Jerry Coyne changes his mind about the lab leak conspiracy theory and now rejects it

Jerry Coyne was initially convinced by Alina Chan's arguments in favor of the lab leak conspiracy theory concerning the origin of SARS-CoV-2. His mind was changed by reading Paul Offit's rebuttal [Lab Leak Mania].

Here's how Jerry describes his conversion in an article posted on his website [The lab leak theory for the origin of the Covid virus is once again deep-sixed].

Fauci claims (incorrectly) that the lab leak conspiracy theory is not a conspiracy theory

Here's Fauci being interviewed on MSNBC as part of his book promotion tour (see below). He's asked about the lab leak conspiracy theory beginning at 10 mins. He points out that there's no evidence that SARS-CoV-2 came from the Wuhan Institute of Virology (WIV) but he's keeping an "open mind" about the possibility that something could be true in the absence of evidence and in the face of considerable evidence for a natural origin.

The most fascinating part of the interview is when he goes out of his way to say that such a possibility doesn't require a conspiracy theory. Really?

David Gorski (Orac) dismantles Alina Chan's lab leak conspiracy theory

This post is just a place-holder for an article that I've already shared on Facebook. I greatly appreciate the fact that Orac referrd to me several times in his article on Respectful Insolence.

The New York Times goes all in on “lab leak”

Earlier this week, the New York Times op-ed page ran an article by Alina Chan, Queen of lab leak conspiracy theories. How is it wrong? Let me count the ways…

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Anti-science New York Times doubles down on the lab leak conspiracy theory

On June 3, 2024,the New York Times published an opinion piece by Alina Chan in which she promoted the lab leak conspiracy theory about the origin of COVID-19. Her views are not shared by the scientific community and the newspaper was criticized by many who pointed out the many flaws in Chan's arguments and her lack of objectivity.¹

I suspect that some people at the NYT might have been somewhat embarrassed by the response to their reckless behavior so they prepared a response. It was written by David Leonhardt who identifies himself as "a senior writer at the New York Times who runs "The Morning", our flagship daily newsletter." He published his article on the website that he runs and the title sounds like it might be an objective appraisal of the evidence in favor of a natural origin of COVID-19 originating in the Wuhan market: Two Covid Theories.

Don't be fooled by the title. Leonhardt makes no attempt to summarize the massive amount of evidence in favor of a natural origin. Instead, he treats the scientific view and the lab leak conspiracy theory as equally probable.

Do you find both explanations plausible? I do.

As I’ve followed this debate over the past few years, I have gone back and forth about which is more likely. Today, I’m close to 50-50. I have heard similar sentiments from some experts.

“No one has proof,” Julian Barnes, who covers intelligence agencies for The Times, told me. “Everyone is using logic.” Julian’s advice to the rest of us: “Be wary, keep an open mind, rule nothing out.”

Let's be clear about what's necessary in order for the lab leak conspiracy theory to be probable.

1. There has to be evidence that SARS-CoV-2 was present in the Wuhan Institute of Virology (WIV) before the pandemic started. There is none.
2. The graduate students, post-docs, scientists, and research technicians at WIV all deny that they were working with SARS-CoV-2 or any closely-related virus before the pandemic started. In order for the lab leak conspiracy theory to be true they must be lying and engaging in a massive coverup. This is totally inconsistent with their behavior over the past two decades. (The woman in the photo is Shi Zhengli, an internationally renowned scientist who Alina Chan accuses of lying—a claim that David Leonhardt thinks is quite possible.)

The latest opinion piece looks to me like an attempt to defend the NYT against accusations that it is anti-science. You would think that in such a defense, the author would be able to present good scientific evidence for the lab leak conspiracy theory, right? Here's the three arguments advanced by David Leonhardt in support of this massive conspiracy.

1. COVID-19 was first detected near the market in Wuhan and the Wuhan Virolgy Institute is in Wuhan.
2. Leaks happen.
3. China controls the evidence (i.e. conspiracy).

I think we are fully justified in claiming that the NYT is anti-science. I think the newspaper owes the scientific community an apology for ignoring the evidence of a natural origin and disparaging the reputations of reputable scientists who reject the lab leak conspiracy theory in favor of a natural origin.

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1. [The New York Times promotes the lab leak conspiracy theory] [Real scientists destroy the Alina Chan lab leak conspiracy theory] [The New York Times goes all in on “lab leak”] [No, gain of function research did not cause COVID-19]

The New York Times promotes the lab leak conspiracy theory

Scientists have been actively investigating the origin of SARS-CoV-2 for the past four years. The evidence strongly favors early transmission from infected animals in the Huanan seafood market in Wuhan, China (Worobey et al., 2022; Alwine et al., 2023; Dwyer, 2023; Holmes et al., 2021; Holmes, 2024). The virus probably originated in bats in China or southest asia. [The case for a natural origin of SARS-CoV-2] [Real scientists discuss the lab leak conspiracy theory]

Some people have suggested that the infectious virus, SARS-Cov-2, escaped from a lab in the Wuhan Institute of Virology in spite of the fact that there's not a shred of evidence that the scientists there ever worked with such a strain before the pandemic and all the scientists deny that they had ever seen the pandemic virus before the pandemic began. Such suggestions have all the characteristics of a conspiracy theory (Lewandowsky et al., 2023; Goodrum et al., 2023).¹

The New York Times has just published an opinion piece that promotes the lab leak conspiracy theory. It just happened to coincide with a Republican witch hunt investigation into Dr. Fauci and the origins of SARS-CoV-2. The article is written by Alina Chan who wrote a book on the subject with co-author Matt Ridley [Alina Chan teams up with Matt Ridley to promote the lab leak conspiracy theory].

Here's the link to the NYT article: Why the Pandemic Probably Started in a Lab, in 5 Key Points. As you can see from the title, Alina Chan has five reasons why the scientists at the Wuhan Institute of Virology were working on SARS-Cov-2 before the pandemic began and why they are denying that the virus escaped from their lab. All of these five points have been discredited and/or discounted but that didn't stop the newspaper from promoting them.²

1. The SARS-like virus that caused the pandemic emerged in Wuhan, the city where the world’s foremost research lab for SARS-like viruses is located.

   This is just about the only thing in the lab leak conspiracy theory that is true.

2. The year before the outbreak, the Wuhan institute, working with U.S. partners, had proposed creating viruses with SARS‑CoV‑2’s defining feature.

This is extremely misleading. The researchers at WIV worked in collabortion with scientists in other countries, including the United States, on investigating the features of coronaviruses that could lead to infection of humans. That's exactly what you would expect them to do. They never created a virus that could be infectious.

3. The Wuhan lab pursued this type of work under low biosafety conditions that could not have contained an airborne virus as infectious as SARS‑CoV‑2.

   The labs followed all the standard procedures for work of this type and passed an international inspection.

4. The hypothesis that Covid-19 came from an animal at the Huanan Seafood Market in Wuhan is not supported by strong evidence.

   That's a lie. There is strong evidence that the outbreak began in the market.

5. Key evidence that would be expected if the virus had emerged from the wildlife trade is still missing.

   It's true that the exact infectious animal carrying SARS-CoV-2 has not been identified but the circumstantial evidence is strong—just as strong as the circumstantial evidence that sends some people to jail. It's crazy to say that evidence for animal transmission is missing when ALL the evidence for the presence of SARS-CoV-2 at WIT is also missing.

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1. The researchers at WIV are highly respected international experts on virology, especially coronaviruses. They published in the best international journals. Since they all deny that they were working with SARS-CoV-2 before the pandemic, the lab leak hypothesis absolutely requires that several hundred reseachers are lying and covering up the fact that the virus leaked from their labs. In other words, a conspiracy is an essential part of the lab leak conspiracy theory [see Most scientists dismiss the lab leak conspiracy theory].

2. It's amazing how many media personalities have assumed that there must be some element of truth in this opinion piece just because it was published in the New York TImes. It's even more amazing that these media personalities couldn't find any real scientists to interview.

Alwine, J.C., Casadevall, A., Enquist, L.W., Goodrum, F.D. and Imperiale, M.J. (2023) A critical analysis of the evidence for the SARS-CoV-2 origin hypotheses, Am Soc Microbiol. 97: e00365-00323. [doi: 10.1128/jvi.00365-23]

Dwyer, D.E. (2023) The origins of severe acute respiratory syndrome-coronavirus-2. Seminars in Respiratory and Critical Care Medicine, Thieme Medical Publishers, Inc. [doi: 10.1055/s-0042-1759564]

Goodrum, F., Lowen, A.C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M.J., Atwood, W., Avgousti, D., Baines, J. and Banfield, B. (2023) Virology under the microscope—a call for rational discourse. Journal of virology 97:e00089-00023. [doi: 10.1128/jvi.00089-23]

Holmes, E.C., Goldstein, S.A., Rasmussen, A.L., Robertson, D.L., Crits-Christoph, A., Wertheim, J.O., Anthony, S.J., Barclay, W.S., Boni, M.F., Doherty, P.C., Farrar, J., Geoghegan, J.L., Jiang, X., Leibowitz, J.L., Neil, S.J.D., Skern, T., Weiss, S., R, Worobey, M., Anderson, K.G., Garry, R.F. and Rambaut, A. (2021) The origins of SARS-CoV-2: A critical review. Cell 184:4848-4856. [doi: 10.1016/j.cell.2021.08.017]

Holmes, E.C. (2024) The emergence and evolution of SARS-CoV-2. Annual review of virology 11. [doi: 10.1146/annurev-virology-093022-013037]

Lewandowsky, S., Jacobs, P.H. and Neil, S. (2023) Leak or Leap? Evidence and Cognition Surrounding the Origins of the SARS-CoV-2 Virus. Covid Conspiracy Theories in Global Perspective, ed. Michael Butter and Peter Knight:26-39. [PDF]

Worobey, M., Levy, J.I., Malpica Serrano, L., Crits-Christoph, A., Pekar, J.E., Goldstein, S.A., Rasmussen, A.L., Kraemer, M.U., Newman, C. and Koopmans, M.P. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377:951-959. [doi: 10.1126/science.abp8715]

The first review of "Viral" is out and it ain't pretty

Michael Hiltzik is first off the mark writing for the Los Angeles Times: These authors wanted to push the COVID-19 lab-leak theory. Instead they exposed its weaknesses.

Hiltzik is one of the few science writers who know what they'r talking about.¹ You should read his entire review—here are some excerpts to tempt you.

... “Viral” is a laboratory-perfect example of how not to write about a scientific issue. The authors rely less on the scientists doing the painstaking work to unearth the virus’ origin than on self-described sleuths who broadcast their dubious claims, sometimes anonymously, on social media. In the end, Chan and Ridley spotlight all the shortcomings of the hypothesis they set out to defend....

“Viral” is built on vague innuendo, dressed up with assertions that may strike laypeople as plausible but have long since been debunked by experienced virologists. An entire chapter, for example, is devoted to the “furin cleavage site,” a feature of the virus’ structure through which the enzyme furin makes the spikes on its surface — which it uses to penetrate and infect healthy cells — more effective.

The furin site was originally described by lab-leak advocates as so unusual that it could have been placed there only by humans. Virologists have since determined that the feature is not all that rare in viruses similar to SARS2, and in any case, it could have emerged through natural evolutionary processes well known to experts. Chan and Ridley place a heads-I-win-tails-you-lose gloss on these findings, writing that if the site “proves to have been inserted artificially, it confirms that the virus was in a laboratory and was altered. ... If, on the other hand, the furin cleavage site proves to be natural, it still says nothing about where the virus came from.” Why write about it at all, then?

Alina Chan's reputation is already about as low as it can get and now it looks like she's dragging Matt Ridely down with her. He was already part way there so he didn't have far to go.

The book is published by HarperCollins. Should American lawmakers look seriously at regulating the publishing industry for spreading misinformation since they're already investigating Facebook for the same crime?

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1. See: Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?.

Alina Chan teams up with Matt Ridley to promote the lab leak conspiracy theory

Harper is set to publish Viral: The Search for the Origin of COVID-19 in just a few days. The authors are Alina Chan, a postdoc at the Broad Institute of MIT and Harvard, and Matt Ridley, a science journalist who has written several respectable books.

The book promises to reignite discussion of the lab leak conspriracy theory with a focus on Alina Chan's role in promoting it. In preparation, you should read this article about her: They called it a conspiracy theory. But Alina Chan tweeted life into the idea that the virus came from a lab.

Science writing in the age of denial

Here's an interesting presentation by Sean B. Carroll, the evolutionary biologist and author of several books on evolution. He's also written a fascinating book on Jacques Monod and he gave a talk at the University of Toronto a few years ago on the role of chance in evolution—I have a signed copy of his book (see the photo and my blog post: Biologist Sean Carroll in Toronto).

Sean likes to emphasize the importance of storytelling in science communication and education. By this he sometimes means stories about individual scientists and sometimes stories about the history of a subject. As Vice President for Science Education at the Howard Hughes Medical Institute in Washington DC (USA) he has helped craft some short videos for high school students and the presentation contains an example of one on evolution. I'm not sure I fully agree with his emphasis on storytelling—as least not to the extent that he promotes it—but some version of it can be useful as long as it doesn't get in the way of understanding important concepts.

I leave it to you to decide whether the short HHMI video is the best way to teach high school students about evolution. I personally don't like the undue emphasis on natural selection and natural history.

The reason for drawing your attention to an old 2012 presentation is to remind you about the charactieristics of science denial. Sean explains the six rules of denialism.

1. Doubt the Science
2. Question Scientist's Motives and Integrity
3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities
4. Exaggerate Potential Harm
5. Appeal to Personal Freedom
6. Acceptance Would Repudiate Key Philosophy

His examples are the denial of evolution by creationists and the rejection of vaccinations by chiropractors. Today, we see how the same rules apply to those who reject COVID-19 vaccinations and to the Lab Leak Conspiracy Theory.

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The case for a natural origin of SARS-CoV-2

Lots of people seem to be confused about the origin of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The investigating committee ot the World Health Organization (WHO) concluded last winter that a natural origin is the most likely scenario but there still seems to be a substantial percentage of the population who think that the virus was being studied at the Wuhan Institute of Virology (WIV) and leaked from there to start the pandemic. This belief in a lab leak scenario persists in spite ot the fact that 21 expert scientists have discounted it and concluded that a natural origin is the best hypothesis. The lab leak speculation persists even when the United States intelligence agencies reached the same conclusion as the scientific experts and said that a natural origin was more likely.

I've published several posts on this topic over the past year trying to emphasize four points: (1) the evidence strongly favors a natural origin, (2) there is no scientific evidence to support the claim that the WIV scientists were working on SARS-CoV-2 before the pandemic started, (3) the most knowledgeable science experts agree that a natural origin is the most likely scenario, and (4) the media is misrepresenting the science and treating the two competing explanations as equivalent.

In this post I want to describe the case for a natural origin in as simple a manner as possible so that people can refer to the main lines of evidence and so that opponents of a natural origin can explain why they dismiss that evidence. I also want to briefly explain why we need to listen to the experts instead of arbitrarily dismissing their views as a argument from authority and assuming that our own research trumps the experts.

Style vs substance in science communication: The science writer perspective

I want to address a recent article on science writing: When editors and scientists meet: communicating science without dumbing it down. The author is Alex Ip and the article is a commentary on a panel session about science writing at the ScienceWriters2021 conference held in early October [Editing experts: How to help scientists meet journalism standards].

Most scientists dismiss the lab leak conspiracy theory

A recent review in Science has the following subtitle, "Why most scientists say it's unlikely that SARS-CoV-2 originated from a lab leak." The title of that article was Call of the Wild but on the Science website it's The hunt for SARS-CoV-2’s ancestors heats up. The website article is behind a paywall but the original magazine article is open access.

21 experts support a natural origin for SARS-CoV-2

Here's a link to a recent review on the origins of SARS-CoV-2 written by 21 scientists from seven different countries. They are all recognized experts on the subject.

Holmes, E.C., Goldstein, S.A., Rasmussen, A.L., Robertson, D.L., Crits-Christoph, A., Wertheim, J.O., Anthony, S.J., Barclay, W.S., Boni, M.F., Doherty, P.C., Farrar, J., Geoghegan, J.L., Jiang, X., Leibowitz, J.L., Neil, S.J.D., Skern, T., Weiss, S., R, Worobey, M., Anderson, K.G., Garry, R.F. and Rambaut, A. (2021) The origins of SARS-CoV-2: A critical review. Cell. (published online Aug. 19, 2021) [doi: 10.1016/j.cell.2021.08.017]

Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a “laboratory escape” scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.

If you are interested in the origin of this virus then you must read this paper, especially if you are a supporter of the lab leak conspiracy theory. The review attempts to put the issues into the proper perspective by looking at the big picture instead of focusing on the kinds of trivia promoted by conspiracy theorists. For example, the review notes that SARS-CoV-2 is the ninth documented coronavirus that has spread to humans and all of the previous ones have zoonotic origins as do the vast majority of human viruses. Four of these viruses are endemic (HCoV-OC43, HCoV-HkU1, HCoV-229E, and HCoV-NL63). They cause minor respiratory illnesses that we classify as common colds. Its interesting to learn about HCoV-HKU1 ...

"These [endogenous] viruses have zoonotic origins, and the circumstances of their emergence are unclear. In direct parallel to SARS-CoV-2, HCoV-HKU1, which was first described in a large Chinese city (Shenzhen, Guangdong) in the winter of 2004, has an unknown animal origin, contains a furin cleavage site in its spike protein and was originally identified in a case of human pneumonia (Woo et al., 2005)."

The authors look at the bat coronaviruses that have been isolated and sequenced before and after the pandemic began. In particular, they examine RaTG13, a bat virus that was identified at the Wuhan Institute of Virology (WIV). They note that this virus is not particularly closely related to SARS-CoV-2 and that three other bat viruses that were identified only last year are more closely related to SARS-CoV-2. The sequences of all these viruses were examined because there has been unfounded speculation that scientists at the WIV created SARS-CoV-2 from RaTG13.

"Collectively, these data demonstrate beyond reasonable doubt that RaTG13 is not the progenitor of SARS-CoV-2, with or without laboratory manipulation or experimental mutagenesis."

Furthermore, the authors note that the RaTG13 virus didn't actually exist. It was just a bunch of sequences assembled in silico from short sequence reads.

The lab leak conspiracy theorists imagine that the WIV was working on SARS-CoV-2 prior to the beginning of the pandemic and they somehow allowed to virus to escape and infect the citizens of Wuhan. The experts examined this speculation and conclude ...

"... there is no data to suggest that the WIV—or any other laboratory—was working on SARS-CoV-2, or any virus close enough to be the progenitor, prior to the COVID-19 pandemic."

This is a very important point. There is no evidence to support the most important part of the lab leak claim. It's just unfounded speculation.

What about the claim that some workers at the WIV were hospitalized with COVID-19 in November 2019? This claim was spread on Reddit and made it's way into some US intelligence briefings in Januray 2020.

"Despite extensive contact tracing of early cases during the COVID-19 pandemic, there have been no reported cases related to any laboratory staff at the WIV, and all staff in the laboratory of Dr. Shi Zhengli were said to be seronegative for SARS-CoV-2 when tested in March 2020 (World Health Organization, 2021), with the laboratory reportedly following the appropriate biosafety protocols during their coronavirus work (Cohen, 2020)."

This is another important point because if it were true that workers had been infected with SARS-CoV-2 then it would support the lab leak theory. But the scientists at the WIV deny that any such infections occurred and reported to WHO that nobody tested positive for the virus. Furthermore, the public version of the American review of intelligence reports on the origin of SARS-CoV-2 published last month failed to mention the speculation that WIV workers were infected [Intelligence Community: Unclassified Report]. The most logical explanation is that the intelligence agencies could not back up the claim. If they had evidence to support the Reddit rumour then you can bet they would have made it public.

What this means is that, in the absence of evidence, the lab leak supporters have to add an additional layer to their accusation. They have to assume that the scientists at the WIV are lying and covering up the fact that they were secretly working with SARS-CoV-2 and allowed it to escape. The speculation becomes a conspiracy theory.

There's another aspect to this false claim that's very interesting. The 21 experts note that in order for there to have been multiple hospitalizations of lab workers in November 2019 there would have to have been widespread circulation of the virus since not all infections result in hospitalizations. However, a close examination of the known cases coupled with extensive modeling indicates that the virus probably started with a single individual around November 1st.

Epidemiological modeling suggests that the number of hypothetical cases needed to result in multiple hospitalized COVID-19 patients prior to December 2019 is incompatible with observed clinical, genomic, and epidemiological data (Pekar et al., 2021).

The conspiracy fans will no doubt claim that this is just part of a massive coverup by the Chinese government. This coverup involves hundreds of patients who were sick with COVID-19 in October and November 2019 and many who were hospitalized. They have all been silenced along with dozens and dozens of health care workers. Not only that, the Chinese government has been clever enough to release just enough information to make it look like the pandemic stated with a few individuals in November and spread slowly until late December as shown in the figure accompanying the review paper.

The available evidence doesn't rule out a lab leak but it's inconsistent with the Reddit rumour that three or four WIV workers were hospitalized with COVID-19 in November.

Nobody can definatively rule out a conspiracy theory—that's why they are so popular. But you can address false claims that presumably support the conspiracy theory. That's why the experts considered whether the scientists at WIV had been working on gain-of-function research or had previously worked with infectious human viruses. They could find no such evidence.

"There is no rational experimental reason why a new genetic system would be developed using an unknown and unpublished virus, with no evidence nor mention of a SARS-CoV-2-like virus in any prior publication or study from the WIV (Ge et al., 2012; Hu et al., 2017; Menachery et al., 2015), no evidence that the WIV sequenced a virus that is closer to SARS-CoV-2 than RaTG13, and no reason to hide research on a SARS-CoV-2-like virus prior to the COVID-19 pandemic. Under any laboratory escape scenario, SARS-CoV-2 would have to have been present in a laboratory prior to the pandemic, yet no evidence exists to support such a notion and no sequence has been identified that could have served as a precursor."

Sandwalk readers will recognize the issue here. You can't prove a negative so the lab leak conspiracy theorists will always be able to say that their conspiracy theory hasn't been disproven. If that's all you have to go on then I feel sorry for you. You are in the same group as those who believe in all other conspiracy theories.

The 21 experts then go on to address the claim that the virus was "pre-adapted" to humans suggesting that scientists at the WIV had selected the virus for its ability to infect human cells. This speculation includes the ridiculous claim that the furin cleavage site had been deliberately engineered. That particular claim has been debunked but so has the general claim of pre-adaption. In fact, the data shows that the virus was a generalist virus that has gradually become more adapted to humans during the pandemic. This fact, that it was a generalist virus, has been known for more than a year but that hasn't squelched the conspiracy theorists.

"SARS-CoV-2 is also notable for being a host generalist virus (Conceicao et al., 2020), capable of efficient transmission in multiple mammalian species (including mink, tigers, cats, gorillas, dogs, raccoon dogs, and ferrets), and large outbreaks have been documented in mink with spill-back to humans (Oude Munnink et al., 2021) and to other animals (van Aart et al., 2021). Combined, these findings show that no specific human “pre” adaptation was required for the emergence or early spread of SARS-CoV-2, and the claim that the virus was already highly adapted to the human host (Zhan et al., 2020), or somehow optimized for binding to human ACE2, is without validity."

The authors conclude that the lab leak conspiracy theory has no merit because there's no evidence to support it. Thus, the only reasonable hypothesis is a natural origin and there's plenty of evidence to support that hypothesis.

"There is currently no evidence that SARS-CoV-2 has a laboratory origin. There is no evidence that any early cases had any connection to the WIV, in contrast to the clear epidemiological links to animal markets in Wuhan, nor evidence that the WIV possessed or worked on a progenitor of SARS-CoV-2 prior to the pandemic. The suspicion that SARS-CoV-2 might have a laboratory origin stems from the coincidence that it was first detected in a city that houses a major virological laboratory that studies coronaviruses. Wuhan is the largest city in central China with multiple animal markets and is a major hub for travel and commerce, well connected to other areas both within China and internationally. The link to Wuhan therefore more likely reflects the fact that pathogens often require heavily populated areas to become established (Pekar et al., 2021).

We contend that although the animal reservoir for SARS-CoV-2 has not been identified and the key species may not have been tested, in contrast to other scenarios there is substantial body of scientific evidence supporting a zoonotic origin. Although the possibility of a laboratory accident cannot be entirely dismissed, and may be near impossible to falsify, this conduit for emergence is highly unlikely relative to the numerous and repeated human-animal contacts that occur routinely in the wildlife trade. Failure to comprehensively investigate the zoonotic origin through collaborative and carefully coordinated studies would leave the world vulnerable to future pandemics arising from the same human activities that have repeatedly put us on a collision course with novel viruses."

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Image credits: The first figure is from the Holmes et al. paper and the second one is from a Scientific American article [A Visual Guide to the SARS-CoV-2 Coronavirus]

Is the media finally realizing that they have been duped into promoting the lab leak conspiracy theory?

I would like to think that the media will eventually wake up and recognize the science behind the origin of SARS-CoV-2. It overhelmingly supports a natural origin and does not support the lab leak conspiracy theory. I was encourgaged by a Los Angeles Times article published a few weeks ago [Column: The lab leak theory for the origin of COVID-19 is fading.]. It was written by Michael Hiltzik who took the time to read some of the scientific papers that have recently been published. He has written an excellent summary of the issues.

Here's the bottom line ....

It would be inaccurate to say that evidence for the lab leak theory is fading. That’s because there never was any evidence for the theory, just conjecture.

Virtually from the outset, the lab leak theory was driven by ideology, not science. It employed the vocabulary of science, but that’s a familiar technique for bamboozling a susceptible public.

"The only evidence for a lab leak, period, is just that the virus emerged in Wuhan, where the Wuhan Institute of Virology is,” Rasmussen told me. “That’s it. Since day one, that has been the only piece of evidence.”

The assertions supporting the lab leak theory are not only conjectures, but in many cases provably wrong conjectures. They’re often based on misinformation, scientific ignorance, or even bad translations from Chinese documents.

Unfortunately, journalists like Michael Hiltzik are rare. Furthemore, there's no evidence that the talking heads on TV are even close to realizing that they have been duped.

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Let's analyze the Newsweek lab leak conspiracy theory article

Lots of people have been sucked in to the lab leak conspiracy theory based on reporting in newspapers and magazines. One of the widely-cited sources is an article published in Newsweek on June 2, 2021. The focus of the article is on How Amateur Sleuths Broke the Wuhan Lab Story and Embarrassed the Media. Those "amateur sleuths" go by the name "Decentralized Radical Autonomous Search Team Investigating COVID-19" or DRASTIC. I'm not interested in them; I'm interested in scientific facts so let's look at all of the so-called "facts" in the Newsweek article. I'll leave it up to you, dear reader, to judge whether the media should be embarrassed by this story.

Newsweek statment #1: Thanks to DRASTIC, we now know that the Wuhan Institute of Virology had an extensive collection of coronaviruses gathered over many years of foraging in the bat caves, and that many of them—including the closest known relative to the pandemic virus, SARS-CoV-2—came from a mineshaft where three men died from a suspected SARS-like disease in 2012.

Some of this is correct. The WIV scientists and their collaborators have been collecting samples from bats all over China and Indochina for several years and many of them have been examined for the presence of coronaviruses. WIV scientists routinely sampled bats from the Yunnan mine cave from 2012 to 2015 after they were informed that four people had been admitted to hospital with severe respiratory disease in 2012 (one of them died). The workers tested negative for Ebola, Nipah virus, and coronavirus so the scientists were looking for a likely unknown virus that caused the infection. (The serum samples were subsequently tested for SARS-CoV-2 and they were negative.)

Several coronaviruses were detected in the bat samples based on short PCR sequences (370 bp) from the RdRp gene and they were classified as either alphacoronaviruses or betacoronaviruses. The data was published in 2016 (Ge et al., 2016) and the sequences were deposited in GenBank in 2016. Improvements in sequencing technology in 2018 prompted a re-examination of those bat samples and an almost full-length sequence of a betacoronavirus was obtained (missing the 5′ and 3′ ends). This virus was named RaTG13 and one of the short GenBank sequences identified as BtCoV/4491 (Accession #KP876546) comes from that virus (Zhou et al., 2020 Addendum).

The bat virus is RaTG13 and it is 96% similar in sequence to SARS-CoV-2—that means that they probably shared a common ancestor about 50 years ago (Zhou et al. 2020). The sequence was deposited in GenBank as Accession #Mn996532. There are parts of SARS-CoV-2 that are not closely related to RaTG13 and this includes the spike protein gene, which is essential for infecting humans. The spike gene sequence is most closely related to a coronavirus from pangolins, Pangolin-Cov.

The data is consistent with a recombination event between different strains of coronaviruses giving rise to SARS-CoV-2 or its immediate ancestors. Such recombinations are a common feature of coronavirus propagation in various animals, including bats. What's clear is that none of the currently known coronavirus sequences could possibly be the ancestors of SARS-CoV-2 so the hunt is on to locate those viruses.

Recently, the scientists at WIV and their collaboratore at the University of Chinese Academy of Sciences in Beijing looked at some of the other samples from bat anal swabs collected in Yunnan in 2015. This in depth analysis was prompted by the discovery of SARS-CoV-2 and the pandemic. They found a number of other bat coronavisus sequences and some of them were more closely related to SARS-CoV-2 in the ORF1b regions but not in other parts of the genome. Again, this is consistent with frequent recombination events that have been documented over the past few decades. Surprisingly, some of these new bat coronavisuses were able to use the bat angiotensin-converting enzyme 2 (ACE2) as a receptor, but they did not bind to human ACE2. (These assays take a lot of time and effort.) This and other data show that the evolution of ACE2 binding can occur in bats giving rise to a generalist virsus, SARS-CoV-2, than can bind to ACE2 from many different species. (MacLean et al., 2021; Guo et al., 2021).

A group of scientists from France, United States, Vietnam, and Cambodia looked at bat samples that were collected in Cambodia in 2010 and found coronaviruses from another species of bats that were cloesly related to SARS-CoV-2 across most of the genome except for a small region of the spike protein gene. In some parts of the genome (ORF1a and ORF8) these viruses were more closely related to SARS-CoV-2 than RATG13 (Hu et al. 2021). The evolutionary history of the Cambodian viruses indicate that they are mosaic viruses due to recombination events. This data indicates that SARS-CoV-2 related viruses are found in Southeast Asia as well as China—that's signficant since pangolins are only found in Southeast Asia and not in China.

SARS-CoV-2-like viruses have also been found in Thailand (Wacharapluesadee et al., 2021).

A group centered in Taian, China, has recently examined coronaviruses from bats at the botanical garden in Mengal county in Yunnan. They have identified four additional SARS-CoV-2 related viruses including one, RpYN06, that is the closest relative to SARS-CoV-2 outside of the spike gene. This is now the leading candidate for the "backbone" that might have given rise to the pandemic virus (Zhou et al., 2021).

CONCLUSION: The Newsweek statement is not wrong but it is highly misleading. The WIV labs had bat samples that contained coronaviruses but so did lots of labs all over the world. In that sense, these labs have an "extensive collection of coronaviruses" but they are stored in bat poop at -80° C! They identified two coronavirus, RaTG13 and RmYN02, by sequencing PCR fragments but the sequences were not complete. It's misleading for Newsweek to imply that the WIV labs had an RaTG13 coronavirus in their labs because that implies that they were working with active viruses. It's true that the RaTG13 virus came from a place where several workers had gotten sick with respiratory disease a few years before the sample was collected. One of these men died (not three) but none of the patients tested positive for coronavirus.

Newsweek statement #2: We know that the WIV was actively working with these viruses, using inadequate safety protocols, in ways that could have triggered the pandemic, and that the lab and Chinese authorities have gone to great lengths to conceal these activities.

CONCLUSION: This is misleading. As far as I know, the scientists are WIV were not actively working with the RaTG13 virus because they had never isolated that virus. Furthermore, it's almost impossible to create SARS-CoV-2 from RaTG13 [Could scientists use the bat coronavirus RaTG13 to engineer SARS-CoV-2, the virus that causes COVID-19, in a lab?]. They were working with other bat coronaviruses but none of them were closely related to SARS-CoV-2 so it's extremely misleading to imply that the escape of these viruses could have triggered the pandemic. They were not using inadequate safety protocols because all of the work with bat coronaviruses was carried out in level 2 labs, exactly as required. There's no evidence that the scientists at the WIV labs have concealed anything. You can only accuse someone of concealing something if you have strong evidence that they did something that they deny doing.

Newsweek statement #3: We know that the first cases appeared weeks before the outbreak at the Huanan wet market that was once thought to be ground zero.

CONCLUSION: This is correct. Chinese scientists and health workers identified a number of earlier cases that appear to be unrelated to the seafood market and they published their results in scientific journals over a year ago. They now conclude that the virus was circulating in the Wuhan population for more than a month before the superspreader event at the market ignited the pandemic. This appears to be a case where Newsweek trusts the work of Chinese scientists.

Newsweek statement #4: The Newsweek article talks a lot about the DRASTIC group as though they have uncovered a huge conspriacy theory. One of their "discoveries" relates to the bat coronavirus RaTG13 that's first mentioned in the paper where the SARS-CoV-2 sequence was published. Here's what Newsweek wrote: "The paper was vague about where RaTG13 had come from. It didn't say exactly where or when RaTG13 had been found, just that it had previously been detected in a bat in Yunnan Province, in southern China.

The paper aroused Deigin's suspicions. He wondered if SARS-CoV-2 might have emerged through some genetic mixing and matching from a lab working with RaTG13 or related viruses. His post was cogent and comprehensive. The Seeker posted Deigin's theory on Reddit, which promptly suspended his account permanently."

CONCLUSION: This is written like it's a big mystery that was uncovered by some clever sleuthing. It's true that the origin of RaTG13 was not discussed in the SARS-CoV-2 paper in January 2020 other than to say that it was found in a bat in Yunnan. I assume that the authors didn't think it was important (and still don't). The origin was explained in November 2020 in an Addendum to the Nature article (Zhou et al., 2020, Addendum). It was one of the viruses discoverd in the bats from the Yunnan mine cave and a partial sequence had been published earlier (Ge et al., 2016). It's not particulary close to SARS-CoV-2 and there's no reason to speculate that it was artificially created unless you are trying to create a conspiracy.

Newsweek statement #5: The key facts quickly came together. The genetic sequence for RaTG13 perfectly matched a small piece of genetic code posted as part of a paper written by Shi Zhengli years earlier, but never mentioned again. The code came from a virus the WIV had found in a Yunnan bat. Connecting key details in the two papers with old news stories, the DRASTIC team determined that RaTG13 had come from a mineshaft in Mojiang County, in Yunnan Province, where six men shoveling bat guano in 2012 had developed pneumonia. Three of them died. DRASTIC wondered if that event marked the first cases of human beings being infected with a precursor of SARS-CoV-2—perhaps RaTG13 or something like it.

In a profile in Scientific American, Shi Zhengli acknowledged working in a mineshaft in Mojiang County where miners had died. But she avoided connecting it to RaTG13 (an omission she had made in her scientific papers as well), claiming that a fungus in the cave had killed the miners.

This reads just like a typical conspiracy theory where "clever" sleuths (i.e. internet anateurs) uncover information that was hidden or covered up by those they are accusing. The origin of RaTG13 was explained in an addendum to the publication of the SARS-CoV-2 sequence in February 2020. The addendum was added in November 2020 in reponse to questions about the origin of RaTG13 but that information was widely known. The sequence of a short fragment of this virus was obtained earlier as explained above.

The WIV scientists were very concerned about the Yunnan mine workers because they had symptoms that were similar to those of SARS patients and that's why they tested serum from the patients. They were negative for all the viruses, including the original SARS-CoV-1. (The serum is also negative for SARS-CoV-2.) The WIV scientists were worried that the infections were due to an unknown virus that could cause a pandemic so they went back to the mine every year to collect samples from the bats. The RaTG13 sequence came from one of those samples but by then the scientists knew that there was no connection between the bat coronaviruses and the sick mine workers. (They were probably disappointed at the lack of connection because they were looking for the cause of the 2002 SARS outbreak.)

The WIV scientists now believe that the Yunnan mine workers had contracted a fungal infection from the fungus growing on the bat guano. There is no reason to connect RaTG13 to the mine workers because it's been known for many years that the workers were not infected with any coronavirus.

The RaTG13 virus is from the bat species Rhinolophus affinis (hence the designation "Ra") but up until the beginning of the pandemic the WIV scientists were much more interested in another cave in Yunnan populated by a number of different species. They reported that this cave represents the most diverse collection of bat coronaviruses in the world. Most of the ones that are SARS-like were from a different species of bat, Rhinolophus sinicus and many of these bound the same ACE2 receptor that SARS-CoV-1 used—the same one used by the more recent SARS-CoV-2 (Hu et al. 2017; Cui et al., 2019).

CONCLUSION: The Newsweek article is repeating innuendos and conspiracies that have been discredited in the past. The DRASTIC team is deliberately making up connections between coroanvirus and the mine workers but all of the data shows that there's no direct connection. It just happened that one of the bat coronaviruses collected in that mine happened to be the one closest to SARS-CoV-2, in part because that was a pretty extensive collection. The RaTG13 sequence is not similar enough to SAS-CoV-2 to be the direct ancestor and, besides, there are now known to be other virus sequences from as far away as Cambodia that are just as similar to SARS-CoV-2.

Newsweek statement #6: That explanation didn't sit well with the DRASTIC group. They suspected a SARS-like virus, not a fungus, had killed the miners and that, for whatever reason, the WIV was trying to hide that fact. It was a hunch, and they had no way of proving it.

At this point, The Seeker revealed his research powers to the group. In his online explorations, he'd recently discovered a massive Chinese database of academic journals and theses called CNKI. Now he wondered if somewhere in its vast circuitry might be information on the sickened miners.

Working through the night at his bedside table on phone and laptop, fueled by chai and using Chinese characters with the help of Google Translate, he plugged in "Mojiang"—the county where the mine was located—in combination with every other word he could think of that might be relevant, instantly translating each new flush of results back to English. "Mojiang + pneumonia"; "Mojiang + WIV"; "Mojiang + bats"; "Mojiang + SARS." Each search brought back thousands of results and half a dozen different databases for journals, books, newspapers, master's theses, doctoral dissertations. He combed through these results, night after night, but never found anything useful. When he ran out of energy, he broke for arcade games and more chai.

He was on the verge of calling it quits, he says, when he struck gold: a 60-page master's thesis written by a student at Kunming Medical University in 2013 titled "The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown Viruses." In exhaustive detail, it described the conditions and step-by-step treatment of the miners. It named the suspected culprit: "Caused by SARS-like [coronavirus] from the Chinese horseshoe bat or other bats."

CONCLUSION: Move along folks; there's nothing to see here. The WIV scientists suspected that the miners were infected with an unknown virus and that's why they were concerned in 2012. They knew that coronavirus wasn't responsible and neither was any other known virus. This is why they went back every year to test the bats in the mine shaft. The know that the stored serum from these workers is negative for SARS-CoV-2, which is not a surprise. They now suspect that the mine workers had contracted a fungl infection and not a viral infection. It's not particulary surprising that a student reported the suspected cause of the symptoms back in the beginning of the investigation.

Newsweek statement #7: Ribera was responsible for solving another piece of the RaTG13 puzzle. Had the WIV been actively working on RaTG13 during the seven years since they discovered it? Peter Daszak said no: they had never used the virus because it wasn't similar enough to the original SARS. "We thought it's interesting, but not high-risk," he told Wired. "So we didn't do anything about it and put it in the freezer."

Ribera disproved that account. When a new science paper on genetics is published, the authors must upload the accompanying genetic sequences to an international database. By examining some metadata tags that had been accidentally uploaded by the WIV along with its genetic sequences for RaTG13, Ribera discovered that scientists at the lab had indeed been actively studying the virus in 2017 and 2018—they hadn't stuck it in a freezer and forgotten about it, after all.

I don't know what this means. The WIV scientists sequenced a bit of what turned out to be the RaTG13 virus when they catagorized all the other viruses back in 2012-2015 (Ge et al. 2016). They then completed an almost whole genome sequence later on in 2018 when their sequencing techniques improved. It's important keep in mind that the WIV never worked with the RaTG13 virus as emphasized by Frutos et al. (2021): "One must remember that SARS-CoV-2 was never found in the wild and that RaTG13 does not exist as a real virus but instead only as a sequence in a computer. It is a virtual virus which thus cannot leak from a laboratory." ¹

CONCLUSION: The scientists at WIV were "working with" the RaTG13 PCR fragments in 2017 and 2018 as they assembled the whole genome sequence. They also assembled the sequences of seveal other viruses at the same time. To say that they were "actively studying" the virus is very misleading and to accuse Peter Daszek of lying is irresponsible.

Newsweek statement #8: In fact, the WIV had been intensely interested in RaTG13 and everything else that had come from the Mojiang mineshaft. From his giant Sudoku puzzle, Ribera determined that they made at least seven different trips to the mine, over many years, collecting thousands of samples. Ribera's guess is that their technology had not been good enough in 2012 and 2013 to find the virus that had killed the miners, so they kept going back as the techniques improved.

He also made a bold prediction. Cross-referencing snippets of information from multiple sources, Ribera guessed, in a Twitter thread dated August 1, 2020, that a cluster of eight SARS-related viruses mentioned briefly in an obscure section of one WIV paper had actually also come from the Mojiang mine. In other words, they hadn't found one relative of SARS-CoV-2 in that mineshaft; they'd found nine. In November 2020, Shi Zhengli confirmed many of DRASTIC's suspicions about the Mojiang cave in an addendum to her original paper on RaTG13 and in a talk in February 2021.

The mine shaft is located in Mojiang county, Yunnan—a map of the location was published in Ge et al. (2016). It contains six different bat species and many of them were infected with coronaviruses. The WIV scientists collected many samples over a number of years in order to determine the phylogeny of the viruses and which species were infected. They also did longitudinal studies to see if the different virus variants changed over time and to see if the infection rates of the various bat species were different from year to year. They also wanted to see if they could detect recombinations between different virus groups.

They obtained 152 partial sequences and then picked 12 of them for more detailed analysis in order to construct a phylogenetic tree from 816 bp of the RNA-dependent RNA polymerase (RdRp) gene. Anyone can read the Ge et al. (2016) paper to see why they were doing these experiments. There's nothing mysterious or unusual about their approach. It's the same one they took with the viruses from the other site (cave) in Yunnan where they identified the two bat coronaviruses that are most closely related to the original SARS virus (Ge et al., 2013) (see: SARS ouotbreak linked to Chinese bat cave)

CONCLUSION: The Newsweek article is making a huge mountain out of a molehill and it's misrepresenting the work of the "amateur sleuths." It's not a secret or a mystery that the WIV scientists were studying the coronaviruses from the mine shaft. That's what they do and they publish in journals that are easy to access.

Newsweek statement #9: "Other databases yielded other clues. In the WIV's grant applications and awards, The Seeker found detailed descriptions of the Institute's research plans, and they were damning: Projects were underway to test the infectivity of novel SARS-like viruses they'd discovered in human cells and in lab animals, to see how they might mutate as they crossed species, and to genetically recombine pieces of different viruses—all being done at woefully inadequate biosecurity levels. All the elements for a disaster were on hand."

CONCLUSION: It's true that the WIV scientists were looking at SARS-like coronavisuses and they were testing for infectivity in humanized mouse cells. The goal was to look for new coronaviruses that could bind ACE2 and they found quite a few of them. In many cases, they expressed the spike protein in recombinant viruses and plasmids just as you would expect them to do if they were looking for the source of the original SARS virus (SARS-CoV-1). All this is described in their grant applications and in their publications. Looks like they didn't make much of an attempt to hide this research. All the experiments were done under the appropriate biosafety measures as specified by international inspectors who visited the lab on several occasions. None of this has anything to do with the pandemic because they were not working with SARS-CoV-2 or any close relative.

The rest of the Newsweek article consists mostly of praise for the DRASTIC heros and the excellent work they have done in uncovering a huge conspiracy to cover up the fact that the WIV scientists started a pandemic. However, one embarrassing fact remains: there is not a shred of evidence that the lab was working with SARS-CoV-2 before the pandemic started. In the absence of such evidence it is irresponsible to accuse these reputable scientists of lying.

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1. One could quibble slightly about the accuracy of this statment since there might be RaTG13 virus particles in the bat fecal samples that are stored in the -80°C freezer.

Cui, J., Li, F. and Shi, Z.-L. (2019) Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology 17:181-192. doi: [doi: 10.1038/s41579-018-0118-9]

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.

Hu, V., Delaune, D., Karlsson, E.A., Hassanin, A., Tey, P.O., Baidaliuk, A., Gámbaro, F., Tu, V.T., Keatts, L. and Mazet, J. (2021) A novel SARS-CoV-2 related coronavirus in bats from Cambodia. bioRxiv. [doi: 10.1101/2021.01.26.428212]

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identified nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a small region corresponding to the spike N terminal domain. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously understood, and suggests that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses.

Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A.A., Zhu, G., Epstein, J.H., Mazet, J.K., Hu, B., Zhang, W. and Peng, C. (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503:535-538. [doi: 10.1038/nature12711]

The 2002–3 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV) was one of the most significant public health events in recent history1. An ongoing outbreak of Middle East respiratory syndrome coronavirus2 suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses3,4,5, attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa5,6,7,8, but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2)9,10. Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness.

Ge, X.-Y., Wang, N., Zhang, W., Hu, B., Li, B., Zhang, Y.-Z., Zhou, J.-H., Luo, C.-M., Yang, X.-L. and Wu, L.-J. (2016) Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virologica Sinica 31:31-40. [doi: 10.1007/s12250-016-3713-9]

Since the 2002–2003 severe acute respiratory syndrome (SARS) outbreak prompted a search for the natural reservoir of the SARS coronavirus, numerous alpha- and betacoronaviruses have been discovered in bats around the world. Bats are likely the natural reservoir of alpha- and beta-coronaviruses, and due to the rich diversity and global distribution of bats, the number of bat coronaviruses will likely increase. We conducted a surveillance of coronaviruses in bats in an abandoned mineshaft in Mojiang County, Yunnan Province, China, from 2012–2013. Six bat species were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus fuliginosus, and Miniopterus fuscus. By sequencing PCR products of the coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high frequency of infection by a diverse group of coronaviruses in different bat species in the mineshaft. Sequenced partial RdRp fragments had 80%–99% nucleic acid sequence identity with well-characterized Alphacoronavirus species, including BtCoV HKU2, BtCoV HKU8, and BtCoV1,and unassigned species BtCoV HKU7 and BtCoV HKU10. Additionally, the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species. Furthermore, coronavirus co-infection was detected in all six batspecies, a phenomenon that fosters recombination and promotes the emergence of novel virus strains. Our findings highlight the importance of bats as natural reservoirs of coronaviruses and the potentially zoonotic source of viral pathogens.

Guo, H., Hu, B., Si, H.-r., Zhu, Y., Zhang, W., Li, B., Li, A., Geng, R., Lin, H.-F. and Yang, X.-L. (2021) Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. bioRxiv. [doi: 10.1101/2021.05.21.445091]

Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.

MacLean, O.A., Lytras, S., Weaver, S., Singer, J.B., Boni, M.F., Lemey, P., Pond, S.L.K. and Robertson, D.L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology 19:e3001115. [doi: 10.1371/journal.pbio.3001115]

Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.

Wacharapluesadee, S., Tan, C.W., Maneeorn, P., Duengkae, P., Zhu, F., Joyjinda, Y., Kaewpom, T., Chia, W.N., Ampoot, W. and Lim, B.L. (2021) Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nature communications 12:1-9. doi: [doi: 10.1038/s41467-021-21240-1]

Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.

Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B. and Huang, C.-L. (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270-273. [doi: 10.1038/s41586-020-2012-7]

Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1,2,3,4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5,6,7. Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.

Zhou, P. et al. (2020) Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 588:E6-E6. [doi: 10.1038/s41586-020-2951-z]

Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Hu, T., Song, H., Chen, Y., Cui, M. and Zhang, Y. (2021) Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv. doi: [doi: 10.1101/2021.03.08.434390]

Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.

Real scientists discuss the lab leak conspiracy theory

Here's an interesting video where the hosts of "This Week in Virology" (Vincent Racaniello, Rich Condit, and Kathy Spindler) discuss the origin of COVID-19 with three scientists who were on the WHO investigation committee that visited the Wuhan Institute of Virology a few months ago (Peter Daszak, Thea Kølsen Fischer, and Marion Koopmans). If you've fallen for the lab leak conspiracy theory then you need to watch the entire video. The rest of you might want to skip to 50 minutes where they discuss the lab leak accusation and relate how they interviewed the scientists at WIV.

The WHO scientists want to emphasize three things: (1) it is extremely unlikely that SARS-CoV-2 was being studied at WIV so it couldn't have escaped from there; (2) there is no evidence to support the lab leak conspiracy theory but if any evidence shows up they are perfectly willing to investigate; (3) it's very likely that SARS-CoV-2 originated naturally in the wild and all efforts should be focused on the most likely scenario and not on an extremely unlikely scenario.

After the interview is over, the three hosts talk about the lab leak conspiracy theory. You should hear what they have to say about Nicholas Wade and his failure to understand the furin cleavage site (1:10 minutes)! And they have lots to say about everything else in the Wade article. Everyone needs to watch that discussion if you are really interested in science and not half-baked conspriacy theories.

The next video is an interview with Robert Garry, a virologist at Tulane University in New Orleans. His area of expertise is emerging infectious viruses. Listen to Garry and the hosts discuss the possibility that SARS-CoV-2 was present in the Wuhan Institure of Virology and released acidentally to start the pandemic (starting at 15 mins). It's good to hear real experts debunk the conspiracy theory.

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World Health Organization (WHO) report on the natural origin theory of SARS-CoV-2

The origin of SARS-Cov-2 is a hot topic these days. As far as I can tell, the consensus view among the experts is that the ancestor is from bats but it evolved in an intermediate host before jumping to humans. However, there's a vocal group who claim that the virus was engineered in a lab in the Wuhan Institute of Virology and accidentally escaped causing a pandemic. A group of scientists from WHO investigated this speculation and decided that it was "extremely unlikely." I posted a summary of their analysis a few days ago [World Health Organization (WHO) report on the lab leak conspiracy theory].

That's not going to put an end to the speculation since proponents of the lab leak hypothesis are now saying that the WHO report, and the opinion of other experts, can't be trusted. They claim that there's a widespread consiracy to lie and cover up the fact that SARS-CoV-2 was created in a lab and leaked to the Wuhan population.

There's not much point in arguing with people once they go down the conspiricy theory path since they will refute every argument by claiming that it's part of the conspriacy. However, it's worth pointing out that there's a perfectly valid alternative explanation; namely, natural origin. For those who still have an open mind I'm posting the explanation of the WHO scientific team who conclude that this is the most likely explanation [WHO-convened global study of origins of SARS-CoV-2: China Part].

Introduction through intermediate host followed by zoonotic transmission

Explanation of hypothesis

SARS-CoV-2 is transmitted from an animal reservoir to an animal host, followed by subsequent spread within that intermediate host (spillover host), and then transmission to humans. The passage through an intermediate host can be without or with virus adaptation.

Arguments in favour

Although the closest related viruses have been found in bats, the evolutionary distance between these bat viruses and SARS-CoV-2 is estimated to be several decades, suggesting a missing link (either a missing progenitor virus, or evolution of a progenitor virus in an intermediate host). Highly similar viruses have also been found in pangolins, suggesting cross-species transmission from bats at least once, but again with considerable genetic distance. Both these putative hosts are infrequently in contact with humans, and an intermediary step involving an amplifying host has been observed for several other emerging viruses (Henipaviruses, influenza viruses, SARS-CoV and MERS-CoV). SARS-CoV-2 infection and intraspecies spread (including further transmission to humans) has been documented in an increasing number of animal species, particularly mustelids and felids. SARS-CoV-2 adapts relatively rapidly in susceptible animals (such as mink). The increasing number of animals shown to be susceptible to SARS-CoV-2 includes animals that are farmed in sufficient densities to allow potential for enzootic circulation. High-density farming is common in many places across the world and includes many livestock species as well as farmed wildlife. There was a large network of domesticated wild animal farms, supplying farmed wildlife. In high-density farms, there often are connections between farms (for instance, through the workforce and food supply), leading to complex transmission pathways that may be difficult to unravel, as was observed in other zoonotic outbreaks involving farmed animals. Optimized conditions for sustained virus transmission chains in large-scale animal farms may also impact on virus seasonality in favour of a year-round endemic transmission pattern, and thereby increasing the zoonotic risk in winter months.

Arguments against

SARS-CoV-2 has been identified in an increasing number of animal species, but genetic and epidemiological studies have suggested that these were infections introduced from humans, rather than enzootic virus circulation. In addition, since the containment of SARS-CoV-2 in China, new outbreaks have occurred for which genomic sequence data was generated. Based on epidemiological analysis and genetic sequencing of viruses from new cases throughout 2020, there is no evidence of repeated introduction of early SARS-CoV-2 strains of potential animal origins into humans in China. There was no genetic or serological evidence for SARS-CoV-2 in a wide range of domestic and wild animals tested to date. The screening of the major livestock species was done across the country and provided no evidence for circulation of a related virus. The scale of testing in these species was such that widespread circulation is extremely unlikely. Screening of farmed wildlife was limited but did not provide conclusive evidence for the existence of circulation.

Assessment of likelihood

Based on the above arguments, the scenario including introduction through an intermediary host was considered to be likely to very likely.

I should note that it's often very difficult to figure out who's right and who's wrong in a scientific controversy but in general there's one group that appears to be thinking critically and one that's not. Critical thinking is also hard to recognize but when I was teaching it we emphasized one important clue. Critical thinkers usually present both sides of an argument and discuss not only their own opinions but also the views of the other side. That's one of the things that impress me about the WHO report. It doesn't mean that they are necessarily correct but they sure look a lot better than proponents of the lab leak conspiracy theory who seem to dismiss out of hand the possibility of a natural origin.

I'd also like to make note of the fact the WHO is not a perfect organization. They have made mistakes during this pandemic as have every single government on the planet (some more than others). I'm not defending everything that WHO has done but I don't see any reason to be overly suspicious of the integrity of the scientists who wrote this report.

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