How to Investigate SARS-CoV-2 Origins

What are the ethics for investigators and researchers under investigation?

SARS-CoV-2 emerged sometime in late 2019, causing a pandemic that killed millions of people. The origin of this virus is unknown, and every week we live without knowing its origin, we postpone the policies and research funding required to reduce the risk of future pandemics capable of killing millions of people.

There are two major hypotheses in play: either SARS-CoV-2 spilled over directly from animals to people via the Huanan Seafood Market, or SARS-CoV-2 spilled over indirectly as a consequence of research on bat coronaviruses conducted at the Wuhan Institute of Virology (WIV). The research in question involved a collaboration between US scientists at EcoHealth Alliance, UNC, and Chinese scientists at the WIV.

Let me share a bit about my background to qualify speaking on this topic. I received a PhD in mathematical biology at Princeton studying ecology & evolution. I did a postdoc at Duke University developing new techniques to utilize evolutionary trees when studying the microbes that live on humans. I was a research scientist at Montana State University studying pathogen spillover from wildlife to people since 2017, and a PI on a DARPA PREEMPT grant studying pathogen spillover from bats to people. Pre-COVID, I was analyzing genomes of pathogens like Ebola to examine their evolutionary origins and running simulations of viral evolution to study early outbreaks and determine the spillover risk of various viruses and mammalian reservoirs. I was familiar with EcoHealth alliance before COVID-19. In fact, they had submitted their own DARPA PREEMPT grant proposing to study SARS coronaviruses in bats. In their DEFUSE proposal to DARPA, they planned to insert a “Furin Cleavage Site” (FCS) into a SARS coronavirus spike protein. Interestingly, SARS-CoV-2 has an FCS in its spike protein where no other SARS coronavirus does, but we’ll get to that later. My main point here is that I’ve established myself as a researcher in this field and the question of whether or not SARS-CoV-2 arose from direct spillover or indirectly as a consequence of risky research is a question I’m actively researching using tools from my pre-COVID toolkit.

I’m aware of methods and standards of evidence in the field, as well as a lot of the social peculiarities like who works with who, who had what reputation pre-COVID, and more. The spillover community was a small community, there were a few large groups, and I was a leading data analyst on the largest group studying bat viruses and NOT studying bat coronaviruses with the WIV.

During COVID-19, I did considerable research on COVID-19 epidemiology in human populations. That research was rather stressful - if you estimated a lower pandemic burden, as I correctly did, other researchers in the field (and obnoxiously vocal researchers from well outside the field) would hold you over a digital pillory on Twitter and say you were going to be responsible for millions of deaths (ironically, using the disproven incorrect high-burden scenarios as their counterfactuals for millions of US deaths). Now that I’ve handed off my last COVID-19 outbreak forecast for medical managers, I’ve put my head to the task of independently examining the origin of SARS-CoV-2 and I’m discovering a highly unusual trail of literature from leaders in the spillover community, a trail of literature that reads to me like an effort to discourage investigations and tamp-down any questions of possible lab origin as a “conspiracy theory”.

There’s unusual behavior from colleagues in the field almost everywhere I look. Kristian Andersen and Eddie Holmes wrote Anthony Fauci in January 2020 they believed SARS-CoV-2 more likely than not arose from a lab. I took one look at the SARS-CoV-2 genome and came to the same conclusion. After Andersen wrote Fauci, Fauci hopped on a call with Andersen, Holmes, Jeremy Farrar (the head of the Wellcome Trust) and others to discuss this issue. Inexplicably, Andersen + Holmes completely changed their minds and later began pushing papers that a natural origin is the only plausible scenario. They wrote the Proximal Origin paper making transparently (to an expert in the field) straw man arguments that use the authors expertise and reputation to pull the veil over the public’s eyes - trust them, there’s no way this leaked from a lab.

To give a specific example, the authors claim that SARS-CoV-2’s Spike protein’s binding of human ACE2 is “not optimal” and therefore this wasn’t likely a bioweapon - but (1) the notion of “optimality” was based on simulations and not measurement (simulations are often wrong), (2) “optimality” in receptor binding is not necessarily the characteristic under selection for an entire virus life cycle which involves far more than binding - at times, too “optimal” of binding can come at the expense of other important functions needed for viral replication - and (3) even a “suboptimal” ACE2 binding in no way precludes other lab-leak possibilities, such as the more realistic (and the more central) hypothesis that perhaps this was a study of wildlife coronaviruses with a FCS inserted that went wrong. This was a straw man argument because the actual argument for a lab origin covers far more possibilities than represented in their paper, and those possibilities make a much stronger case for lab origin. The authors of Proximal Origin take the most extreme possibility (an “optimal” bioweapon) and cast it as the only possibility - that’s like me finding a spherical bullet in a body right next to a DARPA grant proposing to use a musket to kill this exact person and saying there’s no way a musket could’ve killed someone because muskets are suboptimal murder devices.

The Proximal Origin authors also claimed that the FCS may not actually be necessary for SARS-CoV-2 transmissibility in humans and therefore the FCS insert - the only such insert in a large lineage of SARS coronaviruses - isn’t evidence of genetic engineering. However, the FCS is key to SARS-CoV-2’s pathogenesis in humans. So, put simply, this coterie of world leaders were flat out wrong, and they were wrong because their language was too bold, too confident, too unscientific in its certitude. Even before learning that the FCS is key to SARS-CoV-2’s pathogenesis, the language in that paper does not read like it’s intended to convince a scientist like me - it reads like it’s performing a scientific puppet show for some other, unknown audience.

Their first argument on “optimality” is a straw man, and their second argument on the necessity of the FCS for SARS pathogenicity was speculation masquerading as fact that later proved to be wrong. Perhaps this coterie of world-leaders in the field actually believes their arguments, but to me, as a researcher in the field, it is unlikely that these knowledgeable people, after jumping on a call together with all their minds in a room alongside Fauci and Farrar, would make such obvious undergraduate mistakes on such a visible and critical matter concerning the origin of a virus that killed millions. A virus that, if it did leak from a lab, would have likely been funded by Fauci and Farrar, and conducted by the colleagues of these same researchers…

If Usain Bolt suddenly ran a 50 yard sprint in 40 seconds, I would think something is up and I would need to ask Usain Bolt “Why are you doing such poor sprinting today?” Why might there be such a subpar performance from world leaders studying coronaviruses with the Wuhan Institute of Virology, or closely connected with Anthony Fauci who led NIAID as it approved a 2019 proposal for gain of function research on SARS coronaviruses? I simply don’t accept the argument that they have some secret evidence that this was a natural spillover, and so whatever happened they could be the first ones to claim spillover - using whatever botched logic - and later be proven right. I don’t believe that is possible because the evidence required to make that claim - a single CoV genome from a bat sample - would be in the hands of EcoHealth or the WIV and, if they had it, they would release it immediately along with evidence that the sample never made it to Wuhan. They would share the location of the bats containing this progenitor so others could corroborate their finding, and this easily released evidence would be released immediately to absolve themselves and put these questions to rest. Given how easily that evidence would be released if it existed, I simply don’t believe it exists. Something else is happening.

One possibility is that this group of highly intelligent people, with a track record of excellence in the literature pre-COVID, choked under pressure. Maybe all of them, with their hundreds of years of combined expertise, fumbled and bumbled on issues of fact and used overconfident language unbecoming of scientists to present arguments their 2019 selves would reject in peer review. Maybe it’s just bad luck they fumbled when their skills were needed most to guide the world.

However, there’s another possibility we have to consider. As we study a possible research-origin of SARS-CoV-2, there remains the possibility that the researchers and funders connected to the research are worried of being held accountable for research that led to millions of deaths. This next point is crucial: they (Fauci, Andersen, Farrar, Holmes, Daszak) need not actually know if Shi Zheng-Li or others at the WIV inserted a FCS into a SARS coronavirus. It’s possible only one or two people at WIV would know that this experiment was conducted, and all others can be worried about reputational harms they & their colleagues face and the liabilities from the pandemic due to their guilt-by-association or funding of risky research. A class-action lawsuit for 6-20 million deaths could instantaneously evaporate the Wellcome Trust, and the mere fear of liability could dangle over the leader of the Wellcome Trust like a sword of Damocles. The final reputation of Fauci would be ignominy, a tragic fall for someone who spent his whole career jockeying for fame and influence, an Icarus who touched the sun to be hailed as a hero for his highly unusual role leading US COVID public health policy (despite having zero public health policy credentials). Given the circumstances of SARS-CoV-2’s emergence, the collaborations, the funding networks, the inexplicably low-quality work from intelligent authors, and the historically massive stakes, one could easily imagine other plausible explanations for this unusual literature trail I observed. It need not be a massive conspiracy with many people knowing what happened for each person individually to be scared and motivated to quell the questions.

We’re unwise to neglect motives when we see a pattern of deception, distraction, straw men, speculation masquerading as facts, arguments from authority calling their hypotheses facts and other information “misinformation”, and subsequent publications repeatedly insisting lab leak is a “conspiracy theory” and insisting on “dispositive” evidence of a Huanan Seafood Market origin (hint: the evidence was not dispositive). Perhaps this long trail of unusual behavior is benign, albeit extremely unusual and out of character. However, this is a very serious matter and it’s also very possible this behavior is a consciousness of guilt leading researchers to obfuscate and obstruct an impartial scientific investigation into research activities they may have been directly or indirectly involved in.

As I examine SARS-CoV-2 genomes on my laptop, as I try to uncover truth by devouring distasteful literature full of logical fallacies, speculation-as-fact, leaps to conclusions, and complex mathematics hiding simple assumptions that simply are not true, I’m confronted with research ethics questions I haven’t confronted before. At issue is not just whether risky research proceeded with the blessing of the US and Chinese governments (and possibly large foundations like the Wellcome Trust), but whether the parties involved have subsequently tried to use their scientific institutional power and expertise to cover their tracks.

If I were studying the origin of a virus that indisputably came from a bat, I would be incorporating the behavior of bats as I synthesized the literature. I would be thinking about bats in caves, bats eating fruits in trees, bats drinking date-palm sap and peeing into buckets collecting date-palm sap, bats doing all their bat things and I would be wondering whether the bat with the virus that killed people happened to do something unusual, something we could prevent in the future. With SARS-CoV-2, one possibility is that it’s not the behavior of bats, but the behavior of funders and researchers, that caused a pandemic. These researchers have names - they sign their names to papers, emails, and grants, and their laboratory methods leave fingerprints of their idiosyncratic methods. I don’t want to falsely accuse anyone of anything, yet to study the hypothesis that SARS-CoV-2 leaked from a lab, absent some trusted impartial inquiry by an established authority, we have to be private investigators studying the actions of our colleagues and asking questions about the behavior of researchers. As I examine the evidence, I realize this inquiry blurs the lines between a study of SARS-CoV-2, my responsibility as a citizen of the world, and ethical considerations in research of human subjects whose behavior is hypothesized to have caused a pandemic that killed more people than the Holocaust. Again, the stakes are truly, historically massive.

This research involves disproving famous paper after famous paper from famous scientists, all of which make obvious mistakes. Pointing out that a famous scientist is wrong, or that they leapt to conclusions, or that their pattern of publications appear to me to be pushing a particular conclusion and grabbing any argument that might work, will humiliate them. They will hate me, if they don’t already - good thing I’m not applying to them for grants. This research involves uncovering anomalies in SARS coronavirus evolution, analyzing viral evolution, epidemiology, case-ascertainment criteria of the Chinese government, US intelligence memos, FOIA’d documents revealing proposed research and then asking the genomes if such research was conducted, if those idiosyncratic methodological fingerprints from these people are present in the SARS-CoV-2 genome. This research involves a question of whether researchers in the field - the possible peer-reviewers, closely connected to the journal editors and the major global funders of this research - are biased in their beliefs. We have to examine motives for their behavior and biased beliefs, which can include fumbling, willful ignorance, them knowing the consequences for their funding, they themselves being involved in the research under investigation, or possibly they have done geopolitical calculations to believe their actions are moral by some unknown trolley problem (e.g. maybe they’re worried of a war if a virus made in a Chinese lab killed millions of people around the world).

In conducting my research on SARS-CoV-2 origins, I’m balancing my own ethical responsibilities as a citizen & scientist with the requisite expertise to “see something, say something” against the knowledge that the researchers under investigation are real people, innocent until proven guilty. Yet, these researchers are not making it easy to believe their innocence; they are not disclosing their conflicts of interest, they are not voluntarily releasing their data or grants, and they are reliably publishing low-quality work that wouldn’t have passed their own peer-review pre-COVID. I waited nearly 3 years for them to start publishing quality work, disclose their COIs, release the grants, and provide us all the relevant information, but nealry 3 years have passed, and they have not complied with our urgent global scientific effort to understand SARS-CoV-2 origins. In the face of such uncooperative and unscientific actions, I feel it’s necessary to pursue more aggressive lines of inquiry if we really want to understand the biology & the biologists’ behaviors. We have to ask tough, direct questions about the behavior and beliefs of researchers, and we have to consider the uncomfortable possibility that we are being lied to.

What are the ethics for conducting research under such an unprecedented crisis?

I’m examining the usual data - cases, genomes, and such - as well as the behavior of the exact researchers we would normally expect to lead this investigation (in fact, Daszak was the US emissary for the WHO investigation into WIV - does anyone see an issue here?). Not only are the leading bat coronavirus researchers of the world all connected with the WIV, but so too are all the leading health science funders in the world because, pre-COVID, bat coronaviruses were a huge concern. Anthony Fauci has led NIAID since 1984 - since 2 years before I was born - and he was head of NIAID when SARS-CoV-1 threatened to kill millions of people. Francis Collins has led NIH since 2009 and since 2013 Jeremy Farrar has led the Wellcome Trust, the largest private funder of health science research in the world. Anyone studying pathogen spillover pre-COVID or post-COVID will be submitting grants to these agencies and organizations, and the very heads of these agencies and organizations are now called into question for possibly having knowledge of risky research at the WIV, research that they funded.

I’m an unusual figure in this field, in a strange position in my career that provides a unique opportunity for me to contribute to this topic. Pre-COVID, I was working with the largest team in the world studying bat virus spillover and NOT doing research with the WIV. Because COVID was such a warzone, in large part because of unusual top-down narratives from Fauci & Collins, I left academia. I no longer live under the threat of denied NIH, NIAID, or Wellcome Trust funding.

It’s from this perspective of relative independence that I examine the evidence, see a worrisome trend and feel a civic duty to say something: an oligopolistic cartel of the most influential researchers and the most influential funders in this space are all publishing unusually low-quality work that reads like an attempt to persuade the public & not skeptical scientists, failing to disclose conflicts of interest, failing to disclose the role of conflicted funders in ‘leading’ their work protecting funders, and the forceful way this literature has been pushed in major journals and media outlets suggests an effort to obstruct impartial examination of the lab origin hypotheses.

Amidst unjustifiably redacted emails of the researchers in question, we see Kristian Andersen - whose change of mind from lab-leak-is-most-likely to no-way-was-there-a-lab-leak remains inexplicable, thanked Fauci and Farrar for their leadership on the Proximal Origin paper. Farrar himself - alongside Daszak, the president of EcoHealth Alliance - were co-authors of a paper at The Lancet calling lab leak hypotheses “conspiracy theories”, and people like Andersen himself parrot the idea that a lab leak is a “conspiracy theory”, that evolutionary biologists like me are “Creationists” or using creationists’ logic. The trail of evidence - of deception, diversions, and denials later shown to be flat out lies thanks to FOIAs and no thanks to these researchers’ cooperation - is long, and it is getting longer. This mountain of evidence of uncooperative researchers who should be running the research is deeply concerning.

I don’t say “oligopoly” lightly. Yet, how else besides running the NIH, NIAID, a $30B leading funder in a field, and being leading researchers all connected with the WIV and the editors of journals like Science, Nature, and Cell, did these hollow papers get published? If they were written by undergraduates, I would give them a C- for poor logic, yet they were written by leading researchers in the field and published in leading scientific journals and broadcast on the biggest media outlets in the world. How did they get such massive media attention? Why are researchers with a track record of excellence pre-COVID producing such shoddy work, prematurely claiming to conclude the origin while they have undisclosed COIs of working on CoVs with the WIV or funding GoF work in CoVs pre-COVID? Who are the editors overseeing these propaganda pieces (for lack of a better word), and who are the peer reviewers accepting this work?

I’m at a loss of words. I feel like I’m standing outside of Plato’s cave, telling people they live in a cave, and I’m literally being called a conspiracy theorist. I stare at the SARS-CoV-2 genome on my screen and, in more ways than just the FCS, the viral genome reads like Ralph Baric’s lab notebook written by Zheng-Li’s pen on a bat virus that EcoHealth alliance collected in SE Asia. There is a solid case that SARS-CoV-2 arose in a lab, and some of the most damning evidence - such as a grant by EcoHealth proposing to insert the FCS into a sarbecovirus - was not disclosed but rather had to be pried from scientists’ uncooperative hands. What are the ethics about failing to disclose your work and all the data on your database when your work is hypothesized to have killed more people than the Holocaust and your database alone may hold the answer the world needs to know? As we pry damning information and emails from these rogue scientists’ uncooperative hands, I read literature and find these same hands typing the papers, forming a reliable web of connections leading back to Anthony Fauci, Francis Collins, Jeremy Farrar, and affiliated researchers with either close connections to these funders or close connections to researchers at the WIV.

I would be a bad scientist if I weren’t incorporating this human behavior into my epidemiological and genomic analyses. I would be a pathetic, spineless citizen and human if I didn’t speak up about this atrocious behavior.

As we turn over stones, we need to be very careful to not tarnish reputations of our colleagues without strong evidence. However, at some point, the lack of cooperation, the defensive attacks and poor transparency from researchers constitutes a violation of scientific trust, a violation of their ethical duties as scientists to help our world of scientists uncover the truth. While science involves considerable peddling to claim your work is amazing and get everyone to pay attention to it, at some point it is unethical to use one’s authority as an expert in a field to present speculations as facts in a way that prevents people from finding the actual facts. It is unethical to call competing hypotheses “misinformation” and exclude their existence from the public domain. It is unethical to publish papers with hollow arguments and run those papers to media outlets for widespread dissemination and false claims of scientific consensus intended to sway the public while steamrolling over the skeptical scientists who don’t agree. At some point, it is not about the ethics of me asking questions that may harm the reputations of these scientists: they have planted their own reputations in harm’s way by their own questionable conduct, their own research putting them at the epicenter of a pandemic, and their own failure to disclose their grants, their data, and their potential conflicts of interest.

My North Star in my research on SARS-CoV-2 origins is the Truth. The Truth not only of where SARS-CoV-2 came from, but why people behaved the unusual ways they did. If SARS-CoV-2 did spillover directly from an animal and was not brought into the human population as a consequence of research activities, then I really can’t explain the human behavior we’ve observed in these researchers since 2020. I can’t explain their failure to disclose grants proposing to insert a FCS, their uncharacteristically hollow papers, their calling competing hypotheses “conspiracy theories” and trying to win science by mass-media instead of evidence and logic.

I welcome any scientists involved to share their journeys and shine light on how they changed their minds, why they believed the analyses they provided, and more. They should share this information knowing that the person they need to convince is not your average Joe watching CNN, it’s me - someone with a PhD who’s read the literature, who has genomes loaded on his laptop, who is capable of reproducing their methods, and who is familiar with all the jargon of the field. Tell me: why did Andersen change his mind in February 2020? Why did Fauci say he never funded GoF work? Why did Farrar and Daszak publish a paper in The Lancet calling lab leak hypotheses “conspiracy theories” at a time when Daszak knew, and had not yet disclosed to the public, that he had submitted a grant proposing to do gain of function work on CoVs in the WIV? Why didn’t Dazsak - or Fauci or Collins - disclose the 2017 grant proposing to insert a FCS or the 2019 NIH grant funded in 2020 proposing to make chimeric sarbecoviruses & assay them for human infectivity in Wuhan right before an FCS appeared in a human-infectious sarbecovirus in Wuhan?

Perhaps there are good explanations. I remain open to hearing from these people. Perhaps some of them made dumb mistakes and don’t want to admit silly oversights or wrong-in-hindsight analyses in a discipline that prizes being brilliant and being right. Yet, it’s better for them to disclose mistakes, bad insights, and low-quality research than remain quiet and fester this metastasizing suspicion that their uncharacteristically bad research is intentional, designed to mislead the average Joe hearing about “dispositive” evidence on a natural origin, and intended to manufacture the consent of the world to not investigate the possibility their research created a virus that killed millions of people. I hate saying that, but never forget - those are the historically massive stakes.

I don’t want anyone’s reputation to be tarnished, but I also feel a solemn duty to the millions who died of COVID-19 that I use my expertise and my unusual lack of conflicts of interest on this topic to examine the SARS-CoV-2 origins critically, unsparingly leaving no stone unturned until we find the truth. I have a responsibility as a contemporary human being to use my science and knowledge of today’s common practices & standards of evidence to understand how millions of people died so that we can tell the truth to our grandchildren and help them prevent millions of deaths. I have a responsibility to the world, and so too do these researchers whose emails remain redacted, whose grants of risky research are pried from their unwilling hands, whose published papers obfuscate the truth, whose claims of “dispositive” evidence obstruct investigation, whose undisclosed conflicts of interest raise questions. If their behavior raises questions, then it’s my responsibility to ask those questions.

We are playing a game of scientific Werewolf with 6-20 million deaths caused by a virus from Wuhan. Not Laos, not Guangdong, not Vietnam, not Cambodia, not anywhere else in SE Asia. An article by Peter Daszak and colleagues recently estimated nearly 66,000 people are infected with SARS coronaviruses each year all across SE Asia, yet we find a SARS coronavirus causing a once-in-a-century pandemic in Wuhan, of all places. The SARS coronavirus is unlike any SARS coronavirus found previously in nature - it has a Furin cleavage site with unusual codons. Some of the first cases reported were within driving distance of the Wuhan Institute of Virology, a US Intelligence report suggests members of the WIV were sick with a flu-like illness in November 2019 at an institute that proposed inserting a FCS into a SARS coronavirus in 2017, that proposed to make chimeric viruses in 2019, and that may very likely be the true epicenter of the pandemic. Since then, millions have died and a lot of scientists connected with the WIV or funding this risky research have been shady, for lack of a better word. It’s incumbent on those of us alive today to solve this riddle and find the Werewolf before the next virus kills millions more.