Since it's your own personal essay, free free to remove. —PaleoNeonate – 03:00, 8 April 2021 (UTC)[reply]

PaleoNeonate, looks good to me. Thanks for contributing. –Novem Linguae (talk) 06:04, 8 April 2021 (UTC)[reply]

"In my opinion, Trump and the US government want COVID-19's origin to be something that gives China maximum responsibility for the pandemic, and are selectively looking for evidence to support that." I seem to remember that there are sources quoting relevant remarks that don't only make it an editor's opinion and the essay could likely cite some... [1], [2] this wasn't Trump but Missouri, [3] mentions "And he continues to smear the World Health Organization in a transparent quest for scapegoats", [4] mentions CDC defunding, suboptimal handling of the local situation, spreading disinformation about it and blaming China... There's still a more recent source I was looking for but didn't find again though, this was from a Guardian search, so it was likely in another paper. If I eventually fall on it I'll link it, —PaleoNeonate – 06:29, 8 April 2021 (UTC)[reply]

Novem Linguae. could you please get the tense right? "Trump and the US government want". Which US government? The current one? The one under Trump? At the very least it should be "Trump wanted" with a bit of material about what Biden and the current US government wants. --Guy Macon (talk) 15:49, 22 April 2021 (UTC)[reply]

Guy Macon, thanks for the feedback. Has Biden done much to walk back the lab leak idea? If not, then present tense may still be appropriate. –Novem Linguae (talk) 16:04, 22 April 2021 (UTC)[reply]

Judging by stuff like Investigations_into_the_origin_of_COVID-19#Biden_Administration ("On 14 April 2021, the Director of National Intelligence Avril Haines, and other officials of the Biden Administration, said that they had not ruled out the possibility of a laboratory accident as the origin of the Covid-19 virus.[99]"), likely not; though Biden has spared us the shenanigans coming directly from the former on daily twitter posts. RandomCanadian (talk / contribs) 16:13, 22 April 2021 (UTC)[reply]

(edit conflict) I don't keep up with US politics, so I don't know whether US government should be past tense. Certainly Trump should be. A quick search came up with these:[5][6]

Obviously when you wrote that you had particular individuals in the US government in mind. Just the president? Cabinet members that Biden replaced? Senators who are still in office? Agency heads that were retained? --Guy Macon (talk) 16:26, 22 April 2021 (UTC)[reply]

(...Sound of Crickets...) --Guy Macon (talk) 02:51, 30 April 2021 (UTC)[reply]

Trump and Pompeo seemed to be the most egregious offenders. I think it likely Trump directed entire agencies to push the lab leak theory. Some of the statements coming out of the State Department in late 2020/early 2021 were particularly egregious. –Novem Linguae (talk) 04:48, 30 April 2021 (UTC)[reply]

Sounds reasonable. So "Trump and the US government want" should be changed to "Trump and the State Department wanted", thus fixing the incorrect tense and no longer implying that post office letter carriers and national park rangers want the same thing Trump wanted. --Guy Macon (talk) 13:10, 30 April 2021 (UTC)[reply]

Hmm. Has the Biden administration done enough to distance themselves from the lab leak theory? For example, some quick googling "is us government pushing lab leak theory" reveals this NPR article on the Biden administration 1) refusing to rule out the lab leak, and 2) criticizing the WHO report on shaky grounds. –Novem Linguae (talk) 13:48, 30 April 2021 (UTC)[reply]

Interesting. I trust Joe Biden about as much as I trust Xi Jinping or Donald Trump. this is from a source that I trust, but so is this and this. I don't know how to reconcile them. :( --Guy Macon (talk) 19:19, 30 April 2021 (UTC)[reply]

Hey guys. What are your thoughts on how accurate the Chinese COVID death toll is? Statistics of the COVID-19 pandemic in mainland China, 3rd paragraph describes China's numbers as being accurate, and their low death count due to a thorough response. But I'm getting pushback on this idea from some people, so just wanted to double check. Is this argument that China has a very low COVID death toll solid enough to keep in the essay? Thanks. –Novem Linguae (talk) 17:48, 29 April 2021 (UTC)[reply]

I am also interested in the answer. At first glance I am seeing:

1. Sources that are telling whoppers about how high the numbers are.
2. Sources that are telling whoppers about how low the numbers are.
3. Good-faith journalists and scientists trying to figure out the truth but coming up with different numbers because this one is really hard to figure out with all the lies flying about.

I think you might have to give a range of estimates with attribution. In fact, documenting the whoppers would be good information to see who the liars are. Everybody talks about North Korea's claimed 0% Covid-19 rate for the same reason that Kim Jong-un claims to have cured Aids, Ebola and cancer with single miracle drug is so interesting -- and the reason is not because the claims are accurate. --Guy Macon (talk) 22:40, 29 April 2021 (UTC)[reply]

This story from The New York Times is very informative:

• How Steve Bannon and a Chinese Billionaire Created a Right-Wing Coronavirus Media Sensation

--Guy Macon (talk) 13:22, 4 May 2021 (UTC)[reply]

Great article. Thanks for sharing. I added it to the essay. –Novem Linguae (talk) 16:40, 5 May 2021 (UTC)[reply]

Reviews by scientists:

• Statement from Prof Edward Holmes on the SARS-CoV-2 virus --University of Sydney
• The proximal origin of SARS-CoV-2 -- National Center for Biotechnology Information, U.S. National Library of Medicine
• Why misinformation about COVID-19’s origins keeps going viral --National Geographic
• MIT Review #1 --Massachusetts Institute of Technology
• MIT Review #2 --Massachusetts Institute of Technology
• MIT Review #3 --Massachusetts Institute of Technology
• MIT Review #4 --Massachusetts Institute of Technology
• Critical Analysis of the New Preprint that Claims Proof for Bioengineered SARS-CoV-2 --Microbial Instincts
• In Response: Yan et al Preprint Examinations of the Origin of SARS-CoV-2 --Johns Hopkins Center for Health Security
• Still no evidence the coronavirus was made in a lab --New Scientist

Other reviews:

• Cloaked Science: The Yan Reports --Harvard University Media Manipulation Casebook
• How Steve Bannon and a Chinese Billionaire Created a Right-Wing Coronavirus Media Sensation --The New York Times
• Virality Project (China): Coronavirus Conspiracy Claims --Stanford University
• FACT CHECK: COVID-19 Whistleblower Li-Meng Yan Releases Paper With Other Scientists 'Suggesting Sophisticated Laboratory Modification' --Tech Times
• Weird science: How a 'shoddy' Bannon-backed paper on coronavirus origins made its way to an audience of millions --CNN

Related Wikipedia pages:

• Li-Meng Yan
• COVID-19 misinformation
• Investigations into the origin of COVID-19

--Guy Macon (talk) 01:57, 8 May 2021 (UTC)[reply]

Hey Guy Macon. You made a great talk page post recently summarizing the shady origins of the lab leak idea, here. Would it be OK if I copied this into this essay? Thanks. –Novem Linguae (talk) 19:22, 10 May 2021 (UTC)[reply]

Yes. Anyone can copy (with or without modifications) anything I write anywhere unless I say something specific like "Copyright 2021 Yoyodyne", which I do when someone pays me to write, say, a technical manual and thus they own it. Because I feel so strongly about allowing anyone to make copies without any requirements like attribution, asking permission first, etc., everything I write is released under CC0. And BTW, Wikipedia is telling you a fib when they say everything is released under the CC BY-SA 3.0 License. The actual rule is "CC BY-SA 3.0 or any less restrictive license." --Guy Macon (talk) 21:36, 10 May 2021 (UTC)[reply]

Thanks. I added a section just now. Feel free to heavily edit it, since it's your content, and since you seem to have a knack for getting to the bottom of conspiracy theories. Maybe keep the non-collapsed part to two paragraphs, so it's a similar size to the other sections. You can also take a stab at re-wording the "Government misinformation" section if you want. We may want to pepper in some of your citations as well. –Novem Linguae (talk) 21:50, 10 May 2021 (UTC)[reply]

Re. "shady origins" - there's also "shady methods". Daszak and Andersen have a couple of interesting rebuttals to the conspiracists on his Twitter (https://twitter.com/peterdaszak), ex. [7]; [8] - the news articles they cite aren't exactly MEDRS, but they could possibly be cited regarding stuff which is not subject to it (respectively, prior concerns with the sea food market and something to add to the misinfo article). RandomCanadian (talk / contribs) 16:21, 11 May 2021 (UTC)[reply]

Many sources seem to entirely assume a zoonotic origin and not even mention anything else, so I don't know if we should add something about that. For example:

• To, Kelvin Kai-Wang; Sridhar, Siddharth; Chiu, Kelvin Hei-Yeung; Hung, Derek Ling-Lung; Li, Xin; Hung, Ivan Fan-Ngai; Tam, Anthony Raymond; Chung, Tom Wai-Hin; Chan, Jasper Fuk-Woo; Zhang, Anna Jian-Xia; Cheng, Vincent Chi-Chung; Yuen, Kwok-Yung. "Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic". Emerging Microbes & Infections. 10 (1): 507–535. doi:10.1080/22221751.2021.1898291. ISSN 2222-1751.

"The suspected animal-to-human jumping of 4 betacoronaviruses including the human coronaviruses OC43(1890), SARS-CoV-1(2003), MERS-CoV(2012), and SARS-CoV-2(2019) indicates their significant pandemic potential. The presence of a large reservoir of coronaviruses in bats and other wild mammals, culture of mixing and selling them in urban markets with suboptimal hygiene, habit of eating exotic mammals in highly populated areas, and the rapid and frequent air travels from these areas are perfect ingredients for brewing rapidly exploding epidemics." (abstract)
"The origin of SARS-CoV-2 is still unknown. Recombination is a frequent event for the viral subgenus Sarbecovirus, which contains SARS-CoV, bat SARS related CoV, and SARS-CoV-2 [54]. Some studies suggested that the bat SARS-CoV-2-like coronaviruses are recombinants of lineages related to SARS-CoV and SARS-CoV-2, and SARS-CoV-2 may result from recombinations between these bat SARS related coronavirus and the pangolin SARS related coronavirus [55, 56]. However, another study suggested that recombination may not be involved in the generation of SARS-CoV-2, but the RBD of SARS-CoV-2 shares the same ancestral trait as bat viruses [57]. The divergence date between SARS-CoV-2 and bat sarbecovirus has been estimated to be 1948 [57]." (later in the article - no mention of labs or leaks or anything)

• Michelitsch, Anna; Wernike, Kerstin; Ulrich, Lorenz; Mettenleiter, Thomas C.; Beer, Martin (7 April 2021). "SARS-CoV-2 in animals: From potential hosts to animal models". Advances in Virus Research. doi:10.1016/bs.aivir.2021.03.004. ISSN 0065-3527.

Since SARS-CoV-2 very likely has a zoonotic origin, it is important to identify the original animal reservoir to prevent future similar outbreaks. Therefore, during the last months, a significant number of different animal species were either sampled in the field or experimentally infected with SARS-CoV-2, in order to evaluate their susceptibility to infection and to assess their potential as animal reservoirs.

• Osuchowski, Marcin F; Winkler, Martin S; Skirecki, Tomasz; Cajander, Sara; Shankar-Hari, Manu; Lachmann, Gunnar; Monneret, Guillaume; Venet, Fabienne; Bauer, Michael (6 May 2021). "The COVID-19 puzzle: deciphering pathophysiology and phenotypes of a new disease entity". The Lancet. Respiratory Medicine. doi:10.1016/S2213-2600(21)00218-6. ISSN 2213-2600. (I've trimmed the list of authors a wee bit...)

"The zoonotic SARS-CoV-2 virus that causes COVID-19 continues to spread worldwide, with devastating consequences." (abstract)

"The emergence of SARS-CoV-2 has resulted in a health crisis not witnessed since the 1918–19 Spanish influenza pandemic. The most plausible origin of SARS-CoV-2 is natural selection of the virus in an animal host followed by zoonotic transfer."

And then there's the "Clinical pathology of COVID-19" section which describes similarities with all of the other coronaviruses...

• Younes, Salma; Younes, Nadin; Shurrab, Farah; Nasrallah, Gheyath K. (18 November 2020). "Severe acute respiratory syndrome coronavirus‐2 natural animal reservoirs and experimental models: systematic review". Reviews in Medical Virology. doi:10.1002/rmv.2196. ISSN 1052-9276.

"There is a strong evidence that SARS‐CoV‐2 virus originated in bats 64 ; however, the intermediate animal host is still unknown (Figure ​(Figure3).3). Several studies showed that pangolins, snakes, turtles, and mink are all possible intermediate hosts, however, further investigations are needed. 66 , 67 , 68 It is worth mentioning that recent findings that analyse the probable animal reservoir to Covid‐19 suggest the snake as a reservoir, based on relative synonymous codon usage bias. 67 However, the missing link or intermediate link for animal to human transmission of SARS‐CoV‐2 from a recent study suggests the DNA and protein sequence of Malayan pangolins. 69"
"SARS‐CoV‐2 was first identified in Wuhan city in China in hospitalized patients who previously visited the Huanan wet seafood market where various animals including chickens, pigs, pangolins, bats, snakes, frogs, rabbits, and marmots are sold for human consumption, proposing a suitable environment for zoonotic infection spill‐over to humans. 67 , 70 , 71 , 72 , 73 Scientists believe that these traditional Chinese practices might be responsible for the SARS‐CoV‐2 pandemic in humans and that the recurrent interactions between humans and animals without proper biosafety measures present a substantial risk for the occurrence of zoonotic diseases. 74 Zoonotic CoVs have crossed the species barrier twice in the past 2 decades (SARS‐CoV; 2002 and MERS‐CoV; 2012). Thus, scientists have speculated that SARS‐CoV‐2 resulted from a zoonotic spillover event as well. Zoonotic CoVs need to propagate in their zoonotic reservoirs, and then, seek the chances to spillover via intermediate hosts into susceptible human targets, where they can maintain human‐to‐human transmission. Bats have been revealed as the natural hosts for several human CoVs, including HCoV‐NL63, HCoV‐229E, SARS‐CoV, and MERS‐CoV. 75 , 76 Genome sequence analysis confirmed that SARS‐CoV‐2 is 96% identical to the bat CoV RaTG13 at the whole‐genomic level, 77 and hence bats are believed to be the primary source of origin for the novel SARS‐CoV‐2. However, the intermediate host that is yet to be elucidated. 11 , 67 , 70 , 72 , 78 Researchers proposed two hypotheses for the emergence of SARS‐CoV‐2: (1) Natural selection may have occurred in an animal host before transmission to mankind; and (2) natural selection of viruses may have occurred in humans after zoonotic transmission. 79 In this regard, studies involving the use of animal models or cell culture are in need to help clarify these two scenarios. 79"

So, basically, this shows that serious scientists do not give much credence to this. Also note the excellent, recent paper:

• Frutos, Roger; Gavotte, Laurent; Devaux, Christian A. (18 March 2021). "Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover model to the viral circulation model". Infection, Genetics and Evolution. doi:10.1016/j.meegid.2021.104812. ISSN 1567-1348.

Which has a detailed breakdown of existing hypotheses and rebuttals for the nonsense ones. RandomCanadian (talk / contribs) 16:11, 11 May 2021 (UTC)[reply]

Please help to reconcile the contradictory claims documented at Wikipedia:Fringe theories/Noticeboard#Origins of SARS-CoV-2. --Guy Macon (talk) 13:18, 12 May 2021 (UTC)[reply]

Hello, I would like to ask why the essay is titled "There was no lab leak". As far as I know it is a statement not supported by any of the MEDRS that the essay mentions, from what i see there are MEDRS which describe a lab leak as unlikely or implausible, but none which definitely say "there was no leak", right? --Francesco espo (talk) 22:13, 23 May 2021 (UTC)[reply]

The title could be rephrased to e.g. "the lab leak is a fringe theory" or "the lab leak is a [much ]less likely theory than transmission from animals"? Apokrif (talk) 13:22, 25 May 2021 (UTC)[reply]

I just took a quick look at this essay, and several issues in a couple of its sections stood out to me straight away:

In the "China very low deaths, USA very high deaths" section, you apparently take the Chinese government's official death toll (ca. 5K) at face value, when, as far as I'm aware, few others do. Just one example I found just now in a quick Google search: " To date, China has put its nationwide pandemic death toll at 4,735, but that is certainly a huge underestimate." [9] Note that this is from the Washington Post, which is hardly a pro-Trump or pro-Republican outlet!

Moreover, if China did have a significantly lower per capita death rate than the US (which they may well have, but their covid death toll was certainly much higher than 5K), there could be any number of reasons for this, such as: 1) Their authoritarian system allowed them to more quickly effect a robust lockdown. 2) Their population may have had more acquired immunity, due to more previous exposure to other similar coronaviruses. 3) Chinese people may have more innate resistance to the virus than certain other ethnic/racial groups. In particular, people of African dissent seem to be especially vulnerable, and this appears to be due to more than just socioeconomic factors...

It could be a combination of all three, or any number of other potential factors, but ultimately none of this has any bearing on the origin of the virus.

The other section that I find especially problematic is "Suspicious origins of the lab leak idea."

Frankly, this section reads as nothing more than association fallacy, combined with a hefty helping of WP:idontlikeit.

It's basically saying "various immoral/unreliable/suspicious/bad people say X, so therefore X is not true." Anyone with even a cursory knowledge of logic or the scientific method can see that this sort of reasoning is deeply fallacious.

Moreover, the idea that an emergent outbreak of a previously unknown coronavirus strain, which first appeared in the immediate vicinity of a lab which studies and manipulates such viruses, may have escaped for said lab, is hardly a fanciful notion. On the contrary, it's a rather self-evident hypothesis, just as it would be if a new virus were to have first emerged in the vicinity of Fort Detrick, Maryland!

It is of course true that Trump and his allies would have motive to amplify such discourse - in order to deflect from his own less than ideal handling of the pandemic within the US - but this doesn't really say anything (one way or the other) about the actual accuracy of the lab leak hypothesis.

While the knee-jerk compulsion to automatically take the opposite view from Trump on everything probably contributed to many rejecting the lab leak theory early on, these days many more people, including those with views very different from Trump, are taking the idea very seriously. One notable example is the Bulletin of the Atomic Scientists: [10]

-2003:CA:8748:5C71:E17C:1138:2B8B:B9DD (talk) 09:42, 25 May 2021 (UTC)[reply]

Hey there. Thanks for posting. I think many of your counter-arguments are reasonable, although I'm not so sure about this "Chinese people are more immune to COVID" idea, or this "coronavirus springing up in Wuhan is equivalent to coronavirus springing up in Maryland". Chinese horseshoe bats are native to that part of China, so a coincidence is quite plausible. Anyway, the ideas in the "government misinformation" section are not iron clad, but it is my personal opinion that they are stronger and make more sense than alternative ideas I've seen. This is probably one of those things we'll just have to agree to disagree on. –Novem Linguae (talk) 10:03, 25 May 2021 (UTC)[reply]

Hey, thanks for the friendly and civil reply. Of course you're correct that it's plausible that the emergence of covid in close proximity to the Wuhan lab could be purely coincidental. I wasn't asserting that this proximity offered any sort of conclusive proof, but simply that it meant that the lab leak theory was a very reasonable hypothesis, and not some sort of fanciful or unhinged conspiracy theory.

As the article I linked above, from the Bulletin of the Atomic Scientists, notes, at this point there's not direct evidence for either theory - natural emergence or lab leak. Notably, unlike with SARS-1 and MERS, no intermediate host animal has been identified. I definitely recommend that you and others read that article (if you haven't already), as it offers a rather detailed and well informed and articulated summation of the evidence for the lab-leak hypothesis.

This article also notes the danger of group-think:

Science is supposedly a self-correcting community of experts who constantly check each other’s work. So why didn’t other virologists point out that the Andersen group’s argument was full of absurdly large holes? Perhaps because in today’s universities speech can be very costly. Careers can be destroyed for stepping out of line. Any virologist who challenges the community’s declared view risks having his next grant application turned down by the panel of fellow virologists that advises the government grant distribution agency.

None of this requires or implies some sort of grand global conspiracy. It's simply a matter of scientists, while being intelligent and well-educated people, still being human beings, and as such vulnerable to prejudice, group-think, instincts for self-preservation, and even conflicts of interest - direct in the case of people like Daszak, and more indirect in the case of other virologists with a (well founded) fear that public support for, and funding of, the sort of research that they do could be undermined if the lab-leak theory were to gain traction.

Anyway, I've got to get going, but might check back in at some point in the future. Have a good day! -2003:CA:8748:5C71:E17C:1138:2B8B:B9DD (talk) 11:01, 25 May 2021 (UTC)[reply]

Decent points. I hesitate to trust The Bulletin of Atomic Scientists too much, as it is not a biomedical field, but I'll take a look. "Have a good day." Thanks, you too :) –Novem Linguae (talk) 11:13, 25 May 2021 (UTC)[reply]

Hey Novem Linguae and 2B8B:B9DD, just wanted to say I started collecting the many errors Thomas Wade makes in that Bulletin piece. You can find the list over here. I have a PhD in virology and cannot stand when people publish things that are not only outright incorrect, but restate proven falsehoods. I was just amazed at how many mistakes he makes. Really ruined his credibility for me, but that probably started when Wade said race was correlated with intelligence back in 2014.--Shibbolethink ^{(♔ ♕)} 17:59, 25 May 2021 (UTC)[reply]

Shibbolethink, awesome, a subject matter expert. On Wikipedia, you guys are super rare and super needed in these complex topic areas. Maybe you can add Gain of function research to your watchlist. From your Reddit posts, you seem to know quite a bit about that, and the article is not in good shape. Thanks for commenting here, and I'm glad you like the essay. I'll definitely take a thorough look at your Reddit posts. Happy editing :) –Novem Linguae (talk) 22:59, 25 May 2021 (UTC)[reply]

Novem Linguae holy cow, that article really is a tire fire. Makes sense for a hot button issue that even virologists hate to touch, because we think everybody considers us to be mad scientists. lol. Will definitely give it a careful read... thanks for the heads up and happy editing :) --Shibbolethink ^{(♔ ♕)} 23:03, 25 May 2021 (UTC)[reply]

Related: literature review

@Shibbolethink: You might be able to help me with User:RandomCanadian/The origins of COVID-19: literature review - I'm trying to compile the sources I can find on the topic (including the ones cited here, and others) to see what they say, to improve the existing sections on this in the related articles (admittedly, this might be massive levels of overkill, but there's no harm in being too thorough, is there?). Feel free to suggest sources I might have missed or lend a hand in assessing those I have found. Cheers, RandomCanadian (talk / contribs) 22:11, 25 May 2021 (UTC)[reply]

Would love to :) As an aside, I actually acted as peer reviewer on some of the articles you've gathered so far! Can't say which ones ofc. Right now I'm studying for my board exams (and shouldn't be procrastinating on here, haha), but once that clears up I would love to put some work into this. Will keep you posted. --Shibbolethink ^{(♔ ♕)} 22:31, 25 May 2021 (UTC)[reply]

• Hey Novem Linguae, just wanted to say I thought this was really well done. Great essay, gets to the point, cites the right sources, and makes clear the consensus. Also wanted to point you to this longform piece^[1] I wrote on Reddit about this exact question and the evidence for and against. In case you hadn't come across it! Keep up the good work. --Shibbolethink ^{(♔ ♕)} 17:51, 25 May 2021 (UTC)[reply]

  Shibbolethink, I read your PDF cover to cover just now. Exceptionally well done. You achieved a perfect mix of technical, lay-person accessible, and good writing. I'm sure you're already looking into it, but that definitely deserves to be published in a reputable source of some kind and widely distributed. –Novem Linguae (talk) 13:47, 27 May 2021 (UTC)[reply]

  Thank you, you're very kind :) I'm just glad it's still bouncing around these days! Maybe I'll try and clean it up and get it published at Bioessays or another op-ed type place... But I think I also might want to just keep my CV away from this lab leak nonsense, lol. And keep this post in the realm of the internet where the discussion lives. Where the people are--Shibbolethink ^{(♔ ♕)} 00:55, 30 May 2021 (UTC)[reply]

  Shibbolethink, I went ahead and added a "Technical evidence" section today based on your PDF. I hope you don't mind. Feel free to edit it if you'd like. Good luck on your exams. –Novem Linguae (talk) 11:53, 31 May 2021 (UTC)[reply]

"SARS-CoV and SARS-CoV-2 are members of the Sarbecovirus subgenus of betacoronaviruses (family Coronaviridae).

Two sarbecoviruses lineages, GX (Guangxi) and GD (Guangdong), have been identified in Malayan pangolins, Manis javanica, illegally imported into China.

A variety of sarbecoviruses have also been described in bats of the genus Rhinolophus...

The bat coronavirus RaTG13 genome was sequenced from a sample from a Rhinolophus affinis captured at Mojiang cave in Yunnan province, China in 2013.

RaTG13 remains the virus with the highest overall sequence similarity to SARS-CoV-2...

Newly sequenced sarbecoviruses from bats captured in Cambodia, Thailand and Japan possess different combinations of spike motifs in the RBD and the S1/S2 junction that were first described in SARS-CoV-2.

These observations are consistent with the natural origin of SARS-CoV-2 and strongly inconsistent with a laboratory origin".

Source: "Spike protein sequences of Cambodian, Thai and Japanese bat sarbecoviruses provide insights into the natural evolution of the Receptor Binding Domain and S1/S2 cleavage site" by Edward C. Holmes (Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia), Kristian G. Andersen (Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California USA), Andrew Rambaut (Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK), and Robert F. Garry (Department of Microbiology and Immunology, Tulane University Medical Center, New Orleans, Louisiana USA)

URL: [ https://virological.org/t/spike-protein-sequences-of-cambodian-thai-and-japanese-bat-sarbecoviruses-provide-insights-into-the-natural-evolution-of-the-receptor-binding-domain-and-s1-s2-cleavage-site/622 ]

--Guy Macon (talk) 14:45, 1 June 2021 (UTC)[reply]

@Guy Macon: Interesting, but that's all pre-prints/not peer-reviewed. It's easy to find credible sources which provide compelling arguments (for ex. the naturally-occuring FCS in other coronaviruses) against the lab origin claims. We should wait till this gets published in reputable journals. FWIW, the far more interesting paper on that site is the one about COVID likely not having originated from the Wuhan seafood market (an argument made recently by Foster, see Forster, Peter; Forster, Lucy; Renfrew, Colin; Forster, Michael (2020-04-28). "Phylogenetic network analysis of SARS-CoV-2 genomes". Proceedings of the National Academy of Sciences. 117 (17): 9241–9243. doi:10.1073/pnas.2004999117. ISSN 0027-8424. {{cite journal}}: Unknown parameter |lay-url= ignored (help); a hypothesis which, according to our friendly neighbourhood virologist, is also an interesting route. RandomCanadian (talk / contribs) 19:21, 1 June 2021 (UTC)[reply]

The fact that several prominent experts in virology have concluded that the spike protein sequences "are consistent with the natural origin of SARS-CoV-2 and strongly inconsistent with a laboratory origin", combined with the fact that those arguing on the other side have literally zero actual biological evidence, may not be acceptable as an article citation because it is a preprint, but it is excellent at identifying those Wikipedia editors (you know who you are) who are going to ignore the actual biology as being inconvenient facts and continue to believe what they want to believe despite all evidence and arguments to the contrary. --Guy Macon (talk) 21:46, 1 June 2021 (UTC)[reply]

@Guy Macon: The bigger problem is how we reconcile the dramatic difference between how academic sources (preferred per the whole of our policies on reliable sources) present this and how news sources treat this ("journalistic false balance" is not a novel concept). Try explaining that when scientific sources are dismissed as "just one paper" or "outdated" (which is, for matters which are in the news, the natural outcome of following and not leading the sources, but I digress) or a multitude of other reasons (and of course, we don't have quite the same qualitative measurements for the popular press so this is like comparing apples and oranges rotten tomatoes)... RandomCanadian (talk / contribs) 23:32, 1 June 2021 (UTC)[reply]

There are people who in good faith are not convinced that the lab leak theory is highly unlikely, but there are others who know in their hearts that it is true because their favorite bullshit source says so. You can often identify the latter by the fact that they keep confusing "we should investigate further" with "likely" or even "proven". No scientist ever has come out against paying scientists to investigate anything further. --Guy Macon (talk) 23:46, 1 June 2021 (UTC)[reply]

Not science

Guy Macon You’re quoting from a paper forum post by Robert F. Garry and other co-authors of the hardline Proximal Origin paper letter, that reputed fellow co-author W. Ian Lipkin has now distanced himself from [11] [12] [13]. This paper forum post, like the Proximal Origin letter has not been peer reviewed, does not provide any supporting data for Reproducibility, and has been critiqued by scientists in their own forums [14]. What you are demonstrating is that there is a scientific controversy on COVID-19 origins, with scientists holding opposing views, which we should cover with WP:NPOV. CutePeach (talk) 08:47, 2 June 2021 (UTC)[reply]

Note: I no longer read any comments by CutePeach due to repeated snarky comments verging on personal attacks, and I have not and will not read the above.

I find the arguments at User:Novem Linguae/Essays/There was no lab leak#Science to be compelling. --Guy Macon (talk) 14:40, 2 June 2021 (UTC)[reply]

Segretto (whom you're using a tweet of as "critique by scientists in their own forums") is a lab leak proponent, so of course, she'd critique those espousing the majority viewpoint. As for the piece in Nature by Andersen et al., it is being cited by more than 1400+ fellow scientists. It clearly is an influential paper (many citations explicitly espouse it's views, judging it to be reliable), by top virologists, in a prestigious journal. So it clearly has been "accepted by the scientific community", and WP:USEBYOTHERS (papers with 1k+ citations are rare) strongly argues that it is a reliable source (although a primary one, so we're better using the secondary, review papers which comment on it). If you don't like that its viewpoint is not the one you like, well then the problem is not with WP:NPOV, but with your POV. We are biased towards science and scientists. RandomCanadian (talk / contribs) 21:27, 2 June 2021 (UTC)[reply]

Also, take a look at [15] for more details on Andersen et al. @Guy Macon: One thing I noticed from that altmetric page is some tweets from lab leakers which are trying to make noise from the fact Andersen, in a preliminary email to Fauci, seemed to be unsure about the origins; before conducting more in-depth analysis, as described by Andersen here. Of course, something that will likely be arguedmisinterpreted endlessly in the upcoming future... RandomCanadian (talk / contribs) 00:45, 3 June 2021 (UTC)[reply]

Re: "It's an interesting coincidence that China advocates for the theory that gives China the least blame, the frozen food hypothesis":

• China revives conspiracy theory of US army link to Covid
• China pushes conspiracy theories on COVID origin, vaccines
• China counters Biden's Covid origins lab probe ... by calling for a US lab probe
• China Floats U.S. Military Lab as Possible COVID Origin Point, Urges WHO to Investigate

I think the page should say "China advocates for theories that gives China the least blame such as the US army lap leak hypothesis and the frozen food hypothesis" --Guy Macon (talk) 23:05, 1 June 2021 (UTC)[reply]

 Done. Thanks for the feedback. –Novem Linguae (talk) 23:27, 1 June 2021 (UTC)[reply]

I suppose one could call this the US army lap leak hypothesis. :-) —2d37 (talk) 07:50, 8 June 2021 (UTC)[reply]

Also, I notice that that AP article says as fact that Pres. Trump was trying to deflect blame for his government’s handling of the pandemic when he said last year he had seen evidence the virus came from a Wuhan laboratory; I wonder whether that's worth using here or in mainspace. —2d37 (talk) 08:00, 8 June 2021 (UTC)[reply]

The bit about Maatje Benassi is already at COVID-19 misinformation#Patient Zero. There is so much on Trump in the Covid-19 misinformation page that I question whether the AP article really adds anything that we don't already cover. --Guy Macon (talk) 11:28, 8 June 2021 (UTC)[reply]

Let's look at one popular press source that several people have emailed to me:

https://www.vanityfair.com/news/2021/06/the-lab-leak-theory-inside-the-fight-to-uncover-covid-19s-origins

I am going to hold off on commenting for now and let everyone read it with an open mind. Comments welcome! --Guy Macon (talk) 16:37, 4 June 2021 (UTC)[reply]

• Just finished reading that through twice....never thought I'd commend Vanity Fair for such a thorough piece of investigative journalism, but yeah this sums up the current knowledge and history very well. Worth a read for that analysis, and the primary sources/documents they include in the piece. Thanks for dropping that here @Guy Macon: , it's a good read! CatDamon 20:45, 4 June 2021 (UTC)[reply]

The Vanity Fair piece isn't MEDRS, so Wikipedia can't use any of it in support of the LLT, is that correct? —Ashley Y 21:11, 5 June 2021 (UTC)[reply]

Can't be used in an article for biomedical claims, but usable for claims about politics and about events. For biomedical claims, we should go to the sources that VF and evaluate them. VF certainly doesn't claim to be expert in virology.

The restrictions on articles don't apply to essays, but Novem Linguae is only allowing WP:MEDRS sources for biomedical claims, so it amounts to the same thing. --Guy Macon (talk) 21:54, 5 June 2021 (UTC)[reply]

The MEDRS sources in the first section make it clear that lab leak is a conspiracy theory and very poorly regarded by the scientific community, but they do not go into the kind of detail needed to thoroughly debunk it. For the "arguments against lab leak" section, I prefaced it with a warning that it contains opinions and original research, then I snuck some non-MEDRS sources in there. This is allowed in an essay, and I also added a warning to that section, so hopefully there are no objections. Happy editing. –Novem Linguae (talk) 22:36, 5 June 2021 (UTC)[reply]

Leaving aside the essay, what about (in an article) claims about politics and events that tend to support the LLT? —Ashley Y 22:45, 5 June 2021 (UTC)[reply]

@Ashley Y: That discussion is/has been taking place here most recently, though there's been various discussions scattered throughout. Hope this helps! CatDamon 23:03, 5 June 2021 (UTC)[reply]

@Ashley Y: See this and this for my opinion on the matter. In short, yes, we can use non-scientific sources for non-scientific topics (and well, newspapers are obviously reliable sources about politics and recent events, since that is their usual expertise). We however shouldn't use them for arguing claims about scientific topics - we can use them to report the existence of such claims, and notable proponents, and political developments, but we should avoid them (especially if, as in this case, we have better) for actual science. RandomCanadian (talk / contribs) 15:41, 6 June 2021 (UTC)[reply]

The Vanity Fair article claims that the scientific process around COVID-19 origins has been compromised in various extra-scientific ways. These claims, which don't rely on scientific expertise per se, tend to support the LLT. Can we use them in articles? —Ashley Y 19:13, 6 June 2021 (UTC)[reply]

@Ashley Y: I'd be inclined to cite WP:REDFLAG and the well known saying that "exceptional claims require exceptional sources". Trying to discredit mainstream science is also a common "conspiracy theory" theme, so I'd be particularly suspicious of anything like that. As I said, we should strive, as much as possible, to use the best sources. News and recent events, along with political analysis and commentary, is something newspapers are reputed for, but serious science (including criticism of science, and changing scientific positions) is best left to serious scientists publishing with review from their peers, and not people with a journalism degree. RandomCanadian (talk / contribs) 19:42, 6 June 2021 (UTC)[reply]

Just to clarify, you are saying that reliable journalistic claims of, e.g., political manipulation of some scientific process should not be used in Wikipedia articles to cast doubt on the outcomes of that science, is that correct? I do recommend reading the Vanity Fair article if you haven't already. —Ashley Y 19:59, 6 June 2021 (UTC)[reply]

@Ashley Y: I am not seeing anything in that VF piece that would be sufficient (nor would only one article in VF be enough to do so anyway) to throw away the scientific sources. The only concrete political manipulation I see recorded (and, extensively, at that) is that of US government actions by US government actors. The rest, we're better off leaving to scientists than to anonymous intelligence reports and fact sheets. Political blame games, and "efforts to “stove pipe” intelligence analysis" (neither China nor the US government are disinterested parties), isn't particularly new, nor is it unique to COVID. As for China being authoritarian and non-transparent, that's not new either, as the VF piece itself says: "China obviously bears responsibility for stonewalling investigators. Whether it did so out of sheer authoritarian habit or because it had a lab leak to hide is, and may always be, unknown."RandomCanadian (talk / contribs) 20:13, 6 June 2021 (UTC)[reply]

Including this here as fodder for what I will ultimately merge into the essay:

Many previous outbreaks have shown that viruses often emerge or cross-over from animals to humans in suburban or rural settings, only to be first seen in the canary in the coal mine that is the urban center. Lots of people clustered together makes a great setting for the slightly more rare presentation to become obvious. It's where probability dictates we will often find the first cases of a new viral illness, even when cross-over occurs in more rural settings. Examples:

1995 Ebolavirus outbreak in Kikwit (pop. ~500,000) (first case was likely a farmer/charcoal miner who contracted the virus in a very rural setting some 13 miles south of Kikwit, but it quickly spread to the adjacent very urban area),^[1][2][3]

2002 outbreak of SARS-1 in Foshan (pop. 7.2 million) (butchers and other animal-adjacent workers likely got the virus first from civet cats/bats in suburban/rural animal husbandry settings, spread to the very urban area of Foshan),^[4][5]

2012 outbreak of MERS in Jeddah (pop. 4.7 million) (first known case was a 60 year old man with no direct connection to camels who died in a very urban hospital in Jeddah, but the first cases (for this and subsequent outbreaks in Qatar as well) were likely camelmongers and traders who lived in the suburban and rural areas outside the city proper, with spillover happening in warehouses and barns in suburban/rural settings),^{[6][7][8][9][10][11]}

"All roads lead to rome" and more specifically, urban centers represent a canary in the coal mine of viral emergence. The larger the urban center, and the more asymptomatic the disease, the more likely this sort of canary-ing is. Is it possible the emergence actually did happen in Wuhan? Yes, but it would be unique if so. It would be different from known coronaviruses and other emerging virus patterns. All of the outbreaks I linked above, at first, looked like they emerged from the indicated city. Because that's where most if not all of the early cases were. But subsequent epidemiological investigation and sequencing showed the actual emergence was likely suburban or rural, not in the urban center where the first cases were identified. Areas with lots of people tend to have the first hospitalized cases in these things, but that doesn't mean that's where the virus is actually coming from.

I am happy to incorporate the above, but I am rather slow at these things, so feel free to get started without me. I think any and all arguments for why Wuhan is not an "obvious" origin are arguments against the lab leak being extremely plausible.--Shibbolethink ^{(♔ ♕)} 18:21, 8 June 2021 (UTC)[reply]

Shibbolethink. Added. Thank you for suggesting this. I hope you don't mind that I condensed it down to 3 sentences. I suspect that people are more likely to read shorter essays. If you'd like me to use all of this, we can add it collapsed next to the bullet. –Novem Linguae (talk) 22:38, 8 June 2021 (UTC)[reply]

Novem Linguae hahahaha no absolutely. Brevity is the soul of wit, and I have never been very good at it. Thank you!--Shibbolethink ^{(♔ ♕)} 22:55, 8 June 2021 (UTC)[reply]

I recently came across the assertion that there are no sources asserting the existence of a scientific consensus that the lab leak is unlikely, and the zoonotic origin most likely, and this essay was very useful in that discussion. So thank you, Novem Linguae, for writing this and keeping it updated as well as you have. ᛗᛁᛟᛚᚾᛁᚱPants Tell me all about it. 20:04, 9 June 2021 (UTC)[reply]

MPants at work, you're very welcome. Happy to help. –Novem Linguae (talk) 23:16, 9 June 2021 (UTC)[reply]

I just added two things:

1. a point in the "The likely origin of COVID-19" section about timing of the index case likely being mid-October to early November 2019.

2. A mention of same in the "Evidence against a lab leak" section since this is part of why Wuhan and the market are not an obvious origin point.

These two things are based on these two primary articles published in April of 2021 and March of 2020,^[1][2] this news piece in Nature news,^[3] and this secondary review covering the same info.^[4]

Feel free to condense down to just that secondary source as per MEDRS to make it consistent, but I included the April 2021 primary-source article in Science in the citations because I actually just thought it was really cool and well-done and a great example of how we figure things out in early epidemic modelling. Definitely a sleeper hit and worth the read for anyone interested.--Shibbolethink ^{(♔ ♕)} 17:13, 13 June 2021 (UTC)[reply]

Looks great. Thanks for your work on this! –Novem Linguae (talk) 18:52, 13 June 2021 (UTC)[reply]

I included the April 2021 primary-source article in Science in the citations because I actually just thought it was really cool [...] — Would it make sense to put it as further reading rather than as a source (perhaps with commentary explaining what makes it cool)? (Of course I don't speak for Novem Linguae, but) I imagine it would be best if the essay follows its own guidance that primary studies should probably not be used as sources. —2d37 (talk) 09:10, 16 June 2021 (UTC)[reply]

2d37, thanks for your comment. For the "Top quality, WP:MEDRS sources" section, we should only use the absolute best sources. For the other sections, I think it is useful to our readers to loosen our sourcing requirements, so that we can present what we judge to be the best arguments. Luckily this is a userspace essay, so we have some latitude. –Novem Linguae (talk) 17:44, 16 June 2021 (UTC)[reply]

I've written a three part blog series about Wikipedia's coverage of the lab leak theory in my blog. Please read as it intersects on many topics of this excellent essay. Forich (talk) 17:53, 19 June 2021 (UTC)[reply]

Forich. Interesting blog posts. It's an interesting topic and there's a lot to write about. I am infected by the same writing bug... no pun intended ;-) Feel free to post parts 4, 5, etc. here when you release them. –Novem Linguae (talk) 22:10, 19 June 2021 (UTC)[reply]

Thanks, I do have in mind a part IV. I hope when the dust settle on all this lab leak thing, that I can draft something longer that groups all the posts together in a polished form. Since we have many point of intersection and you have good writing skills, please @Novem Linguae: let me know if you are open to collaboration in such an endeavor. We could brainstorm the appropiate format once you agree to jump in the project (I am initially thinking of a modest Original Research preprint in ArXiv). Forich (talk) 22:35, 19 June 2021 (UTC)[reply]

Immense thanks to CutePeach for listing most of the BS sources in one post, here. One journal which comes up often is - yep you've guessed it, Env Chem Lett... I'll do a source text/doi search see how often it is cited here, because it seems rather a dubious source in light of this. RandomCanadian (talk / contribs) 12:16, 21 June 2021 (UTC)[reply]

• https://en.wikipedia.org/w/index.php?search=insource%3A%2210.1007/s10311%22 14 total uses (only one on a directly COVID-related article). RandomCanadian (talk / contribs) 12:22, 21 June 2021 (UTC)[reply]

The use in question is to support the statement After the COVID-19 outbreak in Beijing in June, evidence of food transmission was reported in China in early July 2020 by the discovery of SARS-CoV-2 on frozen foods, packaging materials, and storage environments (Transmission of COVID-19#Food and water). This is marked as a review article, but the relevant part smells like primary research to me; as the caption to Fig. 2 says, Information was compiled from announcements by local authorities. In any case, it should be replaced with a journal that is MEDLINE-indexed. XOR'easter (talk) 17:30, 21 June 2021 (UTC)[reply]

Reminds me of that Bulletin of Atomic Scientists source. Scientists in non-related fields. This topic is complex enough that we should really be looking to experts (virologists) to interpret things for us (furin cleavage sites, etc.) and also let us know the norms of their discipline. I'm not really interested in what a person on Twitter, an atomic scientist, or an environmental chemist thinks about furin cleavage sites. The same way I wouldn't ask a doctor about the design decisions behind a torque converter. –Novem Linguae (talk) 00:17, 22 June 2021 (UTC)[reply]

But I'm an electronics engineer! Surely that makes me an expert on Furin Cleavage Sites, right? The Furin Cleavage Site, or FCS, is the place on a Cockcroft–Walton generator where the electricity "cleaves" into two paths. It was named after Ichabod Furin, who invented it in 1869. Now if you will excuse me, I am off to remove my own appendix. --Guy Macon (talk) 01:57, 22 June 2021 (UTC)[reply]

Another Wuhan Lab Leak page with WP:NPOV problems: Drastic Team. --Guy Macon (talk) 02:21, 22 June 2021 (UTC)[reply]

• Jokes aside, I think Lab leak theory deserves a separate page rather than a redirect because people spent a lot of their time to write this essay (there is also an alternative redirect to [16]). Just reuse the current content and sources of this essay on the page "Lab leak theory". My very best wishes (talk) 04:07, 23 June 2021 (UTC)[reply]

Would Wuhan lab leak theory with a redirect from Lab leak theory be a better title? There is that theory that it came from a US Army lab... --Guy Macon (talk) 04:49, 23 June 2021 (UTC)[reply]

Yes, because it was claimed to come from Wuhan lab, although there are many other labs [17]. One can find whatever. My very best wishes (talk) 05:46, 23 June 2021 (UTC)[reply]

The folks over at Talk:COVID-19 misinformation#Lab leak disagreed with some points in this essay. I'd like to take a closer look at their arguments, evaluate them to see if they are convincing, and then adjust this essay accordingly. –Novem Linguae (talk) 00:52, 9 July 2021 (UTC)[reply]

I've added my responses in-line, with the green text serving as Novem Linguae's summary of the arguments made in the aforementioned article space. My responses follow as indented material responding to each argument. I've grouped similar arguments together and added subsections for ease of reading. I haven't answered all of them, I only answered the ones I could tackle at first reading.--Shibbolethink ^{(♔ ♕)} 01:00, 10 July 2021 (UTC)[reply]

Has WIV not been transparent?

• Argument about WIV not being transparent. Implying they are shady, have a bad safety record, and are covering things up. Of course there are no records of laboratory accidents. After the Laboratory was oppened the Chinese didn't follow through on their promises about transparency towards the French. After SARS-I leaked a total of four times from the lab in Beijing and Chinese sources cautioned at the opening not to repeat those mistakes, there wasn't a lot of transparancy. On the other hand the situation was dire enough so that they told the US in 2018 that they don't have enough people to operate the lab safely and that's why the US helped to train WIV staff.
• Argument that WIV took down their database of viruses. "WIV's viruses are closely tracked" that might be true but the WIV took down their database of viruses and is not willing to share it with anyone.

BSL4 research (and specifically GoFR) conducted at BSL2?

• Argument that BSL4 research was dangerously conducted in BSL2 conditions. But even if the biosafety 4 lab was completely safe that's completely irrelevant given that Shi's lab did their gain of function research in biosafety 2 and not in biosafety 4.
• Argument that gain of function research was conducted at WIV. I'm a bit rusty on this. Did WIV conduct gain of function research, and if so, what was the nature of it?

There is, understandably, disagreement about whether WIV was conducting GoFR. Lots of lab leakers say it was happening, others say it wasn't. But even Alina Chan, one of the lab leak's most voracious proponents, doesn't believe the WIV was conducting GoFR. Regarding the EcoHealth grant:^[1] Alina Chan, a molecular biologist and postdoctoral researcher at the Broad Institute of the Massachusetts Institute of Technology and Harvard, said in a lengthy Twitter thread that the Wuhan subgrant wouldn’t fall under the gain-of-function moratorium because the definition didn’t include testing on naturally occurring viruses “unless the tests are reasonably anticipated to increase transmissibility and/or pathogenicity.” She said the moratorium had “no teeth.” But the EcoHealth/Wuhan grant “was testing naturally occurring SARS viruses, without a reasonable expectation that the tests would increase transmissibility or pathogenicity. Therefore, it is reasonable that they would have been excluded from the moratorium.”

To summarize, if someone like Alina Chan who has lots of experience in biotechnology and genetics, but very little experience in virology, is unclear about whether any of this counts as GoFR, why are the lab leak proponents so sure that it counts? Perhaps because it supports their position?

Regarding Guo et al in JVI, that does not depict GoFR in my expert opinion (and does not depict BSL4 research conducted at BSL2) for two reasons:

1) For any virus that actually causes concerning human disease (meaning SARS-COV-1 AKA "high pathogenicity coronaviruses"),^[2] they used what are called "pseudoviruses." Creating a pseudovirus cannot be described as "gain of function" for one very important reason: pseudoviruses cannot function. They cannot replicate,^[3] they cannot cause disease,^[4] they cannot jump out of the dish and infect humans.^[5] They are incapable of causing an outbreak. Instead of creating a virus, you instead take the packaging of the virus (the membrane and envelope proteins) and remove all the relevant genetic material inside (or make it so incomplete that it cannot function). Then you put the proteins of interest on top, without providing the genetic material that contains the instructions for the protein. One analogy is like if you'd taken a cow to a horses-only rodeo, and put a horse costume on it. The cow still isn't a horse, even if it looks like one enough to get into the rodeo. If you wanted to take your pseudo-horse and make baby horses out of it, it isn't gonna happen, no matter how hard you try. In this scenario, a pandemic would be a horse-pocalypse. Nobody working with these cows dressed as horses is going to create a horse-pocalypse. And, just to clear up any confusion, pseudoviruses are not created using genetic engineering because you, very specifically, are not creating, modifying, or combining any genetic material to create a genome of any kind. Pseudoviruses are, on purpose, created without the genetic material necessary to be harmful. Here's more reading on that [18] [19] [20]

2) Any virus that they actually did perform genetic engineering experiments with (to create a replicating virus), does not infect humans and, therefore, can be safely handled at BSL-2. We here in the US also handle these viruses at BSL-2.^[6] This is standard operating procedure in virology, all around the world. Any experiment involving genetic engineering, you perform it at the highest biosafety level of any part of any virus you're involving in that genetic engineering experiment. You'll notice that in that Guo et al paper, they very specifically followed this standard. They never handled a genetically engineered replication-competent virus that contained any BSL-4 virus at BSL-2. They only performed those experiments on BSL-2 viruses and handled them at BSL-2. To help illustrate this point, we do the same sort of stepping down in biosafety with hantaviruses. If it has never been shown to infect humans, and we're pretty darn sure it doesn't infect healthy immunocompetent humans, then we handle it at BSL-2 or BSL-2+ (e.g. Thottapalayam and Prospect Hill viruses).^[7][8]

So, to summarize, that Guo et al paper does not depict GoFR, by any useful definition, because 1) they used pseudoviruses for any genetic material capable of infecting humans and 2) they did engineering experiments exclusively with bat-viruses swapping genetic material with other bat viruses. Since none of the resulting viruses had any novel tropism or pathogenicity in humans, this also does not meet the US government's definition of Gain-of-Function Research: "research which could enable a pandemic-potential pathogen to replicate more quickly or cause more harm in humans or other closely-related mammals."

As an aside, I want to point out that this entire discussion is one of the many reasons why wikipedia does not allow original research, and cautions so heavily against using non-literature sources (or primary literature sources) to discuss complicated scientific and medical topics like "gain of function." We are getting so deep into the weeds here, as far as what "counts" and does not "count" as GoF or genetic engineering. I would tell you that for the first 2-3 years of my graduate training, working on these viruses and spending almost every waking minute thinking about these laboratory techniques, I had difficulty understanding all these nuances. Why do so many people think they are qualified to understand these nuances with very little formal study? Why would you trust a journalist or non-virologist to get this right, when it's so difficult to understand these nuances as a virologist? This is exactly why peer-reviewed review articles written by experts are so valuable. There's a deep and complex regulatory structure to all of this, involving formal risk-assessments and biosafety committees, staffed with physicians and scientists who have devoted their careers to keeping laboratory experiments safe.--Shibbolethink ^{(♔ ♕)} 13:06, 9 July 2021 (UTC)[reply]

Just to help further illustrate why this argument is bupkis: A quote from the Guo et al manuscript: "all four bat SARSr-CoV strains with the same genomic background but different S proteins could use human ACE2 and replicate at similar levels. However, there are some differences in how they utilize R. sinicus ACE2s." The entire paper is investigating how chimerizing bat viruses with each other makes them more or less able to bind to bat proteins. They all behave similarly in human cells, so chimerizing them will have no impact on their ability to infect human cells. Therefore, it isn't "gaining" any human pathogenicity or transmissibility, and therefore does not qualify for the modern widely-accepted definition of "Dual-use gain-of-function research."--Shibbolethink ^{(♔ ♕)} 01:12, 10 July 2021 (UTC)[reply]

The GoFR moratorium and "increasing biosecurity incidents"

• Argument that the gain-of-function research moratorium was enacted because biosecurity incidents have gotten more frequent lately, not less frequent. As far as leaks decreasing remember 2014 when the US had an anthrax and a smallpox accident in the same year? Things got so bad that the moratorium against gain of function research was created.

To address the events that led up to the moratorium

This is an inappropriate conflation of two things: "Scientists who didn't follow established step-by-step protocols to the letter and put themselves in danger as a result" and "dangerous gain of function experiments involving pathogens that can cause pandemics." The series of events that spurred the creation of the moratorium involved accidental screw-ups where a pathogen was stored incorrectly or not inactivated rigorously enough. But, in all of these cases, the follow-up procedures worked as intended and the system self-corrected.

Importantly, none of these events involved "gain of function" research in any way, and no one actually got sick as a result of these incidents. It was simply a set of events that made people go on "higher alert" for biosafety/biosecurity practice regulations. And so the Cambridge Working Group seized this opportunity to advocate for enhanced regulations that they'd wanted for several years before these events occurred.^[29] Lipsitch reignited this debate with the 2012 H5N1 studies in the Netherlands and in Wisconsin, that have very little, if anything, to do with the events described above (CDC anthrax, FDA smallpox, NIH H5N1). He just saw this as a further reason to be upset about GoFR.

And you'll notice, that's why many other scientists were confused about the conflation of the two. Scientists for Science, for example, advocated for a review of biosafety practices at the federal level, poor application of which is the actual cause of the events above. These are relatively isolated incidents, that all occurred in a short span, igniting debate and concerning researchers and the public alike. It was a bad few months in 2014 where a few of these events happened. But it is extremely misleading to use these events as evidence for the statement "laboratory accidents are happening more frequently" because you're selecting 2 or 3 isolated events that have not re-occurred in subsequent years, and appear to have been isolated incidents that have been thoroughly investigated and used to design remedies. Science (and, by extent, biosafety) is a process that course-corrects as time moves on.--Shibbolethink ^{(♔ ♕)} 17:12, 9 July 2021 (UTC)[reply]

Are lab accidents becoming more or less common?

As to the question "are lab accidents becoming more or less common?" we need to look at a broader set of data and ask a more specific set of questions. We need to be careful about whether we're talking about accidents which result in an infection or accidents in general and also, whether we're talking about procedural errors or actual exposures of researchers to an infectious agent.

Among these modern developments is the enhanced requirement for reporting every single alteration in protocol, even if it does not put any researchers (or the public) at risk.^[11] CDC and the DHHS require reporting of any such incident that occurs in Select Agent labs.^{[12][13][14][15]} In the past, incidents were often only made public or reported to government officials if an illness occurred, or if substantial risk was interpreted to exist for the public. But now, every tiny little thing is reported. In a 2019 report of incidents that occurred at Boston University's NEIDL, for example, you can see two incidents which pose no risk to the public whatsoever.^[14] In the 50s or 60s, probably neither of these would have been reported to anyone. Is this change in standards a good thing, that we report more and more benign stuff? Yes! It allows regulators to actually decide what counts as "concerning" and what does not. However, with that change, comes the responsibility to more precisely choose our words when discussing these incidents.

Several studies of "laboratory acquired infections" (so-called "LAIs") have found that the overall number of LAIs has been decreasing since the 1950s, due to all of the improved biosafety practices described above.^{[16][17][18][19][20]} In the U.K., for example, 82.7 cases of LAIs occurred per 100,000 person-years of work occurred in 1988,^[21] versus 16.2 per 100,000 in 1994.^[22] This is just one of many examples of decreasing LAIs over time.

Overall, this question represents a similar problem to the vaccines and autism misinformation conundrum. Autism represents a disease for which we have much better diagnostic criteria now than we did 30 or 40 years ago.^[23] We catch a lot more autistic kids earlier in the course of disease and at younger ages.^[24] Unfortunately, the timing of that diagnosis often coincides with the administration of many vaccines against childhood illnesses.^[25] This has led to widespread misunderstanding and misinformation about a purported link between autism and vaccines, for which no credible evidence exists.^[26]

My point in bringing up this example is this: More reports of X do not always mean an increase in X. More reports of Y thing related to X that is a broader definition, do not always mean that X has increased. In the case of autism spectrum disorders (ASD), the last several decades have resulted in a broader definition of ASD, and a resulting increase in diagnoses. However, the actual number of autistic children has likely not changed. We're just finding it more. Likewise, with laboratory incidents, the criteria for what is a "reportable" event has broadened, resulting in a perceived increase in notable accidents, but there is no evidence that actual "accidents" which endanger the public have increased. Indeed, actual infections of laboratory workers have decreased. Surely, that is the more important metric for determining risk to the public.--Shibbolethink ^{(♔ ♕)} 15:43, 9 July 2021 (UTC)[reply]

False positive COVID tests

• Argument that false positives from COVID tests are not an insurmountable problem, you just re-test with a better test that has no false positives. While COVID tests have false positive rates, any specific finding of a COVID case would lead to DNA sequencing of the involved blood which is more expensive but has no false positive rate and more importantly tells us the exact sequence of the virus.

This is a grave misunderstanding of how clinical testing works. I wrote a long explainer about this exact problem, with numerous peer-reviewed scientific journal article references, back in April of 2020. But here I'll just write a shorter summary answering this specific question. If you want more detail, check out that explainer.

You cannot create a test which has "zero false positives." That's statistically and physicochemically impossible. You can reduce the number of false positives, and better tests make that possible, but you cannot eliminate them entirely. If any clinical diagnostic test is given to a large enough group of people, there will be some false positives.^[1][2] All we can do to increase the utility of the test is reduce that number. Many experts describe clinical diagnostic tests as a "resource" which itself should be conserved.^[3] Meaning we should not indiscriminately administer clinical diagnostic tests, if we want to maximize their usefulness. In medicine, we have pre-test inclusion criteria, which narrow down the population actually given the test,^[4] so that we can reduce the number of false positives. This is because we are increasing so-called "pre-test probability."

For example, let's say you want to give an antigen capture test (checking for antibodies against COVID-19) to the general population of a country. You need to first make sure your test captures as few antibodies generated against common-cold coronaviruses as possible.^[5] But you cannot completely eliminate the binding of these antibodies. The viruses are too structurally similar, and antibodies are too good at binding to things. All you can do is try to find the most distinct possible regions of the viruses, and use those as the "bait."^[6][7] But some patient out there could still have developed a "broadly-binding antibody" against this region, after being infected with a common cold coronavirus.^[8][9] You cannot eliminate that possibility completely. Instead, you make the biochemistry of the test as good and specific as possible, and then you add pre-test criteria to try and remove such people from the testing pool (e.g. "did they have COVID symptoms in the last year?" or "have you been hospitalized with COVID-19 symptoms in the past year?"). These questions may affect the generalizability of the study's findings, but they make the test results more accurate.^[10] You also can combine multiple tests (either the same test multiple times or multiple tests which assess different areas of the virus or different mechanisms (e.g. antibody capture tests and B cell sequencing assays).^[11] Of these, multiple tests with different mechanisms and different "targets" are the most effective at reducing false positives).^[12] In this framework, you would only count someone as positive if they are positive on all the included tests. This substantially reduces false positives, but again it does not eliminate it completely. If you give the test to a large enough group of people, it will still produce some false positives.--Shibbolethink ^{(♔ ♕)} 16:18, 9 July 2021 (UTC)[reply]

If you're knowledgeable about these topics, feel free to chime in, and I'll summarize your responses and adjust this essay accordingly. Thanks. –Novem Linguae (talk) 00:52, 9 July 2021 (UTC)[reply]

Is it alright if I edit inline? Just a lot of points to cover and it will be easier that way. --Shibbolethink ^{(♔ ♕)} 11:43, 9 July 2021 (UTC)[reply]

As an aside, this entire talk page section is an exercise in Brandolini's Law: "The amount of energy needed to refute bullshit is an order of magnitude larger than to produce it." --Shibbolethink ^{(♔ ♕)} 17:29, 9 July 2021 (UTC)[reply]

Discussion re: additional WIV manuscripts (PMIDs 27170748 and 29190287)

@Novem Linguae: I tend to agree with the points raised by soibangla, ChristianKl and Tisthefirstletter in Talk:COVID-19_misinformation#Lab_leak.

Shibbolethink Regarding WIV doing live virus SARSrCoV work at BSL2 labs, the paper that Ian Lipkin and Ralph Baric expressed concern about was PMID: 27170748, as reported in this Minerva article [21]. It seems you may be conflating this paper with the Guo et al paper in your analysis above.

Regarding what counts as GoFR, as you are surely aware, there is no scientific consensus on what constitutes "Gain of function research" let alone "Gain of function research of concern". The P3CO framework serves as recommended policy guidance for federally funded research, and is currently under review. The paper that is most oft cited WRT GoFR at the WIV is PMID: 29190287, and this work meets the definition of PPP enhancement under the 2014 Pause and the 2017 P3CO framework [22] [23].

Regarding your comments on decrease in LAIs, you are surely aware that even a minute decimal percentage is a concern with enhanced PPPs, as it only takes one infected lab worker taking the subway home to spark a global pandemic. I remind you again of Lipsitch’s position that virologists should not be the only ones allowed to discuss epidemiology or matters of science policy [24] [25]. Hath not a non virologist hands, organs, dimensions, senses, affections, passions? Fed with the same food, hurt with the same weapons, subject to the same diseases, healed by the same means, warmed and cooled by the same winter and summer, as a Virologist is? If you prick us, do we not bleed? CutePeach (talk) 12:38, 11 July 2021 (UTC)[reply]

@CutePeach:, re: manuscripts and whether the work within them counts as "GoFR," I have only answered the papers I have been presented with. As I will continue to do. Re: PMID 27170748, I have great respect for Lipkin and Baric, but I would point out again (as I did above) that US researchers were also conducting work with these viruses at BSL-2. Does that make it right? No, of course not necessarily. I'm simply demonstrating that it was commonly accepted that these particular bat viruses (WIV1 and WIV16) are not human-pathogenic, and therefore can be safely handled at BSL-2.

There are many multiple examples besides the hantaviruses that I provided, where a non-human pathogenic close relative of a human pathogenic virus can be safely handled at a lower biosafety level. Tamiami virus (a close relative of Lassa virus), Ross River virus (a close relative of Semliki Forest virus), or non-neurovirulent strains (e.g. Kunjin) of West Nile all come to mind. All of these are examples of viruses closely related to BSL-3 and 4 viruses that are themselves handled at BSL-2 (and BSL-2+) because they lack a concerning virulence in humans. In fact, I believe Dr. Lipkin himself has benefited from this commonly accepted practice, in his West Nile/Kunjin work [26] [27] [28].

This is a cornerstone of biosafety, enabling researchers to conduct experiments without over-burdening them with unnecessary and expensive restrictions. This allows experiments to be conducted more easily (plaque assays, antibody inhibition assays, flow cytometry of cells, etc. which are all quite frustrating to conduct at BSL-3 and 4) which enables faster generation of treatments and vaccines. Of course, eventually, the findings are later replicated on the real-deal human pathogenic viruses, but at the appropriately higher biosafety level. Doing the experiments first on closely related viruses that are more easily (and still safely) handled at BSL-2 (and BSL-2+) means less time is wasted at BSL3 or 4.

Of course, any genetic engineering work that combines or chimerizes viruses to create replication-competent clones must be conducted at the highest biosafety level of any of the involved pathogens. As I said above. I would also point out that in this paper (PMID 27170748), there was no gain in any function. And neither Lipkin nor Baric are claiming that there was. How could this be "Gain-of-Function research of concern" if no function was actually gained? Indeed, the viruses, when ORFX was deleted, lost the function of interferon inhibition and NF-κB activation. There certainly was not any gain in human virulence.

"Regarding what counts as GoFR, as you are surely aware, there is no scientific consensus on what constitutes "Gain of function research" let alone "Gain of function research of concern"" -- Yes, exactly as I said above. Is this a straw man argument? The controversy is exactly why it would be inappropriate for us to describe this work as "gain of function" in wiki-voice. We must instead use attributed quotations as sourced from duly weighted RSes. This is what I have already said in a discussion on the Investigations talk page.

Re: PMID 29190287, my argument about this is the same as above, they are chimerizing bat viruses with bat viruses, and not altering their human infectivity. Again, there is no gain in any function here, so my opinion is that it would be inappropriate to describe this work as "gain of function." Re: P3CO, these experiments do not enhance the ability for any included virus to infect humans more than it already did. How does that meet the P3CO definition?

"I remind you again of Lipsitch’s position that virologists should not be the only ones allowed to discuss epidemiology or matters of science policy." I don't believe I've ever disputed this, or if I have, I don't recall it. I would characterize this as another straw man argument. I think experts in adjacent fields such as Alina Chan, Richard Ebright, Lipsitch, or other biosafety experts are perfectly qualified to debate whether something is "gain of function research." That's why experts in these fields serve on expert government panels and IBCs and so on. Above, I argued that completely unqualified individuals probably should not be the ones we are citing about this (e.g. Yuri Deign has expertise in "entrepreneurship" and "life extension" and software engineering, with an MBA and a bachelor's in computer science. He is clearly unqualified). But absolutely I would agree that we should duly weight quotations from experts such as Ebright, Lipsitch, and Relman. I haven't looked much into the overall set of RSes about their thoughts on these matters, but we would need to make sure their statements are weighted based on the coverage in those RSes. However, no matter how much it is covered, I do not believe it would rise to the level of wiki-voice inclusion. The controversy in topic-relevant well-respected widely-circulated scientific literature sources would prevent this.--Shibbolethink ^{(♔ ♕)} 16:21, 11 July 2021 (UTC)[reply]

@Shibbolethink: I didn’t say Lipkin and Baric expressed concern with PMID: 27170748 over possible GoFR at the WIV. We’re talking here about a species of virus which the WIV produced some research on in 2013 claiming it could directly infect humans without an intermediate species [29]. Relman expounds on Lipkin and Baric’s concerns, in this webinar he gave the other day [30].

On PMID 29190287, construction of novel chimeric SARS-related coronaviruses able to infect human cells is something that as per the P3CO framework, should have undergone a risk-benefit review, but apparently did not. That is something that Fauci has to answer to, and has less to do with the WIV’s safety record, though it's not entirely irrelevant here. With this and similar reports of their activities, I think there is reasonable concern about the WIV, the undisclosed viruses it holds, and the undisclosed ways it may have worked on them. It may have been an affiliated lab, as you will have read in Shoham’s report, that they are allegedly part of an undisclosed network of labs.

On your last point, we are in agreement. I thought you were discounting the opinion of Chan WRT to GoFR definitions and her say on future policy planning. I actually share your POV about GoFR WRT to lab origins, which is why I pointed you to the proposal from Drs Latham and Wilson on your talk page [31], as its the only lab origins hypothesis that doesn’t involve any significant form of bioengineering. Deigin’s finding WRT to the double CGG sequence is significant, and remains anomalous, but his claim of it being strong evidence of gene splicing is somewhat tedious, as it rests on only a tiny handful of nucleotides. When we take Latham and Wilson’s thesis, against the backdrop of white space that is everything we don’t know about this virus and its early spread - it is IMO the most plausible version of the lab leak hypothesis. It is not given any consideration in your thesis posted to Reddit, so I do hope you find the time to read it, as its clear from this Reuters piece that Fauci has [32]. CutePeach (talk) 13:27, 12 July 2021 (UTC)[reply]

CutePeach, the issue isn't whether a virus can infect a human, the issue is whether it has virulence in humans. Lots of viruses can infect different species, but cause no symptoms or extremely mild symptoms. One example would be Vesicular stomatitis virus, which we also handle in BSL-2. Also, you cannot say that research did not undergo risk-benefit review, when all we have is the manuscript. They have an IBC at WIV, we have no idea from the available data whether it underwent a risk-benefit review and IBC protocol review. Have you gone through their IBC meeting minutes? Are they available somewhere? I would love to see those, if so.

I've discussed this double arginine CGG elsewhere, but it is not actually that unusual as double CGGs appear many hundreds of times throughout the genomes of other alpha and betacoronaviruses. I would describe this overall as pareidolia. Deigin is looking for something to explain the opinions he already holds, and he takes whatever he's found and claims it is significant. When we all should be doing the inverse of this as good scientific practice.--Shibbolethink ^{(♔ ♕)} 16:55, 12 July 2021 (UTC)[reply]

@Shibbolethink:, SARS is pretty virulent, so one would assume other SARS-like viruses are virulent too. Your comparison to Vesicular stomatitis is completely out of left field, so I remind you again that Lipkin and Baric have expressed serious concern with the WIV and its safety practises, and they had very good reasons for doing so.

Regarding risk-benefit review, the controversy is exactly around that process, as it is completely confidential and out of the public record. Scientists like David Relman of the CWG have advocated for this process to be made public and for the names of the review panelists to be made public for many years. They even want the review panel to be spun off into an independent agency.

As for the WIV’s IBC, you probably aren’t going to get to see any of their minutes as in case you weren’t aware, the Chinese government has been busy covering up the origins and early spread of the virus from the start. On your next trip to China, you might want to learn a bit more about how the Chinese government actually governs. CutePeach (talk) 07:48, 13 July 2021 (UTC)[reply]

On your next trip to China, you might want to learn a bit more about how the Chinese government actually governs. CutePeach, if you're going to be snarky, you can stop posting in my userspace. Thanks. –Novem Linguae (talk) 08:05, 13 July 2021 (UTC)[reply]