COVID-19 origins — a review of the lab leak saga.
Disclaimer: This post doesn’t reflect views of my employer or any other entity, other than me in my personal capacity.
Nearly two years into the COVID-19 pandemic, there has been scant progress in understanding its origins. In this post, I write how one hypothesis has seen a rebirth from being a “conspiracy theory” to a plausible hypothesis with some circumstantial evidence supporting it.
Prologue
The “dominant” view among scientists seems to be that COVID-19 was the result of a zoonotic spillover. There have been many names who have called for an open investigation into this by considering all possibilities, but it hasn’t been embraced wholeheartedly by the scientific community is what I’ve observed.
It should be significant to note that till date, we don’t have a trail of evidence for a zoonotic spillover as the origin of COVID-19. Just claiming that “this is what happens in nature all the time so COVID-19 happened because of it” or that this is the “scientific consensus” is plain intellectual dishonesty. During the 2003 SARS epidemic, civets were quickly identified as the intermediary host of the virus. Now, it might be the case that Chinese authorities obliterated potential evidence in Wuhan’s wet markets, but I find this excuse to advocate zoonosis to be tenuous. Also, it very much would be in the interest of Chinese authorities to provide irrefutable evidence of zoonosis so that their labs and scientists are cleared of suspicion, but notably that hasn’t happened as well.
Lab leaks are frequent
Some months back, New York Times ran a very interesting story (I’m not a big fan of NYT, but I’ll acknowledge that they often publish interesting stories). It pertained to an anthrax outbreak in the erstwhile Soviet Union:
In 1979, there was an outbreak of Anthrax in Yekaterinburg, Russia (formerly Sverdlovsk in Soviet era). There was a military research facility in this town, where an accident caused an anthrax outbreak killing many people. The West got to know of this a few months later (Iron curtain and all) and initially, it was reported to be from a lab accident. Soviets later permitted an American scientist to conduct an “investigation” there, where their explanation of a natural origin of this outbreak was accepted. Only later was this story blown apart, when a Wall Street Journal reported deployed to Russia found out this story was inconsistent and then Boris Yeltsin admitted this was due to a lab accident.
Recently, Taiwan (which is following a zero COVID policy very assiduously) reported a COVID case, curiously in a scientist working in a lab handling viruses. It was quickly traced to indeed be a safety incident in the lab and the entity, Academia Sinica received a fine for lax safety practices.
In 2004, there was an outbreak of SARS in Beijing, which was traced back to a lab there. Heck, WHO itself issued a bulletin about this, conclusively stating that this outbreak was because of a lab incident. Funny enough, a similar incident seems to have happened in National Institute for Viral Disease Control, Beijing in February 2020, where a researcher got infected with COVID-19 due to some such accident. This came out from a public records request done by US Right to Know in the state of Ohio.
While looking up this stuff, the scariest case I came across has nothing to do with viruses, but with stuff called prions, which are misfolded proteins. Contacting prions can lead to deadly diseases leading to very painful deaths. France had an incident where a retired lab worker handling prions died in 2019 due to an incident in her lab where she contacted prions a decade before. This led to France issuing a moratorium on this research to look into measures to prevent such incidents.
By this point, it is clear to us that lab accidents can happen and they do happen. They can lead to disease outbreaks. And, it can get deadly, as the SARS leak in Beijing in 2004 and the Soviet Anthrax leak in 1979 have shown us.
One argument proponents of “COVID-19 due to zoonosis” use is that animal to human virus spillovers keep happening in nature. By that logic, accidents in labs handling deadly pathogens and biological agents do happen. What is bad is that there seems to be no standardized mechanism to report such incidents, as pointed out by this 2016 survey. Whether COVID-19 was a lab leak or not, I believe its high time the authorities come up with rigorous frameworks to minimize lab incidents, rigorously record such incidents and launch containment measures. The way nuclear research and work is regulated heavily, the world needs to come up with similar measures for research into dangerous pathogens and agents.
The cult of science and scientists
This is a strange name to give to this section. I felt compelled to include this considering the stuff I came across, alongside some observations I wish to make.
A few months back, the comedian Jon Stewart appeared on his friend Stephen Colbert’s late night show and, had a bit of a meltdown where he suggested that COVID-19 was due to a lab leak:
The reaction to this was, interesting to say the least. Colbert suggested that Stewart worked for Sen. Ron Johnson (R-WI), who has engaged in misleading statements about COVID. Some have even suggested that Stewart was being sarcastic, although I felt he was being sincere. Some reaction tweets below to show how upset some folks were with Stewart:
The premise of some folks here seems to be that, since genuine science is under attack by some segments of American politics, we must defend science and scientists at all costs, even when there is a chance the science might have caused something bad and scientists might be engaging in bad faith due to immense conflicts of interest. Personally, I oppose this kind of rhetoric. We should never put anything on the pedestal of being divine and infallible.
Recently, Republicans on two committees of the US House of Representatives were given access to some email exchanges between Dr. Fauci and many other scientists in early 2020. These emails were initially released in heavily redacted versions in response to FOIA requests. So, the notes Republicans released of what was contained in these emails were interesting:
The initial impression of many scientists involved in these exchanges was that, the virus has some unusual features which is difficult to explain as having originated in nature. They also noted the existence of techniques called serial passage, where one passes naturally occurring viruses through human tissues etc and see how they evolve. So, a lab incident was definitely on the table as an explanation for the origins of COVID-19, as of the first week of February 2020. But within a month, there was a paper named “The proximal origin of SARS-CoV-2” in the journal Nature medicine which heavily downplayed a lab origin in favour of natural origins of the virus. Many authors of this paper, including the lead author Kristian Andersen took part in those calls with Fauci et al. Within weeks, a possible hypothesis was severely downplayed in an influential research paper, which was used by Fauci and others to downplay a lab leak scenario. Dr. Andersen stated that they had “new data” which changed their minds, but that new data has never really come to light:
Some emails by Francis Collins, the former head of NIH are pretty damning:
The reply by Dr. Fauci to Dr. Collins’ above email has aged like rotten tomatoes:
Freedom of Information requests to NIH by various entities in US have run into roadblocks. One entity, US Right to Know even wrote an article on their website detailing their travails:
The Intercept, a left leaning news organization has sued NIH for information:
Possibly the worst instance of bad faith discourse came in a letter in “The Lancet”, published in February 2020:
The above letter seems innocuous, but it turns out Peter Daszak, president of EcoHealth Alliance orchestrated it behind the scenes:
Peter Daszak and EcoHealth Alliance have been key players in this saga, acting as conduits for US taxpayer money to fund bat coronavirus research in China. Thus, they had an absolutely blatant conflict of interest here. Ideally, that Lancet letter should have been withdrawn, but all we ever got was an “addendum” addressing these conflicts of interest:
Thankfully, some signatories of this letter have withdrawn their support for it, with one supposedly going as far as saying “I’m convinced that what happened is that the virus was brought to a lab, they started to work with it…and some sloppy individual brought it out.” (This was reported by Wall Street Journal)
Jeremy Farrar, a British scientist who head Wellcome Trust (focusing on health research) was involved in those calls with Fauci and co in early 2020. Recently, he said this:
It’s one thing to drag law enforcement, intelligence or military agencies to court for information under FOIA. But, when a supposed health concerned agency is fighting to keep information of it’s funding and deliberations secret, it doesn’t inspire confidence. Nor does the fact that people like Peter Daszak who have blatant conflicts of interest in denying a lab leak ever happened have been given 200 decibel microphones by influential segments of the media subserviently does us any good. Questioning these bad faith actions shouldn’t be issues dictated by our political leanings, but it’s sad that in USA, this has come down to that mostly. We cannot be caught up in cults, whether its in being anti-science cranks or scientists are gods cranks.
Why don’t virologists speak out about this? A tweet by a MIT Media Lab scientist might clarify why:
It’s astounding how scientists become beholden to authority figures like Fauci and might become hesitant to speak what’s on their minds. Sounds Trumpian.
Intermission
In the next sections, I’ll cover the events that have transpired in China which is the circumstantial evidence for why a lab leak might have happened. There is a vast amount of stuff to cover here, which goes beyond the scope of this post. I’ll cover certain key events briefly and point the reader to persons on the internet who cover all this, if one is more curious.
The curious case of the Mojiang mine
In April 2012, six workers were cleaning out bat guano from a mineshaft in Mojiang, Yunnan province, China. They came down sick with persistent coughs, fever, headaches and breathing issues. They were eventually admitted to a hospital in Kunming, the capital of Yunnan. Three of these unfortunate workers eventually died. Curiously, those symptoms resemble COVID-19. Ofcourse, it should be beyond obvious that these workers didn’t contact COVID-19 itself, since it appears that beyond those 6, nobody else who came in close contact with them caught the disease/virus that inflicted them.
This event was captured in a thesis by an University of Kunming student named “The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown Viruses” which apparently described the conditions of those workers. This thesis was hunted down by an intrepid, anonymous Indian who goes by the pseudonym The Seeker (his twitter handle is TheSeeker268).
The Seeker also hunted down another thesis linked to a student at Chinese CDC which confirmed much of the contents of the University of Kunming thesis. This event was described by these theses to have been “Caused by SARS-like [coronavirus] from the Chinese horseshoe bat or other bats”. Shortly after The Seeker’s exploits, Chinese authorities blocked access to this theses database.
For more information on this, the interested reader can google “Mojiang Mine” and results will pop out. I used a Newsweek article for this section.
In late 2020, it seems like there was an interest among some western journalists to explore this mine, which didn’t happen as access to it was blocked by Chinese authorities. Here are some stories:
A Wall Street Journal reporter apparently managed to reach the mine through mountain bikes, but was detained, as per a story from them:
Enter Wuhan Institute of Virology
Scientists of WIV have made trips to the Mojiang mineshaft, collecting bat coronaviruses, as acknowledged by WIV’s leading bat coronavirus researcher Shi Zhengli to Scientific American (curiously, she claimed that those workers died due to a fungal infection). One such virus was named RaTG13, which has made appearances in research papers by WIV. This virus is said to be 96.2% similar to SARS-CoV-2 (but do remember that these viruses might have a few tens of thousands of nucleotides, not as complex as human beings, chimpanzees etc).
If WIV was just collecting and storing bat coronaviruses, it wouldn’t be such a big deal. Here we enter the murkiest waters, where scientists enhance these viruses through various techniques to see how they might evolve and affect human beings. This body of research is called “gain of function (GOF)”, which has led to a massive amount of controversy since WIV was performing GOF on bat coronaviruses. Now, WIV and its backers like Fauci might dispute this research being characterized as GOF by using some arcane descriptions of their own, but many experts (Richard Ebright of Rutgers University for example, who actively writes about this on Twitter) have termed WIV’s work with bat cooronaviruses as GOF.
NIH has given grants to WIV through EcoHealth Alliance (run by our friend Peter Daszak). Some of those grant progress reports were obtained by US publication The Intercept.
One such report outlines plans by Peter Daszak to screen thousands of bat samples for coronaviruses, screening people working with live animals and conducting research work with such viruses on humanized mice at BSL 3 labs:
Prof. Richard Ebright and Dr. Alina Chan (two people actively posting about this topic on twitter) have gone through this report, giving comments to The Intercept. The details they’ve flagged are fascinating:
Alina Chan, a molecular biologist at the Broad Institute, said the documents show that EcoHealth Alliance has reason to take the lab-leak theory seriously. “In this proposal, they actually point out that they know how risky this work is. They keep talking about people potentially getting bitten — and they kept records of everyone who got bitten,” Chan said. “Does EcoHealth have those records? And if not, how can they possibly rule out a research-related accident?”
According to Richard Ebright, a molecular biologist at Rutgers University, the documents contain critical information about the research done in Wuhan, including about the creation of novel viruses. “The viruses they constructed were tested for their ability to infect mice that were engineered to display human type receptors on their cell,” Ebright wrote to The Intercept after reviewing the documents. Ebright also said the documents make it clear that two different types of novel coronaviruses were able to infect humanized mice. “While they were working on SARS-related coronavirus, they were carrying out a parallel project at the same time on MERS-related coronavirus,” Ebright said, referring to the virus that causes Middle East Respiratory Syndrome.
Commenting on this story from The Intercept, New York Times noted:
In some of their experiments, the researchers isolated genes from bat coronaviruses that encode a surface protein, called spike. Coronaviruses use the spike protein to bind to host cells, the first step to an infection. The spike protein latches onto a cell-surface protein called ACE2.
According to the materials published, the researchers then engineered another bat virus, called WIV1, to carry spike proteins from other bat coronaviruses. They then conducted experiments to see if the engineered WIV1 viruses became better at attaching to ACE2 on cells.
Such experiments reignited a debate that has been going on for years about what sort of research is simply too dangerous to carry out, regardless of the insights it may provide. Experiments that can endow viruses with new abilities — sometimes called “gain of function” — have caused particular concern.
Another alarming piece of research that happened at WIV was flagged by Prof. Ebright:
Manipulating original viruses to cause viral loads upto 10,000 times, to have higher pathogenicity is simply alarming stuff. Also, we should note that this is stuff we’ve learned from the documents NIH was forced to release under FOIA. WIV definitely gets lot more funding from Chinese authorities and we simply have no way to know what research happened under those grants, and considering China’s amazing record in transparency, we don’t have much hope of knowing everything that happened in WIV. But, the picture we have so far isn’t comforting and it raises a lot of questions. Also, it’s important to note that Prof. Ralph Baric, who is an authoritative figure on coronavirus research has noted that it’s possible to manipulate viruses without leaving traces of such manipulation:
Not only that, but they’d figured out how to perform their assembly seamlessly, without any signs of human handiwork. Nobody would know if the virus had been fabricated in a laboratory or grown in nature. Baric called this the “no-see’m method,” and he asserted that it had “broad and largely unappreciated molecular biology applications.” The method was named, he wrote, after a “very small biting insect that is occasionally found on North Carolina beaches.”
Spooky happenings in WIV
WIV maintained a database of viruses they used to work on, which was mysteriously taken offline in 2019. This was first flagged by members of DRASTIC. The Print (an Indian publication run by veteran journalist Shekar Gupta) noted:
There have been repeated contradictions by key people about the reasons for the final removal of the database in 2019, and about the exact contents of it. DRASTIC listed out the following as instances of these contradictions.
“In Dec 2020, Pr. Shi Zhengli explained in a BBC interview that access to the DB [database] was stopped to prevent cyber security attacks.”
“On the 26th January 2021, Pr. Shi Zhengli confirmed again that the database has been taken offline ‘during Covid-19 pandemic’ in an email answer to Tommy Cleary.”
“On the 10th March 2021, during a Chatham House interview, Peter Daszak repeated the exact reason given by Shi Zhengli in her email to Tommy Cleary above.”
“These three statements do not make any sense since the main database was taken offline on the 12 Sep 2019, 3 months at least before the official start of the pandemic. So either the reason given for taking the database off is not correct (which raises more questions), or the statement points at an outbreak in Sep 2019.”
Zhengli was the administrator of the database.
It’s notable that there has been no pressure on WIV by their key Western allies to release this database for public consumption.
A few months back, Wall Street Journal reported that US Intelligence found a case of three researchers from WIV became sick enough to seek hospital care in November 2019:
Now, the above could well be a nothing-burger since we don’t know the nature of this sickness, whether those researchers worked on bat coronaviruses and I don’t attach a ton of weight to it, but it definitely is a curious coincidence.
In April 2020, Josh Rogin of Washington Post reported that US State Department had warned about less than adequate biosafety at WIV:
The above report should increase one’s anxiety about how safe things were at a place which was messing around with dangerous viruses.
DEFUSE ing the lab leak theory
In September 2021, someone leaked a grant proposal named “Project DEFUSE” written by EcoHealth Alliance to DARPA (Defense Advanced Research Projects Agency) to the group DRASTIC. EcoHealth hasn’t refuted this document’s authenticity and various news outlets have covered it as being authentic (including Washington Post, The Atlantic and The Intercept). The details in this grant proposal, as reported by The Intercept are alarming to say the least:
Among the scientific tasks the group described in its proposal, which was rejected by DARPA, was the creation of full-length infectious clones of bat SARS-related coronaviruses and the insertion of a tiny part of the virus known as a “proteolytic cleavage site” into bat coronaviruses. Of particular interest was a type of cleavage site able to interact with furin, an enzyme expressed in human cells.
But the proposal describes the process of looking for novel furin cleavage sites in bat coronaviruses the scientists had sampled and inserting them into the spikes of SARS-related viruses in the laboratory.
“We will introduce appropriate human-specific cleavage sites and evaluate growth potential in [a type of mammalian cell commonly used in microbiology] and HAE cultures,” referring to cells found in the lining of the human airway, the proposal states.
The new proposal, which also described a plan to mass vaccinate bats in caves, does not provide conclusive evidence that the virus that caused the pandemic emerged from a lab. And virus experts remain sharply divided over its origins. But several scientists who work with coronaviruses told The Intercept that they felt that the proposal shifted the terrain of the debate.
“Some kind of threshold has been crossed,” said Alina Chan, a Boston-based scientist and co-author of the upcoming book “Viral: The Search for the Origin of Covid-19.” Chan has been vocal about the need to thoroughly investigate the possibility that SARS-CoV-2 emerged from a lab while remaining open to both possible theories of its development. For Chan, the revelation from the proposal was the description of the insertion of a novel furin cleavage site into bat coronaviruses — something people previously speculated, but had no evidence, may have happened.
“Let’s look at the big picture: A novel SARS coronavirus emerges in Wuhan with a novel cleavage site in it. We now have evidence that, in early 2018, they had pitched inserting novel cleavage sites into novel SARS-related viruses in their lab,” said Chan. “This definitely tips the scales for me. And I think it should do that for many other scientists too.”
Richard Ebright, a molecular biologist at Rutgers University who has espoused the possibility that SARS-CoV-2 may have originated in a lab, agreed. “The relevance of this is that SARS Cov-2, the pandemic virus, is the only virus in its entire genus of SARS-related coronaviruses that contains a fully functional cleavage site at the S1, S2 junction,” said Ebright, referring to the place where two subunits of the spike protein meet. “And here is a proposal from the beginning of 2018, proposing explicitly to engineer that sequence at that position in chimeric lab-generated coronaviruses.”
Martin Wikelski, a director at the Max Planck Institute of Animal Behavior in Germany, whose work tracking bats and other animals was referenced in the grant application without his knowledge, also said it made him more open to the idea that the pandemic may have its roots in a lab. “The information in the proposal certainly changes my thoughts about a possible origin of SARS-CoV-2,” Wikelski told The Intercept. “In fact, a possible transmission chain is now logically consistent — which it was not before I read the proposal.”
Some experts tried refuting this by saying the genetic engineering work was proposed to be done in US rather than China, but they were refuted by others:
But others insisted that the research posed little or no threat and pointed out that the proposal called for most of the genetic engineering work to be done in North Carolina rather than China. “Given that the work wasn’t funded and wasn’t proposed to take place in Wuhan anyway it’s hard to assess any bearing on the origin of SARS-CoV-2,” Stephen Goldstein, a scientist who studies the evolution of viral genes at the University of Utah, and an author of the recent Cell article, wrote in an email to The Intercept.
Other scientists contacted by The Intercept noted that there is published evidence that the Wuhan Institute of Virology was already engaged in some of the genetic engineering work described in the proposal and that viruses designed in North Carolina could easily be used in China. “The mail is filled with little envelopes with plasmid dried on to filter paper that scientists routinely send each other,” said Jack Nunberg, director of the Montana Biotechnology Center at the University of Montana.
Thankfully, DARPA rejected this proposal, but we will have to question if WIV undertook any of this proposed work by obtaining funding through other channels. I’ll add a personal note here. In my graduate student time, I was involved in preparing material for a DARPA proposal by my former advisor. We were basically proposing extending research work we had already done. Proposals you submit will incorporate a lot of your previous work and how you plan to extend it. Thus, I find it reasonable to assume that WIV might have found funding elsewhere to perform some of this work that was proposed to DARPA, but we again have no way of knowing it unless we can breach the great wall of opacity built by China.
The Laos connection
In September 2021, Bloomberg reported that the closest relatives of SARS-CoV-2 was found in Laos, something enthusiastically shared by Peter Daszak:
But it turns out Daszak omitted stating the fact that WIV scientists were studying samples from Laos, which was reported in November 2021:
So, we have another case where Daszak was caught lying, which at this point doesn’t surprise me one bit.
What does US Intel community know?
Early into his presidency, Joe Biden ordered a time bound review by the US Intelligence Community on the origins on COVID-19. The unclassified release by the ODNI office had an interesting tidbit:
Four IC elements and the National Intelligence Council assess with low confidence that the initial SARS-CoV-2 infection was most likely caused by natural exposure to an animal infected with it or a close progenitor virus — a virus that probably would be more than 99 percent similar to SARS-CoV-2. These analysts give weight to China’s officials’ lack of foreknowledge, the numerous vectors for natural exposure, and other factors.
One IC element assesses with moderate confidence that the first human infection with SARS-CoV-2 most likely was the result of a laboratory-associated incident, probably involving experimentation, animal handling, or sampling by the Wuhan Institute of Virology. These analysts give weight to the inherently risky nature of work on coronaviruses.
Analysts at three IC elements remain unable to coalesce around either explanation without additional information, with some analysts favoring natural origin, others a laboratory origin, and some seeing the hypotheses as equally likely.
Variations in analytic views largely stem from differences in how agencies weigh intelligence reporting and scientific publications, and intelligence and scientific gaps.
One US Intelligence agency (we don’t know which one, although some have speculated it could be FBI, which does counterintelligence and is considered an element of US Intelligence community) is said to have concluded with moderate confidence that this was a lab leak. Now, there is a massive gap between how US Intel folks assign low confidence, moderate confidence and high confidence to a conclusion:
High confidence generally indicates judgments based on high-quality information, and/or the nature of the issue makes it possible to render a solid judgment. A “high confidence” judgment is not a fact or a certainty, however, and still carries a risk of being wrong.
Moderate confidence generally means credibly sourced and plausible information, but not of sufficient quality or corroboration to warrant a higher level of confidence.
Low confidence generally means questionable or implausible information was used, the information is too fragmented or poorly corroborated to make solid analytic inferences, or significant concerns or problems with sources existed.
It would have been nice to know the material US Intelligence used in writing their overall report on COVID-19 origins, but I’m curious how one agency said with some degree of confidence that this was a lab leak and what material they used to support this assessment. Also, another curiosity here would be if the Intelligence folks scoured their own government for data. But, Katherine Eban of Vanity Fair had reported in July 2021 that many officials in US government had stonewalled efforts by their peers on investigating the Wuhan lab and it’s link to US government, so one shouldn’t be too hopeful:
Epilogue
Can we ever find the origins of COVID-19? I’m not sure. A zoonotic origin favours the scientific establishment, but funny enough we have close to zero progress on it. A lab leak origin involves extensive forensic investigation into what happened at WIV, but its being stonewalled by various entities to varying degrees.
At this point, I’m personally in favour of this being a lab leak. The amount of circumstantial evidence I’ve come across has led me to this place, but if it indeed is traced to be a zoonotic origin conclusively, I’ll accept it. What I find unacceptable is how a credible avenue of investigation was derided as a racist conspiracy theory for more than a year, a gaslighting effort of epic proportions which was spearheaded by scientific figures with questionable motives and was successfully propagated by sections of US media, all because the lab leak angle was espoused by Donald Trump and his conservative allies. Science is supposed to go beyond political leanings, but it’s unfortunate that US media is letting politics colour this (yes, I’m aware of the shenanigans of American conservatives about stuff like climate change, but you can’t use it to defend your bad faith actions).
What are your thoughts on this? Let me know!
Credits
Many people have done stellar work in this arena. The Seeker, Alina Chan, Richard Ebright have been stellar contributors. The Intercept and US Right to Know have spearheaded FOIA efforts in this front. Josh Rogin of Washington Post and Katherine Eban of Vanity Fair have also contributed insights in this regard.
