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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Pentagon ran secret anti-vax campaign to undermine China during pandemic

This is a Reuters report about misinformation spread by the United States military in order to discredit China's Sinovac vaccine. It was directed at the Philippines and other countries who were purchasing the China vaccine.

Reuters suggests that by undermining public trust in government health initiatives the US military might have cost thousands of lives in the Phillippines.

A REUTERS INVESTIGATION: Pentagon ran secret anti-vax campaign to undermine China during pandemic

The U.S. military launched a clandestine program amid the COVID crisis to discredit China’s Sinovac inoculation – payback for Beijing’s efforts to blame Washington for the pandemic. One target: the Filipino public. Health experts say the gambit was indefensible and put innocent lives at risk.

It shouldn't surprise anyone that nations engage in propaganda wars in order to destabilize or demonize their perceived enemies. The world is a complicated multinational environment and meddling in the affairs of other countries is a routine part of modern international relations. It's important to emphasize that it's not only the "bad guys" who do this sort of thing. Your own country and your friends and allies also spread misinformation in order to convince you that you are one of the "good guys" (e.g. defenders of morality, decency, democracy, and freedom).

I emphasize this for two reasons. One, here in Canada there's a lot of pearl-clutchng these days about foreign interference and the main focus is on China and India and how they might have influenced our elections. I think this is pretty minor stuff compared to what else is going on and the foreign influence from other countries, including the United States.

Second, as mentioned above, we all need to be aware of the fact that misinformation is rampant and that doesn't just include misinformation spread by Russia, China, Iran, and Hamas. We also need to be skeptical about information being spread by the governments of Ukraine, Israel, and the United States. Do not assume that everything they say is truthful.

These days, I find that it's almost impossible to hear, read, or watch any "authority" who convinces me that they are critical thinkers without an agenda. Almost all of them seem to be victims of propaganda.

Note: I'm aware of the fact that this report may not be accurate—it may, in fact, be misinformation. I'm mostly using it as a vehicle to point out that you can't trust anyone these days, including your friends. That's very upsetting because I grew up thinking that the mainstream news outlets (TV, radio, newspapers) could be (mostly) trusted.

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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]

NPR vs CDC on the new COVID-19 guidelines

NPR tweeted out a summary of the new CDC (United States) guidelines on COVID-19. The figure was posted under the name of Dr. Marcus Plescia, chief medical officer for the Association of State and Territorial Health Officials. I've posted a screenshot of the figure on the right.

Before discussing the four bullet points, I want to emphasize that Marcus Plescia issued a press release on August 11, 2022 when the new guidelines came out and it did not mention the points in the NPR figure. In fact, it seems to me that he would not agree with the NPR sumary.

Akiko Iwasaki talks about mucosal immunity

Akiko Iwasaki is a Professor of Immunology at Yale and a former student in my department (Dept. of Biochemistry, University of Toronto). She got her undergraduate degree in biochemistry in the mid-1990s¹ and then did her Ph.D. in the Dept. of Imunology under my friend and colleague Brian Barber.

Alex Pallazzo is a keen podcast listener and he alerted me to an interview with Akiko Iwasaki on the EMBO podcast channel: The Right Place at the Right time. There are several reasons why listening to this podcast is worthwhile if you are interested in science and immunology. The most important reason is that it gives you a good idea of the depth of knowledge in the field because the level of the interview is pitched at those who have a considerable understanding of imunology. I'm not one of those people but I recognize good science when I hear it.

Another reason is that she discusses COVID-19 and how vaccines work. As you know from earlier posts, the serum antibody levels induced by the current vaccines wane after a few months so that vaccinated people can get infected by the SARS-CoV-2 virus. The secondary response then kicks in protecting you from serious illness. In order to stop the initial infections and prevent the spread of the virus we might have to get booster shots every six months or so and that's not a satisfactory solution.

Iwasaki works on something called mucosal immunity, which is new to me but very familiar to the experts. Here's a brief description from her website and a figure from Wikipedia.

The mucosal surfaces represent major sites of entry for numerous infectious agents. Consequently, the vast mucosal surfaces are intricately lined with cells and lymphoid organs specialized in providing protective antibody and cellular immunity. One of the most fundamental issues in this field concerns how antigens in the mucosa are taken up, processed, and presented by antigen presenting cells. Our laboratory's goal is to understand how immunity is initiated and maintained at the mucosal surfaces, particularly by the dendritic cells (DCs), through natural portals of entry for pathogens that are of significant health concerns in the world.

We focus on understanding how viruses are recognized (innate immunity) and how that information is used to generate protective adaptive immunity.

I hope I understand this well enough to explain it in simple terms. Mucosal immunity means that there are IgA antibodies in the mucosa that surrounds cells in certain parts of the body. For our purposes, the cells in the respiratory tract are important in COVID-19. The memory B-cells and T-cells that respond to the antigen are located right under the mucosa. Imagine that you could produce a vaccine that induced IgA against SARS-CoV-2 in the mucosa. The antibodies would be located right where the virus enters the body and they don't disappear over time like IgG in the blood stream. Furthermore, the secondary response is induced right near the site where the virus is attacking the body.

I think you need a nasal/throat spray vaccine to make this work and such vaccines are under development. They would probably have to be given in conjunction with the intra-muscular mRNA vaccines. I wish I could get Brian Barber to explain this but I can't seem to contact him. He gave a short lesson in immunology on his daughter, Jill Barber's Instagram account last year so I know he could do it.

I learned one other thing from listening to Akiko Iwasaki. We know that SARS-CoV-2 is more virulent in cold weather, especially during the winter months. She explains that the mucosal layer needs to be kept moist but during the winter months it can dry up due to the low humidity. The outside air is cold, therefore the humidity is low, and we import that air into our homes and workplaces. This dry air promotes spread of the virus.

Maybe we should be installing extra humidifiers to keep the humidity at higher levels?

It's a bit of a stretch from Akiko Iwasaki to Jill Barber but we've known Jill since she was little and my wife and I are big fans so here's a musical interlude to take your mind off COVID-19.

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1. She must have taken my Molecular biology course and that's probably why she knows so much!

Omicron variant: lessons from Denmark

Danish scientists have looked at the first 785 cases of Omicron variant in Denmark. The most important lesson is that 83% of the cases were fully vaccinated. (Mostly two doses of an mRNA vaccine). This includes 7% of the total cases that had also received a booster shot. 76% of the Danish population are fully vaccinated.

Espenhain, L., Funk, T., Overvad, M., Edslev, S.M., Fonager, J., Ingham, A.C., Rasmussen, M., Madsen, S.L., Espersen, C.H. and Sieber, R.N. (2021) Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021. Eurosurveillance 26:2101146. doi: [Eurosurveillance: Full Text]

This is similar to the results in other countries where a large percentage of the population are vaccinated. The spread of Omicron in those countries is largely driven by infection of the vaccinated group and the only way to blunt this spread is to limit contacts among vaccinated people. That means lockdowns or partial lockdowns for everybody and that seems to be working.

As usual, the United States is going to serve as a good control on these measures since the dominant message from American government, media, and health officials is that you are pretty much okay if you are vaccinated and you just have to be a bit more carefeul. No need to change your holiday travel plans.

The cases in Denmark cover all ages groups but the 20-29 age group had the highest number of infections. Quite a few of the cases could be traced to a "seasonal gathering" of 150 people and a large concert but most others seem to be due to community transmission once the variant became established. The original cases came from people who had travelled from South Africa and other countries.

Since the identification of the first Omicron case in Denmark, a steep increase in the number of cases has been observed. A major driver of this development was a large party with young adults – a population group with more social and close connections than adults and children.

We find several reasons for concern: (i) the rapid spread shortly after introduction despite extensive contact tracing efforts, (ii) the occurrence of several superspreading events with high attack rates and (iii) the high proportion of fully vaccinated Omicron cases.

So far, there haven't been many hospitalizations or deaths due to infection with the Omicron variant but that could come later.

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The omicron variant evades vaccine immunity but boosters help

Scientists are very interested in the omicron variant and why it is so dangerous. Since vaccinated people are getting infected, it must mean that the omicron variant isn't effectively neutralized by vaccine-induced antibodies. Several preprints on this topic have been posted and they all reach the same conclusion. I'll discuss one of them.

Garcia-Beltran, W.F., St Denis, K.J., Hoelzemer, A., Lam, E.C., Nitido, A.D., Sheehan, M.L., Berrios, C., Ofoman, O., Chang, C.C. and Hauser, B.M. (2021) mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. medRxiv. doi: 10.1101/2021.12.14.21267755

Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of vaccine-induced neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that were vaccinated recently (<3 months), distantly (6-12 months), or recently boosted, and accounted for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinated individuals. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron only 4-6-fold lower than wild type, suggesting that boosters enhance the cross-reactivity of neutralizing antibody responses. In addition, we find Omicron pseudovirus is more infectious than any other variant tested. Overall, this study highlights the importance of boosters to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.

On the effectiveness of vaccines

I've learned a bit of immunology from hanging out with immunologists so I'm going to try and explain how vaccines protect you from the worst consequences of an infection and why booster shots aren't as necessary as you think. This will be an illustration of how difficult it is for the media to keep you correctly informed about real science and why we should have more scientists explaining these things instead of doctors

Dozens of papers on this topic have been published over the past year or so and they all say the same thing. SARS-CoV-2 vaccinations induce an immediate production of antibodies in response to the spike protein antigen whether it's presented on the surface of a viral vector such as adenovirus or synthesized in your cells by mRNA. The antibodies are produced by a small number of B cells that just by chance happen to recognize the viral protein. These cells multiply rapidly so that within a few days you have enough antibodies being produced to fight off any infection.

Over time, the antibody production declines if there's no infection but some of the B cells become memory B cells that lie in wait for the next infection when they can be rapidly stimulated if you get infected months, or years, later. There's another type of cell called a T cell that also forms memory T cells that are very long-lasting and help fight off future infections.

Imagine that you encounter the virus several months after you've been vaccinated. As soon as the virus enters your body the memory cells are activated and the virus is attacked. You may have a mild case of COVID-19 for a few days but you are protected against the most severe forms of the disease. The point is that a reduction in antibody levels is perfectly normal. What's important is whether you have a robust level of memory B cells and memory T cells that can be activated. The hype in the media has convinced people that the vaccines are no longer effective after six months and you have to get a booster shot to protect you from COVID-19.

Here's a very recent paper that presents the data. It was published in Science on December 3, 2021.

Goel, R.R., Painter, M.M., Apostolidis, S.A., Mathew, D., Meng, W., Rosenfeld, A.M., Lundgreen, K.A., Reynaldi, A., Khoury, D.S. and Pattekar, A. et al. (2021) mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science 374:eabm0829. doi: 10.1126/science.abm0829

Vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proven highly effective at preventing severe COVID-19. However, the evolution of viral variants, and waning antibody levels over time, raise questions regarding the longevity of vaccine-induced immune protection. Goel et al. examined B and T lymphocyte responses in individuals who received SARS-CoV-2 messenger RNA vaccines. They performed a 6-month longitudinal study of individuals who never had SARS-CoV-2 infection compared with people who had recovered from SARS-CoV-2. Humoral and cellular immune memory was observed in vaccinated individuals, as were functional immune responses against the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) viral variants. Analysis of T cell activity suggested that robust cellular immune memory may prevent hospitalization by limiting the development of severe disease.

The authors looked at the immune reaction in three different groups. The first was the naive group of people who have never had COVID-19 but got the vaccine (blue). The second group was people who had already survived COVID-19 and then got vaccinated (red). The third group was composed of people who had mild cases of COVID-19 and never got vaccinated (purple).

This is a long paper with lots of experiments but the data can be summarized in the figure below. The authors looked at antibodies to the spike protein and to its specific ACE2 binding site. They also looked at neutralizing antibodies or the abiity of circulating antibodies to neutralize whole virus particles. The results are summarized in the first graph and they show that the antibody levels rise to maximum levels about one week after receiving the second dose of vaccine (administered four weeks after the first dose).

The antibody levels fall to about 10% of the maximum value over the next six months. (The x-axis is a log scale.) This is exactly what you expect for a typical vaccine. Note that the levels for people who had already been infected were higher to begin with but the rate of decline was similar to the naive group. This suggests that booster shots will have a similar effect on antibody levels.

The levels of memory B cells and memory T cells rise to a maximum at four months, right at the time of the second dose. They remain high at the end of six months.

Taken together, these data demonstrate that mRNA vaccines induced a population of memory B cells that was durable for at least six months after vaccinaton, and these cells were capable of rapidly producing functional antibodies against SARS-CoV-2, including neutralizing antibodies against VOCs [variants of concern], upon stimulation....

Taken together, these data indicate that mRNA vaccination generates durable SARS-CoV-2-specific CD4⁺ T cell memory in individuals who were not previously infected with SARS-CoV-2 and only transiently boosts these responses in SARS-CoV-2-recovered individuals.

What this means is described by the authors in the concluding remarks,

These data may also provide context for understanding potential discrepancies in vaccine efficacy at preventing infection versus severe disease, hospitalization, and death. Declining antibody titers over time likely reduce the potential that vaccination will completely prevent infection or provide near-sterilizing immunity. However, the durability of cellular immunity, here demonstrated for at least 6 months, may contribute to rapid recall responses that can limit initial viral replication and dissemination in the host, thereby preventing severe disease.

In other words, if you are fully vaccinated (two doses of mRNA vaccine) then you are well-protected against severe disease although you may suffer mild symptoms for a few days. You may be able to avoid the mild symptoms if you have gotten a recent booster shot but that effect is likely to decline in a few months.

The hype about booster shots is extremely misleading. The media is making it sound like all of your vaccine protection declines after six months and you need the boosters to have any chance at all against the omicron variant. How many times have you heard that your vaccine protection drops to 33% after six months?

You could argue that boosters aren't even necessary but that ignores the possibility that even a mild infection may be harmful to some people. It also ignores the possibility that by preventing even a mild infection you could be blocking the spread of the virus. I don't know of any data on viral loads after vaccination but I suspect that a booster offers some protection against spread.

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Image Credit: The coronavirus figure is from Alexy Solodovnikov and Wikmedia Commons.

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.

The origin of SARS-CoV-2 and gain-of-function research

I'm currently discussing the meaning of "function" with a small group of scientists and philosophers and it's not easy to come up with an acceptable definition. Imagine how much more difficult it is to identify research that results in a gain of function!

Gain-of-function research has been in the news recently because there are a group of conspiracy theorists who accuse the scientists at the Wuhan Institute of Virology of conducting gain-of-function research on bat caronaviruses leading to the creation of SARS-CoV-2 which then escaped from the lab to cause the pandemic. Some of these conspiracy theorists even accuse the American NIH of funding this gain-of-function research.

How do you define gain-of-function research in a meaningful manner? That's the question posed by Amber Dance in a recent Nature article. (Amber Dance is a freelance science journalist.) The first reference below is the title and subtitle of the article that was published in the magazine and the second reference is the online version.

Dance, A. (2021) The Truth About Gain-of-Function Research: Granting new abilities to pathogenic microbes sounds dangerous, but what has the research told us? Nature 598: 554-555. [doi: 10.1038/d41586-021-02903-x]

Dance, A. (2021) The shifting sands of ‘gain-of-function’ research: The mystery of COVID’s origins has reignited a contentious debate about potentially risky studies and the fuzzy terminology that describes them. Nature 598: 554-555. [Nature website]

The only relevant gain-of-function research is the type specified by NIH as "gain-of-function research of concern" (GOFROC). This is research that makes a potential pathogen more likely to cause disease in humans. This is the kind of research that would be carried out in a lab devoted to biological warfare but it could also apply to some research that was carried out in the past, as described in the article. There is no evidence to support the accusation that scientists in China, or anywhere else, were doing such research on coronaviruses.

There are other kinds of research that involve constructing chimeric viruses in order to test whether they have the potential to cause a pandemic. This is perfectly normal, even necessary, research but conspiracy theorists have claimed that this is forbidden gain-of-function research. The article does a good job of explaining this research and why it's not a problem.

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Image Credits: The coronavirus figure is from Alexy Solodovnikov and Wikmedia Commons.

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.

Characteristics of COVID-19 in the United States during 2020

An interesting paper on COVID-19 infections in the USA during 2020 was recently published in Nature. The take-home lessons are:

1. about 78% of infections were probably undocumented so the actual number of people with COVID-19 is almost twice the number that's been reported
2. about 31% of the population was infected during 2020 giving rise to a considerable level of natural immunity
3. by the end of 2020 the case fatality rate (CFR = number of deaths per estimated cases) fell to about 0.30% due to better reporting of cases and better patient care
4. the case fatality rate of 0.30% is about four times higher than that of seasonal influenza (<0.08%)

Sen, P., Yamana, T.K., Kandula, S., Galanti, M. and Shaman, J. (2021) Burden and characteristics of COVID-19 in the United States during 2020. Nature 598:338-341.
[doi: 10.1038/s41586-021-03914-4]

The COVID-19 pandemic disrupted health systems and economies throughout the world during 2020 and was particularly devastating for the United States, which experienced the highest numbers of reported cases and deaths during 2020. Many of the epidemiological features responsible for observed rates of morbidity and mortality have been reported; however, the overall burden and characteristics of COVID-19 in the United States have not been comprehensively quantified. Here we use a data-driven model-inference approach to simulate the pandemic at county-scale in the United States during 2020 and estimate critical, time-varying epidemiological properties underpinning the dynamics of the virus. The pandemic in the United States during 2020 was characterized by national ascertainment rates that increased from 11.3% (95% credible interval (CI): 8.3–15.9%) in March to 24.5% (18.6–32.3%) during December. Population susceptibility at the end of the year was 69.0% (63.6–75.4%), indicating that about one third of the US population had been infected. Community infectious rates, the percentage of people harbouring a contagious infection, increased above 0.8% (0.6–1.0%) before the end of the year, and were as high as 2.4% in some major metropolitan areas. By contrast, the infection fatality rate fell to 0.3% by year’s end.

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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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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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Asymptomatic and presymptomatic spread of SARS-CoV-2

It is widely believed that a substantial amount of viral spread is due to individuals who are transmitting the virus but have no symptoms (asymptomatic spread) but there's so much misinformation about COVID-19 out there that I'm having trouble sorting out real science from fake science so I've become skeptical of just about everything.

I'm not talking about the kind of fake science being spread on FOX News, I'm also talking about misinformation spread by ordinary people like me and the typical readers of this blog. We might do it inadvertantly but it's still wrong.

What's the real data on asymptomatic spread? I don't know, but here's a summary of the issue in a recent issue of Science. It sounds good to me because the authors take steps to address questions that seem obvious.

Rasmussen, A.L. and Popescu, S. V. (2021) SARS-CoV-2 transmission without symptoms. Science 371: 1204-1207. [doi: 10.1126/science.abf9569]