Orthocoronavirinae or Coronaviruses: FCS is common
   1. Genus Betacoronavirus: We don't know how common it is, at least from the sources you provided
      1. Subgenus Sarbecovirus: FCS is not observed in all related viruses belonging to this subgenus (This wording is kind of ambiguous, I'd prefer we double check with other sources for a more accurate description of how common it is). Forich (talk) 15:46, 1 June 2021 (UTC)

@Forich: Wu and Zhao (cited above) give a diagram as a graphical abstract for Betacoronavirus which highlights multiple examples of FCS in other subgenera (but not in Sar.). I think that clarifies the matter. RandomCanadian (talk / contribs) 16:09, 1 June 2021 (UTC)

• Note: Article has been updated to reflect the above. RandomCanadian (talk / contribs) 16:26, 1 June 2021 (UTC)

Nice work @RandomCanadian:. This is the current information: A distinguishing feature of SARS‑CoV‑2 is its incorporation of a polybasic site cleaved by furin, which appears to be an important element enhancing its virulence. Although such sites are a common naturally-occurring feature of other viruses, including members of the Beta-CoV genus and other genera of coronaviruses, SARS-Cov-2 is unique among members of its subgenus for such a site. . Please compare with this phrase from the WHO report (p. 83) in order to assess whether there is room for improvement (i.e. the WHO report says that most Betacoronaviruses do not have the FCS which is more informative than saying that in members of betacoronvairuses FCS sites at the S1/S2 junction occur naturally): This furin-cleavage site is not present in most other betacoronaviruses (for instance, SARS-CoV). Forich (talk) 22:28, 2 June 2021 (UTC)

Agreed, good catch all around. The paper cited by the WHO report is this one, which states more directly: Furthermore, SARS-CoV-2 has a unique furin cleavage site insertion (PRRA) not found in any other CoVs in the Sarbecovirus group (fig. S3), although similar motifs are also found in MERS and more divergent bat CoVs. This PRRA motif makes the S1/S2 cleavage in SARS-CoV-2 much more efficient than in SARS-CoV and may expand its tropism and/or enhance its transmissibility. A recent study of bat CoVs in Yunnan, China, identified a three–amino acid insertion (PAA) at the same site. Although it is not known whether this PAA motif can function similar to the PRRA motif, the presence of a similar insertion at the same site indicates that such insertion may already be present in the wild bat CoVs. The more efficient cleavage of S1 and S2 subunits of the S glycoprotein and efficient binding to ACE2 by SARS-CoV-2 may have allowed SARS-CoV-2 to jump to humans, leading to the rapid spread of SARS-CoV-2 in China and the rest of the world. Best not to dive too deeply into details, but I agree we want to get it right. It seems the gap is between 'commonly occurring' and 'present in most'. The former doesn't necessarily imply the latter, but we also don't want to unintentionally suggest that it is implied here. Bakkster Man (talk) 22:57, 2 June 2021 (UTC)

Maybe some grammatical re-jigging could make this clearer? "Although such sites are a common naturally-occurring feature of other viruses, including in some members of the Beta-CoV genus and in other genera of coronaviruses, [...]"? Wu and Zhao, however, seem to be less cautious, and are also more recent that Li et al., and their abstract is rather clear that there are multiple examples. RandomCanadian (talk / contribs) 00:33, 3 June 2021 (UTC)

I think that works well, if we continue to use the word 'common'. If the concern is with 'common' itself, then perhaps removing common and including a reference to MERS? Bakkster Man (talk) 13:31, 3 June 2021 (UTC)

Three points I'd like to ask are: 1) What is the DUE taxonomical category to mention: the subfamily, the genus or the subgenus? Our readers interested in general information on the virus may have different needs than readers of the specialized papers. 2) Once we pick what levels to report, should we go with most/common/rare or with "there is multiple examples". I think "most/common/rare" is still a more accurate descriptor given that a particular subgenus can have hundreds of strains, and having "multiple" of them with a particular characteristic won't make it common. 3) If we bring an example of other well-know virus, do we pick one that has the FCS or one that lacks it? Or we bring examples of both? I like the WHO report quote because they went for the genus, they used "is not present in most" (which we can convert into "is present in few" for brevity), and used a negative example (SARS-CoV-1 lacks a FCS despite being a well-know relative). Forich (talk) 17:37, 3 June 2021 (UTC)

1. I'm not sure it befits us to make that decision ourselves. We should follow what our reliable, secondary sources consider the most relevant.
2. This one really depends on why we're mentioning the frequency of occurrence in the first place for it to be notable. The simple presence of the Furin cleavage site, and its effect on human infectiousness, is obviously notable on its own. But I'd suggest the inclusion of the frequency in nature relates directly to the origin debate, specifically the argument from lab-origin advocates that the FCS is an indicator of lab modification. See #1, we should mirror the reliable secondary sources on this, not the fringe ones, in order to keep the NPOV. Of note, the WHO report describes the FCS as "not present in most other betacoronaviruses", but also that "both RmYN02 and RshSTT200/182 share part of the furin-cleavage site unique to SARS-CoV-2." So we don't need to go in blind on this one, and can provide context that 'being rare' doesn't mean 'unlikely' (not necessarily mentioned in sources, but a possibility of survivorship bias. FCS/ACE-2 may be rare in nature, but the viruses with them may be the most likely to jumpt to humans).
3. Personally, I think both SARS and MERS would be the appropriate comparison, absent an WP:RS guiding us elsewhere (though both the RS and fringe sources tend to make these comparisons, from what I've seen). They're the two other major human CoVs causing severe symptoms, one with each of these structures, making good sense as comparisons.

Good focusing questions. Bakkster Man (talk) 13:50, 4 June 2021 (UTC)

Re: positive selective pressures on the furin cleavage site, is one of these the paper you were referring to RandomCanadian? The first establishes how crucial the furin site is to pathogenesis, and the second shows via conservation analysis of known sequences that the cleavage sites are all relatively non-mutagenic.--Shibbolethink ^{(♔ ♕)} 14:21, 13 June 2021 (UTC)

References

Nucleotide skewness of SARS-CoV-2

In biology, markov models that describe changes over evolutionary time of the genetic sequence of SARS-CoV-2 are called Substitution models. Its genes are sequence of symbols (RNA has a four nucleotide alphabet) which can used to compute the likelihood of phylogenetic trees using multiple sequence alignment data. When we see the famous estimate of evolutionary distance of SARS-CoV to RatG13 being between 20 and 90 years, that was made by the use of Substitution models. The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). Wang, Pipes, and Nielsen (2020) observe that the literature has been inconclusive on fully reconstructing the evolutionary history of SARS-CoV-2 because nonsynonimous mutations suggest different conclusion than synonimous mutations. The estimation of synonimous mutations is "complicated" by the skewed distribution of nucleotide frequencies in synonimous sites of SARS-CoV-2. Therefore, I propose we include the fact that SARS-CoV-2 has a skewed distribution of nucleotide frequencies in its synonimous sites. Forich (talk) 15:40, 6 June 2021 (UTC)

The reference: Hongru Wang, Lenore Pipes, Rasmus Nielsen, Synonymous mutations and the molecular evolution of SARS-CoV-2 origins, Virus Evolution, Volume 7, Issue 1, January 2021, veaa098, https://doi.org/10.1093/ve/veaa098 Forich (talk) 15:43, 6 June 2021 (UTC)

While interesting, I'm curious why the focus on the 'skew'. The paper appears to suggest this is just a complicating factor in determining the phylogenetic tree, and I didn't see any particular conclusions based on it beyond just refining the estimate of divergence with RaTG13/RmYN02. Am I missing something? Bakkster Man (talk) 18:48, 6 June 2021 (UTC)

@Forich: in case you missed. Bakkster Man (talk) 23:02, 7 June 2021 (UTC)

@Bakkster Man: Frutos et al. describe that "The lower presence of CpG (intrachain Cytosine-Guanosine dinucleotide linked by a phosphate bond) in human pathogens has been shown to be a selective process. CpGs trigger direct B-Cell activation and therefore these dinucleotides provide a selective disadvantage (Krieg et al., 1995)." We can certainly mention this, and the theorised reason behind it. RandomCanadian (talk / contribs) 00:45, 8 June 2021 (UTC)

@Bakkster Man: You are right, although the skewness is notable for virologists working on molecular clocks, the paper by Wang et al seem to have found a quick fix to the bias. So it should be important to include it in an article on the Phylogenetics of SARS-CoV-2 (which does not exist), but not on the general article on the SARS-CoV-2. The info posted by RandomCanadian I couldn't understand and can't comment. Forich (talk) 02:26, 8 June 2021 (UTC)

@Forich: Trying to put this in somewhat more complete terms (I'm no expert, so I might be wrong): "The skew against cytosine [C] and guanine [G] in human pathogens is caused by natural selection, since the presence of C and G in single-stranded genetic material (viral RNA, at least in the group of viruses SARS-CoV-2 is part of, is single-stranded) triggers an immune response from B-cell lymphoma which hinders the virus". RandomCanadian (talk / contribs) 02:45, 8 June 2021 (UTC)

@RandomCanadian:, oh thanks for explaining further. You seem to be mentioning another implication of having nucleotide skewness, that it is caused by natural selection and therefore shows clues of how the virus evolved. I mentioned the skewness originally because it was distorting the molecular clock studies, but this other implication seem ok, maybe we should ask in Wikiproject Viruses if it makes it notable. Forich (talk) 02:59, 8 June 2021 (UTC)

Uh, doesn't § Genome already mention the nucleotide skew? The article text cites Rice et. al. 2021 and Wang et. al. 2020. The sources even discuss host immune targeting of CpG sites and making sure the RNA doesn't form stem loops that stop translation. Rotideypoc41352 (talk · contribs) 03:36, 8 June 2021 (UTC)

Yes, I missed it. Thanks for spotting it. My case is done. Forich (talk) 20:17, 13 June 2021 (UTC)

Last paragraph poorly worded

"..some people have recovered from confirmed infections" is quite misleading and might worry some people. Many many people have recovered from confirmed infections especially in developed countries with widespread testing regimes. Galund (talk) 19:43, 13 June 2021 (UTC)

Agree, have removed it. The general sentiment of that sentence wasn't wrong, but it was both uncited and phrased in a fairly misleading way. I don't think that information really needed to be at that point in the article anyway. ~ mazca ^talk 21:34, 13 June 2021 (UTC)

RFC that may interest those of you on this talk page

Talk:Investigations_into_the_origin_of_COVID-19 (edit | article | history | links | watch | logs)

Investigations_into_the_origin_of_COVID-19 has an ongoing RFC: "joint WHO-China report" or "WHO-convened report?". A discussion is taking place. If you would like to participate in the discussion, you are invited to add your comments on the discussion page. Thank you. Shibbolethink ^{(♔ ♕)} 19:25, 25 June 2021 (UTC)

I've advertised this here because the different uses of terms for the report include a section that is transcoded from this article! So please add your input. Thanks! --Shibbolethink ^{(♔ ♕)} 19:25, 25 June 2021 (UTC)

FYI, I withdrew this per WP:SNOWBALL. It was overwhelmingly in favor of option B. For more nuance see the withdrawal notice linked above.--Shibbolethink ^{(♔ ♕)} 02:06, 30 June 2021 (UTC)

Fringe theories again

(See Severe_acute_respiratory_syndrome_coronavirus_2#Reservoir_and_origin, starting from "Early in the pandemic, conspiracy theories spread on social media...") In my opinion, conspiracy theories should not even be mentioned here. This conspiracy theory is a social phenomenon and it is irrelevant to the article about a virus (article about pandemic/disease could be a different case). Because it is out of scoupe. Compare it to the article about HIV. AIDS denialism, as well as a theory about AIDS artificial origin (see Operation INFEKTION) are extremely well documented, but still we do not have a word about them in the article about HIV itself. And HIV is a GA, so I suspect that such an approach reflects general consensus. And also "amplified by echo chambers in the American far-right". Who cares about American far-right? There are articles about pandemic in specific countries for it. --Hwem (talk) 11:09, 17 June 2021 (UTC)

I agree with your assessment. This is an article about the science of a virus. It is not an article about society and politics. There are other articles to cover those topics. Previously, there have been also other non-involved editors who have noted how the paragraph is out of place. The paragraph should be removed. --Guest2625 (talk) 12:10, 17 June 2021 (UTC)

Those whom the American far-right has harmed care about the American far-right. Let's better global coverage without dismissing that. We could all use a little more compassion here. That said, I see no problem removing anything that isn't essentially biomedical information supported by WP:MEDRS. Rotideypoc41352 (talk · contribs) 13:27, 17 June 2021 (UTC)

I would agree, this article doesn't need this information. I suspect the transclude to Investigations into the origin of COVID-19 is part of the reason why it has stuck around here so long. I'm quite in favor of moving the final two paragraphs to Investigations into the origin of COVID-19, and removing them from this article. Probably best from someone with good citation tools or enough time to ensure all the citations move as needed. Bakkster Man (talk) 15:02, 17 June 2021 (UTC)

I'd say that a short mention here is probably due (compare with Moon landing, which has a short section on conspiracies), but if it isn't done by then I'll get around to moving it to the suggested article this evening. RandomCanadian (talk / contribs) 17:05, 17 June 2021 (UTC)

I'd suggest this article is better compared to Moon, which references the actual landings but not the conspiracies. We link to Investigations into the origin of COVID-19, the analogous article to Moon landing where the conspiracies are more due. Bakkster Man (talk) 17:28, 17 June 2021 (UTC)

 Done The only thing that's left to check is whether there is any source duplication. I'll go take a look at updating the main pandemic article, for consistency. RandomCanadian (talk / contribs) 21:57, 17 June 2021 (UTC)

Is this paper appropriate for the "Reservoir and origin" section?

https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691 Sadly, not yet accepted for publication in a journal, even though a month passed (perhaps more like a working paper than a preprint, IDK). Still being cited however. Ain92 (talk) 19:27, 18 June 2021 (UTC)

Not sure. It could qualify as a WP:SPS (the author is, without question, a subject-matter expert), but that would not be ideal since there are surely much better sources for this. The citation you give is also a pre-print... I see there's at least one other link to virological.org in the article. Will try finding better sources. RandomCanadian (talk / contribs) 19:38, 18 June 2021 (UTC)

I would say, categorically, no. If it's good enough for us to use, it'll get peer-reviewed and published (one month isn't a lot of time for that process). Bakkster Man (talk) 20:04, 18 June 2021 (UTC)

LDR

Special:Diff/1029589934 by Coffeeandcrumbs (talk) leads me to ask if maintaining LDR is worth the effort. Potential transclusion issues aside, people tend to add citation templates inline, as is common, so one of the regulars has to move it into the {{reflist}}. Also, the template throws an error every time the article stops citing a defined reference. I was just wondering if anything other than precedent stops us from switching to the usual citation style. Rotideypoc41352 (talk · contribs) 02:24, 21 June 2021 (UTC)

Extended-confirmed-protected edit request on 25 June 2021

The variants portion should be renamed to "Variants of concern". SARS-CoV-2 has many variants, mostly harmless. Alpha, Beta, Gamma and Delta are variants of concern. 2001:1970:4822:9600:6075:21E8:4598:33B1 (talk) 05:05, 25 June 2021 (UTC)

I don't see how most COVID-19 variants are harmless. The big 4 are mostly noted for increased transmissiblity compared to the ancestral strain, not increased deadliness. Hemiauchenia (talk) 05:10, 25 June 2021 (UTC)

Yeah, "harmless" isn't the right word. It's more like "have limited clinical differences from the wild strain". But the section covers variants of all kinds, including the Variants of Concern. Bakkster Man (talk) 17:40, 25 June 2021 (UTC)

 Not done for now: please establish a consensus for this alteration before using the {{edit extended-protected}} template. ScottishFinnishRadish (talk) 10:50, 25 June 2021 (UTC)

Extended-confirmed-protected edit request on 10 July 2021

CHANGE FROM

is not an uncommon occurrence

CHANGE TO

is a common occurrence

BECAUSE

Remove over complex double negative to aid comprehension Missionstatus (talk) 12:22, 10 July 2021 (UTC)

 Note: Both means the same. I did not find it complex enough to change. Run n Fly (talk) 14:34, 10 July 2021 (UTC)

Transclude material to COVID-19 lab leak hypothesis

I'd like to transclude information on this page about virus origins to the new page that's been created, COVID-19 lab leak hypothesis. I don't know if that page will be kept, merged or deleted, but while it exists, we should include what's known in scientific literature about this virus' origins at that page.

Is anyone here willing to help with transclusion of some kind? -Darouet (talk) 06:17, 19 July 2021 (UTC)

Text copied from Severe acute respiratory syndrome coronavirus 2#Reservoir and origin to COVID-19 lab leak hypothesis#Scientific consensus on likely natural zoonosis from bats

Per my comment above, I've copied text and sources from Severe acute respiratory syndrome coronavirus 2#Reservoir and origin to COVID-19 lab leak hypothesis#Scientific consensus on likely natural zoonosis from bats. I or other editors might copy additional material, and possibly modify it slightly, from this article into that one in order to contextualize the discussion about a possible laboratory origin with strong scientific references. -Darouet (talk) 11:55, 19 July 2021 (UTC)

You can see the diff of the copying here [27]. -Darouet (talk) 12:03, 19 July 2021 (UTC)

First scientifically accurate atomic model in WP and Commons

Dear Colleagues! Please change the outdated image in the Virusbox article for a new, more detailed and scientific one (High quality large image. FP on Commons. Illustrates article well. Published on the N+1 popular science website):

Scientifically accurate atomic model of the external structure of the SARS-CoV-2. Each "ball" is an atom.
● Cobalt: envelope
● Turquoise: spike glycoprotein (S)
● Crimson: envelope proteins (E)
● Green: membrane proteins (M)
● Orange: glucose

Sources

• Thank you for your attention. — Best Regards, Niklitov (talk) 01:06, 1 August 2021 (UTC)

 Done Thanks, @Niklitov. See diff. ––𝗙𝗼𝗿𝗺𝗮𝗹𝗗𝘂𝗱𝗲^(talk) 04:09, 1 August 2021 (UTC)

what is technical name for the spike protein

Does it have a unique name if we were to have an article just about the spike protein?

There is also a December 2020 paper I would like to see put into context called "The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease" which can be found at https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1.full

Are there any other concerns about the spike protein besides microvascular disease in cardiac pericytes? WakandaQT (talk) 09:22, 2 August 2021 (UTC)

Cell types

I propose to list the cell types that the virus typically infect. So far I was able to find only a couple of sources on that. E.g.: [28] AXONOV (talk) ⚑ 13:36, 3 August 2021 (UTC)