Using Occam's Razor to open Pandora's Box: The Origin of COVID-19 (Updated 1/30)
(11/27/20)
“Life was such a wheel that no man could stand upon it for long. And it always, at the end, came round to the same place again.”
-Stephen King, The Stand (1978)
<>The first time I read those words (at the end of Stephen King's 1,200*-page uncut post-apocalyptic 'Lord of the Rings' saga) they made quite an impression on me. Given that I was 14 years old, it shouldn't be too surprising to learn that a blood-soaked, raw portrait of what civilization might look like in the wake of a global pandemic would be memorable - but the older I get, the more disturbing that 'history repeats' warning becomes. The picture below, from the epilogue of the 1990 edition of the book, perfectly encapsulates the evil that can emerge whenever humanity succumbs to our curiosity and decides to peek inside Pandora's Box.
<>I didn't know that the book was foreshadowing my later academic study of history and military career as a WMD specialist, the COVID-19 pandemic, the threat of biological weapons and/or the confirmation that Las Vegas is the root of all evil, but sometimes the signs are so obvious that one can miss the forest for the trees.
<>In the last few weeks, a number of important pieces to the puzzle have emerged; the purpose of this update (in truth, a complete re-write) is to lay out the big picture, followed by my perspective on one particular study that I believe points in the direction of the final answer to the origin question. We may never know the answer to the question of COVID-19's origin, but we are guaranteed to fail if we lack the courage to ask the right question.
{For anyone seeking broader context for the true impact of the pandemic, I recommend my article that projects the long-term/cases/deaths trajectory for the US}
The Circle Opens
<>As early as March, I began to question the logic of ignoring the massive elephant in the room (perhaps the Elephant in the Huanan Market?) when scientists resoundingly rejected the possibility of COVID-19 having escaped from one of the laboratories in the city of Wuhan. My curiosity was entirely appropriate, because I was less than 2 years removed from a 15-year career as a WMD (CBRN-Chemical, Biological, Radiological, Nuclear) defense specialist, including nearly 8 with the Marine Corps Embassy Security Group & 3 years as an instructor for new Warrant Officers in our job field. Threat analysis is an essential part of preparation and mitigation, and ignoring the presence of the Wuhan Institute of Virology (the only BSL-4 lab in a nation of 1.4 billion people) and the Chinese Centers for Disease Control (CDC) in a city of 11 million people (more than twice as large as Atlanta, the home of our CDC) would be a massive failure for the global community.*
*Spoiler Alert: there's been a massive failure on the part of the global community.
<>When I first published this article in July, support for an investigation into a possible lab escape as the source for the pandemic was 'limited,' to put it mildly. It took two weeks to find a dozen sources of information on the topic, and yet today the bibliography below has 224 references (more than twice as many as the master's thesis for my M.A.).* As I write this update, an official WHO investigation is beginning, and a growing number of scientists are calling for far more transparency than anyone dared at the beginning. On 11/17, Dr. Zheng-Li Shi and her WIV team finally addressed a few aspects of the 2012 outbreak that spurred their heightened collection efforts in a peer-reviewed article, as well as aspects of the 'conspiracy theory' that the SARS-CoV-2 virus may have come to Wuhan through a lab accident, rather than a human-animal species jump a year ago.
*[The original text of the article can be found here. That version also contains some information about my background, for anyone curious or skeptical. A more complete explanation of my purpose can be found here, and if masochism intrigues you, then my pile of sources is a good place to start.
<>The vast majority of new information that continues to emerge about research into the origins of the pandemic has mostly weakened the support for alternative explanations, but attempting to lay out detailed information as I did in the first iteration of this article would exceed the character limits of what LinkedIn allows for articles, and so I will rely on that first version (linked below) and link or highlight the best of the primary research as time allows. Despite the dozens of news articles linked below, no real effort was made to draw attention away from the election, even though this issue could become the central theme of the next presidential administration. It might not, but the picture that's now coming into focus is not 'flattering;'
In 2012, an outbreak of a SARS-like virus occurred in Yunnan Province in southern China, which infected 6 miners and killed three of them, after they had spent about 2 weeks working to clean out a section of cave within an old gold mining complex.
This event prompted the return of virus-hunting expeditions led by Dr. Shi Zheng-Li, one of the world's foremost authorities on bat coronaviruses. She gained prominence after an earlier hunt successfully found the animal reservoir of the first SARS virus nearby, in 2005.
Despite the circumstances at the time, no information or reference to that incident ever appeared in the WIV’s published papers, even though the possibility of a new species of human coronavirus (CoV) would have enormous potential for disaster (including COVID-19, there are only 7 known species of human CoV’s : the 4 that cause the common cold, SARS and MERS).
Dr. Shi knowingly lied about the nature of that outbreak in the spring, telling Scientific American that that event was the result of a fungal infection. However, Dr. Shi (“BatWoman”) personally led the sampling team; as a renowned expert on coronaviruses, there would have been no reason for her and a team of virus researchers from the WIV to travel there.
The Chinese have also avoided referencing the 2013 miner incident despite its obvious resemblance to COVID-19 symptoms. That’s probably because most people don’t know that the RaTG13 strain (the closest relative of COVID-19) was taken during the aforementioned trip, which was undertaken specifically to investigate the earlier outbreak. RaTG13 is the strain that whose genome is a 96.3%match for SARS-CoV-2, but didn’t compare as well with the original SARS-CoV from 2003.
The first public acknowledgement of this omission was published a week ago - 7 months after her interview - however, the WIV doesn't actually point out that their explanation has changed, even though the article appears to be a pre-emptive strike against the WHO investigation that has just begun. The document made no effort to clear up any of the other obvious concerns arising from that research, or the initial response of the Chinese to the COVID-19 pandemic (including the destruction of many early samples, as ordered by Wuhan officials in early January).
The most prominent early advocates of the natural emergence theory in were Peter Daszak and Ralph Baric; the former is an advocate of medical research into sources of potential animal pathogens, and the latter was the lead researcher from the University of North Carolina that helped Shi and the WIV practice techniques that help 'nudge' virus evolution without direct genetic manipulation. This was the main defense against those who claimed that the COVID-19 virus had a suspicious origin and may have been fully engineered, but it ignored the fact that 'natural' evolution could include repeated passaging experiments which repeatedly combine viruses with animal cells in order to induce favorable mutations. Or, exactly what the WIV did in studies they later published the results of (2016-2019).
If not for the discovery of a master's thesis that linked the WIV to the 2013 mystery illness investigation, we might have never known the full story behind the acquisition RaTG13 and other samples by the WIV.
Shi partnered in publishing results of experiments involving “gain of function” (GOF) by exposing coronaviruses to human, monkey and mouse cells to encourage adaptive evolution to make the affinity even greater. Her papers are readily available online.
Many of the detractors arguing against an accidental lab release have pointed to the time needed to produce evolutionary changes that could account for the 3.7% gap between the genomes of RaTG13 & SARS-CoV-2, estimated at 20-50 years. There is broad agreement that the genome doesn’t seem to have artificial insertions, but RaTG13 was an obvious candidate for gain-of-function experiments, and the methods used could explain the exponential condensing of evolutionary progress & the absence of evidence of human gene modification
In late May, China announced that the evidence no longer supported the claim that the Wuhan Live Market was the location where zoonotic transmission to humans took place.
Lastly, a new study from a senior M.D./PhD, discussed below, has provided compelling evidence for the specific location of the pandemic's emergence within the city of Wuhan.
<>Almost exactly a year has passed since the first proven cases of COVID-19 appeared in early December of 2019, during which 60 million people have been infected (and 1.4M of those people have died); my 10/1 projection of the winter 'peak' (based on historical patterns of flu seasons) projects that the US final death toll will be nearly double where it is now, just above 500K by May. It is a travesty that 10 months passed before the scientific community at large was willing to openly question the Chinese narrative; regardless of the final outcome of any investigation, the lack of courage amongst politicians and academia has undermined honest attempts to share information with other researchers.
'Peer Reviewed'
<>To put the shift into better perspective, a simple scan of the references reveals that the first peer-reviewed article to aggressively question the orthodox narrative didn't appear until August 12th, and the first article to accuse the WIV of withholding evidence wasn't published until October 20th,10 months after the city of Wuhan had been closed. Prior to last month, every article submitted to every journal that implied the possibility of a lab accident was rejected. This includes the 10/20 article, which had sat on a preprint server since May, and first publicized the existence of a 2013 thesis that described the role of the WIV in searching for the virus that sparked an outbreak in Yunnan Province in 2012.
<>The purpose of my original article was to aid in the dissemination of an analysis by Jonathan Latham, PhD and Allison Wilson, of a Master's thesis describing an unknown illness that killed 3 of 6 miners after they had been infected while clearing out an abandoned gold mine in Mojiang, Yunnan Province. Spoiler Alert: the simplest answer that explains the stability of the COVID-19 virus (its lack of exponential mutations that results when a virus first transitions to human hosts) is that the virus had made the jump 7 years earlier - or that further evolution most likely occurred at the Wuhan Institute of Virology, where China’s "BatWoman" and a team of researchers had brought samples from the cave, 900 miles to the south, to add to their collection and conduct research in 2013. Much of the debate over provenance has been framed by the speed of virus evolution, but natural mechanisms can account for the gap with or without direct genetic modification.
<>When I wrote that private message on May 28th (referencing an excerpt from my original article), the primary focus of origin research had centered on connecting the dots for a presumed zoonotic (animal) jump or series of jumps, because direct transmission from a bat to a human would be much less likely due to the relatively weak link between bat and human cell/immune systems – as opposed to the similarity between humans and pigs (a la swine flu). Despite a broad effort, no local coronavirus strains came close to indicating a recent ancestral connection with SARS-nCoV-2, the RNA virus that causes COVID-19 infection. The prime target species, pangolins, registered a genome similarity of 93%, which in viral terms represents a huge gulf in time and evolution, whereas the Wuhan Institute of Virology had bat samples above 96.3%; this is a correlation getting stronger in the direction of direct transmission.
<>However, there are at least two other major issues that have vexed scientists seeking zoonotic transmission, and the first is incredibly simple yet seemingly ignored – even if a bat managed to travel 800 miles from Yunnan Province to reach Wuhan, it would have probably been hibernating at the time a transmission took place in November. The more complex issue is based on the very low incidence of mutation observed despite more than 16 million confirmed cases; this is clear evidence that COVID-19 is already well adapted to human hosts. It’s so well adapted, in fact, that it’s statistically impossible for COVID-19’s infectivity prowess to have come via gene editing, because no simulated virus has come close to matching the complexity nature has provided.
<>I must note that one of the primary pieces of the Latham/Wilson hypothesis is the argument that newer techniques for nudging genome changes in viruses have been developed, and the most common option simply uses human cells to force evolutionary changes to strengthen affinity for human hosts by pairing them together over and over again. This method speeds up evolution without requiring manual editing, accomplishing similar results with zero human fingerprints.
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Pandora's Box
<>The map above depicts my attempt (this summer) to begin looking at the geographic distribution of early COVID cases; I've long felt that seeing the pattern of diffusion in spatial terms would make it much easier to determine whether COVID-19 was brought to Wuhan by random human or animal vectors, or emerged from an internal event such as an accidental lab escape. For scale, understand that the distance between the Huanan Market (the red pin) and the Wuhan Institute of Virology (bottom right corner biohazard marker) is about 7.5 miles. That is a sizable distance, when considering that Wuhan has 12 million residents and several million more in the metropolitan area, and the 2002-2003 SARS epidemic did come from a live market - thus making the hypothesis very simple and attractive. The problem was that the first cases had no connection to the market, and very little information has been released about those patients.
<>Once I discovered that there was no identifying information about the residence or treatment of the index cases, I gave up trying to map the outbreak. And then last week, I discovered that someone had found the missing link, and built an extensive model of the implications. Dr. Steven Quay calculated the hospital locations using the genome sequencing databank, metro rail traffic and information pulled from the earliest journal articles:
<>This five minute video is straightforward, but the evidence is explicitly laid out in the 32-page pre-print article on Zenodo. Triangulating the first case locations didn't just point back to the first hospital - it showed exactly how COVID-19 spread through Wuhan, and reached the outside world through the airport. If the odds of every early case occurring next to the the Subway are 1:68,500, then it's also highly unlikely that the first case of COVID-19 randomly appeared in the center of Wuhan.
<>The map above indicates the position of the 9 rail lines that run through Wuhan. The table to the right shows the hospitals, WIV and Huanan Market and their closest train station on Line 2.
<>In other words, the very first case of COVID-19 emerged 900 miles from its suspected natural source (the equivalent of driving from my house in Dallas, TX to Tallahassee, FL), and randomly popped up somewhere within a 20 minute walk from the WIV, rather than any other location in a city of 12 million, in a country of 1.4 (ish) billion. During its travels, the virus managed to infect no one on the journey, until it made it to the exact location where it could best implicate the only BSL-4 lab of its kind within a couple thousand miles, that also stored the closest direct genetic ancestor and more than 1,300 other CoV specimens.
Furthermore, each of the direct-flight routes of the airport correspond perfectly with the earliest cases of COVID-19 to appear outside of China. Finally, every sequenced genome taken from infected patients (141,000+) is a direct descendant of the true index case that first appeared at the PLA hospital. It is possible that someone became infected in Yunnan Province, rode a train directly to Wuhan, only to become sick soon after. However, the possibility of that person randomly living within blocks of the WIV are stupendously small, especially since they would have had to come into contact with raw bat-meat or fresh guano from a bat species that was already in hibernation for the winter.
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Occam’s Razor
This article is far from a complete review of the Latham/Wilson or Quay findings, much less of the other articles I’ve included, but in order to maintain the slightest pretense of brevity I must conclude that the evidence can provide far more answers than a wild goose chase for pangolins and civet cats in southern China.
<>The director of the Wuhan Institute of Virology is one of the world’s leading authorities on coronavirus research; her stature grew dramatically after she assisted in the cataloging and study of coronaviruses after the emergence of SARS-CoV in 2002. 10 years later, her institute had become the epicenter and repository of coronavirus research and hundreds of different strain samples gathered over several expeditions. She led her team to Yunnan once again in 2013, and among the samples gathered were the two closest relatives of the virus that caused our global pandemic. The presence of such a close cousin was bound to intensify the natural scrutiny that emerged as a result of the laboratory’s presence within the city that sparked the pandemic. However, the enthusiasm with which Chinese officials embraced the Huanan Market theory {and the willingness of the West to accept the notion first advanced by an American journal} seemed to negate any interest among scientists to buck conventional wisdom when the prospect of a global pandemic was looming.
<>As time wore on, the reluctance slowly pushed a lab-accident hypothesis out of the accepted mainstream, and then into the realm of conspiracy. I was very surprised by the reaction to President Trump's claims about the topic in March, as if his (admittedly reckless) accusation could only be based in xenophobia. It was far more likely that his opinion came directly from intelligence assessments that only he was privy to, and I saw no reason to question the veracity of an assertion that would certainly have been among the potential origins investigated by those same institutions. I have very little faith in the comments of 'former intelligence officials' who denied the existence of any evidence to that end, because political enemies without current 'need-to-know' are not reliable sources. The sudden explosion of peer-reviewed articles questioning the actions of the WIV is a consequence of prior censorship, not new information, because the articles are mostly the same ones that have sat in pre-print obscurity for several months. If the Chinese did have something to hide, then they've been gifted a year's time to clean up any evidence of wrongdoing.
<>Why does my CBRN/Marine/Historian/analytical intuition find this proposal so plausible? The best answer is that China has meticulously ignored, obfuscated, erased or ‘forgotten’ many of the details within the timeline laid out by Latham and Wilson; the Chinese also took deliberate actions to obfuscate the background information concerning the geographical distribution of the first 41 cases, which would've directly pointed to the research labs in the center of Wuhan, not to a remote part of Yunnan Province 1,000 miles away.
<>Actions speak louder than words, especially when China isn’t saying much to begin with. Even the publication of the full gene sequence in early January was unplanned; Shi’s team had completed the task more than a week before the milestone was announced, but an unauthorized release from another research group forced the hand of the WIV. Not until January 23rd did the WIV release the full sequence of RaTG13, a virus it had held for seven years. And, ignoring the 2013 outbreak leads to greater attention being given to the search for an intermediate species; why would scientists want to focus on a less attractive theory, when the possibility exists that the first emergence of human COVID was in 2012, not 2019? Even if we trust that last week's claims were true, and the miners weren't infected with SARS-CoV-2, there are dozens of β-CoV strains still stored within the WIV, and some of them were used in publicly documented experiments to increase human transmissibility using methods that can't be detected within the genome (one they perfected under the guidance of the American researcher Ralph Baric).
<>These articles and hypotheses deserve greater attention, so why haven’t more media outlets investigated the most plausible analysis of the pandemic’s genesis? China’s intransigence is unusual, because many possible outcomes could help exonerate the country from suspicions regarding the origin of the pandemic. The alternative is that China’s silence is a natural result of being stuck in a corner, unable to offer any evidence that could clear their name because none exists; the reluctance to consider a lab accident has raised eyebrows in Europe and Australia, but the presidential elections sucked all of the oxygen out of the room here in the US. Dr. Quay's spatial analysis and genomic forensics show that the first four cases were identified and treated at the hospital closest to the WIV, of which 3/4 were likely patients or doctors in close contact with the first.
The Circle Closes
<>I'll go a step further; the provincial and national officials would've been alerted not long after the initial creation of a slot meant to store an unidentified coronavirus sometime around 10 December, not at the end of the month. Why would concerned physicians at the military hospital (where the first patients were treated) wait 3 weeks before notifying the world's best coronavirus research team located a mile or two away? At every opportunity, officials concealed information until private doctors and researchers publicly released their own findings: the genome sat for 10 days after being identified, until one team released a partial segment on the 11th. The next day, Shi's WIV announced and released the complete sequence, which they had finished on the 2nd.
<>It wasn't until Jan 20th that Xi Xinping (the leader of the country) said he received word of the crisis and took over publicly, but later revelations showed showed that his direct involvement actually began on January 7th. Nor did they tell the public or WHO that clear human-to-human transmission was taking place, until after the New Year's celebrations on January 18th. In the 5 days before a lock-down was announced in the city of 12 million people, an estimated 5 million left the city - perhaps hundreds of thousands which then flew back to their homes all across the globe using the no. 2 subway train that ran directly to the international airport.
<>I further contend that the existing facts point to deliberate actions taken by officials to conceal any information that could tie cases to the Wuhan Institute of Virology. It's logical to assume that the information Dr. Quay used to triangulate the hospital locations of the first patients is accurate, because there would have been no reason to fabricate evidence that would strengthen the case against the facility (as the location tags for the genome samples indicate). Conversely, there would be little sense in refusing to release non-personal treatment information if it clearly showed a favorable pattern centered somewhere else.
<>Ironically, the same evidence that points to an accidental release of an experimental virus also argues against an intentional release; if the Chinese wanted to engineer and then release a bio-weapon, the last place that they would do so is the city where their CDC & Virology nexus is located. For a regime constantly focused on self-preservation, killing untold numbers of their newly middle-class society with an engineered virus would run counter to their long-term geopolitical objectives. Mao's reforms and Kai-shek's intentional flood led to millions of deaths in the middle portion of the 20th century, but those were strategic calculations during a war and its aftermath; exposure of such an event would destabilize the very society that the Chinese Communist Party has aggressively sought to maintain control over.
<>William of Ockham may or may not have been a believer in the principle attributed to him, but his razor has highlighted a possible solution that demands a thorough investigation. Continued Chinese resistance would further imply that their unwillingness to help discover Pandora’s opened Box stems from the fear that investigators might find their fingerprints on the lid. My hope is simply that we start looking for the fingerprints at all.
For Further Reading - I've moved my growing list of sources to this post, mostly because 224 references don't fit.
C.H. Rixey