BOOK EXCERPT: The Code As Witness: How the COVID Genome Reveals Its Lab Origins

The origin of COVID-19 has sparked relentless debate since 2020. But if we truly follow the science, the evidence for a lab-based beginning is undeniable.

30 minute read

In an interview on The DisInformation Chronicle Podcast, physician-scientist and entrepreur Steven Quay discussed his new book “The Code As Witness” explaining how scientific evidence shows that the COVID pandemic started in a Wuhan lab.

Science Magazine has published several false and misleading studies that allege the pandemic started in a market in December 2019, and then defended those deceitful conclusions and defamed critics in their news section. But even the head of China’s Centre for Disease Control, Gao Fu, has noted that the scientific evidence does not support inaccurate claims that COVID arose in a market.

Gao was involved in collecting samples at the Huanan Wholesale Seafood Market that Science Magazine claims was the pandemic’s origin. However, he told the South China Morning Post, “We first believed the virus originated in the seafood market, but now it looks like that the market is just another victim. The virus existed [before the infections happened in the market].”

Examining the virus’s genetic data, Quay also finds that the virus was circulating many months before it began spreading in December at the market in Wuhan.

You can purchase Quay’s book at this link on Amazon: “The Code as Witness: How the Covid Genome Reveals its Lab Origins and How to Prevent Future Outbreaks.”

An excerpted chapter follows, below.

Update: Last month, I reported that NIH virologist Vincent Munster was caught smuggling dangerous viruses into the United States while conducting research in Africa. The Department of Justice has announced that both Munster and his assistant have been charged with smuggling monkeypox into the United States and giving false statements to federal law enforcement.

Both NIH scientists now face a maximum sentence of five years in prison.

THE CODE AS WITNESS

CHAPTER ONE

Ground Zero

On my first trip to Wuhan in 2014, I knew little about the city. I was there to visit a laboratory testing site and negotiate a contract for research related to my work as the CEO of Atossa Therapeutics, a pharmaceutical company mostly dedicated to finding solutions to the prevention and cure of breast cancer.

I had assumed that Wuhan might be something like Chicago: not the biggest city, nor the most important, but a big site for industry and a crucial center for transportation. When I arrived at Tianhe International Airport, I slipped into the underground Line 2 of the subway. I knew from looking at maps before the trip that the original, ancient city of Wuhan lies on the east side of the Yangtze River. On the west side lies the modern, sleek portion of the city, and when I emerged from the subway to find my hotel, it was immediately clear to me which side of the river Line 2 had brought me to.

I stood in the center of a city so modern that it makes Manhattan look like something out of a Charles Dickens novel. The glistening skyscrapers, bustling traffic, and high-speed trains seemed out of a postmodern utopian dream.

Wuhan itself is a major business hub for several international corporations. After checking in, I returned to Line 2 to travel eastward. I exited at the eleventh stop along Line 2, located near Optics Valley, where my meeting was to take place. You can think of Optics Valley as China’s version of Silicon Valley, as it is a hub for technological innovation and entrepreneurship. The zone retains forty-two institutes of higher learning, including Wuhan University and Huazhong University of Science and Technology. Within its planned area of 322 square miles and a permanent population of about 1.8 million, it holds fifty-six scientific research institutes at the national, provincial, and ministerial levels and more than 300,000 professional and technical personnel, which makes it one of the three most talent-rich areas in the country. It has also been recognized as a major hub for biotechnology and bio-industry. The Wuhan Institute of Virology’s two locations are within Optics Valley.

During my stay, I continued to be impressed with beautiful, brand-new stations that dotted the subway system, and I was struck by how easy it was to travel from Wuhan to anywhere else in China—from the center of the city, one can easily travel deep into the rural southern province of Yunnan, or to an international airport, or north to Beijing. All this and more is connected via Wuhan’s hypermodern mass transportation system that weaves through and around the city with nine lines used by millions daily.

Line 2, however, is of particular interest to this story. Before the pandemic, Line 2 alone carried an average of one million passengers per day, commuters going into the city center and then home to the outlying areas each night. The line begins in the east at Fozuling, moves through Optics Valley Square, and travels a zigzaggy course, going under the river and then continuing sixteen miles north of the city center before terminating at Wuhan Tianhe International Airport.

Wuhan Tianhe is the busiest airport in central China, and one can easily fly nonstop from Wuhan to major international destinations, such as New York, San Francisco, Tokyo, Rome, Istanbul, Dubai, Sydney, Bali, Bangkok, Moscow, Osaka, Seoul, and Singapore. Terminal 3, which services international flights, has a whopping passenger capacity of thirty-five million passengers per year. This steady flow of traffic lends credence to the airport’s name, Tianhe, which literally translates to “sky river.”

So, when I began hearing rumors in early 2020 that a virus had broken out in Wuhan, a virus that was a close genetic relative to a virus from Yunnan in the south, I was suspicious of the idea that what would be named SARS‑CoV‑2 was the result of a natural process. I had experienced firsthand how far Yunnan—the geographic location of the origin of the closest natural virus based on the virus’s genetic sequence—was from Wuhan, and I had also experienced the dense, urbanized, impressiveness of the city. Rumors held that the virus had broken out at a certain wet market, and I also knew just how close this suspected wet market was to China’s, and arguably the world’s, largest coronavirus-research laboratory, the Wuhan Institute of Virology, which was conducting some of the most dangerous viral research in China at the time—research that some scientists outside China worried, well before the COVID-19 pandemic, would lead to pathogens escaping. Like the rest of the world, I hadn’t ruled out that the virus had a natural origin, but my gut told me that I should dig deeper and discover from where this virus had emerged.

When we look closely at Wuhan as the virus’s ground zero, we can clearly see that the most significant locations for tracing the early days of the virus run along Line 2. In a later chapter, I will show why I believe that Line 2 was the “COVID-19 conduit” that allowed the virus to leave Wuhan and spread throughout China and the world before we even knew it existed. But for now, let us ride the rails of Line 2 through Wuhan and see where it takes us.

General Hospital of the Central Theater Command Hospital of the People’s Liberation Army of China

627 Wuluo Road, Wuchang District Wuhan Metro Line 2: Baotong Temple Station

On December 27, 2019, a forty-four-year-old man developed pneumonia-like symptoms and was taken to the General Hospital of the Central Theater Command of the People’s Liberation Army of China. The PLA hospital is located in the middle of China’s joint civilian-military operations, which were under development in the academic, scientific, and military facilities in this part of Wuhan. The medical staff tested him for pneumonia. Bronchoalveolar lavage, as this procedure is known, is common when diagnosing lung cancer, bacterial, viral, and fungal infections, and persistent coughs of unknown origin. What the lab found when it studied this man’s sample, however, was anything but common. It was unlike anything the world had seen before.

The patient was infected with a virus that we would soon come to know as SARS‑CoV‑2, and he was one of the first documented patients to develop the resulting disease, COVID-19.

In virology, the term patient zero refers to the (usually unknown) first patient afflicted with a virus that becomes an outbreak. This forty-four-year-old man was not the very first person to come down with COVID-19, so we won’t call him patient zero. As we will see later, our key witness, the virus genome itself, will report that it probably first entered the human population of Wuhan months earlier, sometime in the summer or early fall of 2019. While this man was not patient zero, we could effectively call his affliction Virus Zero.

Allow me to explain. The way scientists trace a virus’s progression is by looking at its mutations—single-letter genetic mistakes that it occasionally makes as it replicates itself. As a virus is passed from person to person or animal to animal, its genetic composition changes at a predictable rate. About twice a month, or every two weeks, the virus makes a random mistake when it copies the roughly 30,000 letters of its genetic blueprint. We call this its molecular clock. Because these mistakes are then copied into the virus’s progeny, we can use computer programs to walk back in time through the historical record of all the mutations that arise in a pandemic. This technique allows us to identify the earliest version of a virus that infected humans.

This man was infected with a strain of SARS‑CoV‑2 that was later named Lineage A. The specific Lineage A virus from this patient was called WHO04. For viruses, lineages are akin to ethnic groups while WH004 would be a surname for a family within that ethnic group. Although this SARS‑CoV‑2 virus was identical to known bat viruses in over 96 percent of the length of its genetic code, it still had over eleven hundred mutations that were different from any previously known coronavirus. That is over forty years on the coronavirus molecular clock.

This forty-four-year-old man was infected with what we will call Virus Zero because he was infected with the first known variant, or clade, of the novel coronavirus—a fact that made this middle-aged man among the earliest patients infected with what was called Clade A, a virus from an infected human that is genetically closest to it ancestor host, the bat.

The determination of which variant of a virus arose first relies on using the molecular clock as well: The more time a bat virus has to jump from host to host, the more mutations it will have, until its genome changes enough that it is able to spread among humans. Clade A and the next variant, labeled Clade B, became the first SARS‑CoV‑2 viruses to infect humans. Two mutations differentiated Clade A from Clade B, with Clade A being identical to bat viruses at those two positions, and Clade B had changed the code letter for each of those two spots.

Being the first infected was no honor, as other patients were soon to discover. On December 31, 2019, another sample was collected at the PLA hospital, this time from a forty-three-year-old male. The following day, another patient—a twenty-one-year-old female—became the hospital’s third known case of COVID-19. This patient is especially noteworthy because her residence lay on the east side of the Yangtze River, not the west side, where the wet market that many have pointed to as the origin point of the pandemic is located. This patient also lived within a short walking distance of the Wuhan Institute of Virology and Wuhan University, both institutions with active coronavirus research programs. She was thus a potential candidate for having acquired SARS‑CoV‑2 from the laboratory she worked in. Finally, on January 5, 2020, a thirty-nine-year-old male experiencing pneumonia-like symptoms also made his way to the PLA hospital for testing. These three patients all had Clade B. By then, it was clear: The PLA hospital was experiencing the earliest patient cluster of sequenced SARS‑CoV‑2 viruses, and the virus was spreading quickly.

Chinese officials had been tight-lipped about the virus’s outbreak, and to piece details together, I began in February 2020 to sift through the dozens of scattered reports, internet genetic databases (places where scientists deposit the raw information, called Sequence Read Archive, or SRA, and final, assembled genetic sequences of viruses), and academic papers that had trickled out in reports from doctors on the ground.

The research process began with a publication out of China, authored by thirty-four Chinese doctors and one Australian scientist, Eddie Holmes. The paper states that “nine patients with viral pneumonia and negative for common respiratory pathogens, who presented to at least three hospitals in Wuhan, were included in this study.”

Nowhere in the paper do the researchers name the PLA hospital as one of the three hospitals. Theirs, however, was not the only paper with this opacity. The few published reports of early patients in Wuhan conspicuously omit information about the hospitals where patients were seen. Early reports include such vague statements as, “We report the epidemiological data of nine inpatients, from at least three hospitals in Wuhan, who were diagnosed with viral pneumonia of unidentified cause.” It took some serious digging through genomic databases to discover where the founder patients were treated.

I was only able to find the PLA hospital records because someone had uploaded the PLA patient samples to a server in Germany and—likely by accident—included the hospital’s address. If the information was posted by mistake, it was never made again. No other SARS‑CoV‑2 genome sequence from a patient at the PLA hospital has ever been made public.

Not only was the location later obscured, but also serious digging was required to find out that this cluster of patients even existed at all. There is also evidence that “problematic” patient records were simply changed or removed from databases completely. We can see an example of this in the first paper that describes the hospital course of COVID-19 patients. This Chinese peer-reviewed publication on SARS‑CoV‑2 was written by twenty-seven Chinese doctors, all of whom were working in the major Wuhan hospitals. They documented one patient with disease onset on December 1, 2019, and three with onset of December 10, 2019, and then noted that the first patient and three of these first four patients had no history of visiting any wet markets.

Their methods were rigorous, as they stated: “To ascertain the epidemiological and symptom data, which were not available from electronic medical records, the researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data.”

Interestingly, this peer-reviewed paper was never corrected or retracted. Yet the subsequent WHO report that claimed to be based on this very paper deleted, without comment, any and all references to the three non-market patients. And nowhere in the WHO report is there a reference to the original PLA cluster. It seems as if someone wanted to create the impression that these four patients—all treated within the same military hospital, a ten-minute taxi ride from the WIV—or any patient who did not visit a wet market, never existed at all.

Central Hospital of Wuhan

26 Shengli Street, Jianghan District Wuhan Metro Line 2: Jianghan Road Station

Thirty-three-year-old physician Li Wenliang had been working as an ophthalmologist at Wuhan Central Hospital since 2014. The BBC reported that he was well-known as a “responsible doctor and a loving husband.” And his wife, Fu Xuejie, was a devoted mother to their four-year-old and pregnant with their second child.

During the last few weeks of December 2019, Li noticed seven patients who had come to the hospital with symptoms resembling those associated with SARS. Li had been a teenager when the first reported case of SARS emerged in 2002 in Guangzhou (about 621 miles south of Wuhan), and he had seen firsthand how bad a public-health crisis could get. He had witnessed the subsequent eight months, how the disease had killed 349 people and infected more than 5,000 nationwide by the end of 2002. By the time the Chinese government brought the disease under control, the SARS epidemic had caused a severe sociopolitical disaster for the Chinese leadership. In May 2003, China’s health minister and the mayor of Beijing were dismissed from their jobs as well as their Communist Party posts over the outbreak. A detailed inquiry into the ways the health minister tried and failed to manage the damage SARS caused to both his and China’s global image explains why he was ultimately fired from his post.

Seventeen years later, on December 30, 2019, Dr. Ai Fen, the director of the Central Hospital of Wuhan emergency department, treated a patient whose pathology report bore the words, “SARS coronavirus.” She circled the words and forwarded a photograph to a medical colleague. The image began making the rounds among certain specialists, and that evening, it hit Li’s phone.

Naturally, Li was concerned for his colleagues and friends, so that same night, he sent a message to a group of fellow doctors on the social media platform WeChat. He warned them to be careful because an outbreak of an illness resembling SARS might be underway. When later asked why he did it, Li responded, “It’s always better to be cautious and take protective measures.” And “there were discussions among our colleagues,” he said, “that SARS might come back. We needed to be ready for it mentally. Take protective measures.”

Several days later, police appeared at Li’s home and he was summoned to the Public Security Bureau in Wuhan, where local authorities chastised him for “making false comments” that had “severely disturbed the public order.”

Before allowing Li to return to work, the police forced him to sign a statement that included the warning, “If you keep being stubborn, with such impertinence, and continue this illegal activity, you will be brought to justice—is that understood?” He inked the statement with a red thumbprint and wrote, “Yes, I do.”

Little did he know that with that simple act, he may have signed his death warrant.

Wuhan Huanan Seafood Wholesale Market

207 Fazhan Avenue, Jianghan District Wuhan Metro Line 2: Hankou Railway Station

Squawking birds. Flapping wings. Wild yelps. Plaintive braying. The humid gurgle of fish tanks. The splash of water on blood-spattered cement. Stall beside stall beside stall. Friendly calls between sellers and customers. The tense patter of fast-paced bartering. The hot press of bodies in narrow lanes.

Pre-pandemic, this was daily life in the Wuhan Huanan Seafood Wholesale Market—a sprawling live-animal market, on either side of Xinhua Road and Jindun Street, nestled within the bustling Jianghan District. Covering twelve acres, the market contained the wares of more than one thousand sellers on any given day. It was the largest seafood wholesale market in central China, but many of its products had nothing to do with the sea. Poultry, livestock, and other exotic animals found buyers within the market’s walls. The wild-animal section in the market’s western zone was especially eclectic, boasting thirty-eight terrestrial wild species. These included everything from Siberian weasels, Chinese hares, and Malayan porcupines to red foxes, minks, and wild boars.

Many of these exotic animals were intended for luxury consumption, not everyday meals. The most expensive wild mammal sold for food was the marmot, which would put you out more than $25 per kilogram. Raccoon dogs and badgers sold for a slightly more modest $15–20 per kilogram, while hedgehogs cost $2–3 apiece. Indian peafowl was the most expensive avian food source, at $56 per bird, while the sharp-nosed pit viper was the most prized edible reptile, costing $70 per kilogram.

Other species, such as squirrels, were sold as pets rather than food. While a single squirrel cost only $25, luxury-pet owners might have been drawn to the captive-bred crested myna birds, which can imitate human speech. These sold for around $300.

The wild-animal section of the Huanan Seafood Market comprised only ten stalls, a small but veritable zoo, and it was widely known that such animals were capable of hosting a variety of zoonotic diseases. “Zoonosis” literally means “zoo disease” because it refers to a disease that arises in animals before jumping to humans. Because these diseases are new to humans, we have very little natural immunity, so they hold devastating potential. The good news about natural spillover zoonoses is that, at least early on, they have limited ability to cause a serious outbreak. This is a trait of natural biology: The viruses have adapted to their nonhuman hosts, and it takes some time and experimentation to adapt to humans and support robust human-to-human spread. In the case of a natural zoonosis, the time it takes a virus to adapt from an animal host to a human host gives the healthcare community an important opportunity to develop protocols for the diagnosis and treatment of the new affliction.

Nonetheless, after the first SARS epidemic, in which a SARS virus adapted to civet cats sold in wet markets jumped to humans, the Chinese government already had some protocols in place to prevent the spread of zoonotic diseases in the market. For example, Wuhan Forestry Bureau enforcement officers issued permits to market vendors, and policy dictated that animals must have an origin certificate and spend time in quarantine to ensure they didn’t exhibit overt disease symptoms before they were allowed into the market. Law-enforcement officers also had full access to trading practices, including the right to inspect animals for gunshot wounds or snap-trap injuries that might indicate the animals were captured in the wild. In China, wild animals are considered state property, and any trader convicted of selling protected species can face up to fifteen years in prison.

Unfortunately, these policies were rarely enforced. Animals were frequently stacked in cages in unhygienic conditions. A broad study of wet markets prior to the outbreak of SARS‑CoV‑2 revealed that many animals suffered from wounds, implying they were illegally sourced. Of seventeen shops surveyed during the outbreak, none posted origin certificates or quarantine certificates for their animals, which meant that their entire trade was illegal.

These certainly weren’t favorable conditions for health, and history has shown that the best way to kick off a devastating human pandemic is to start it with animals. SARS‑1, MERS, and modern influenza all began as zoonoses. There was a good reason that Chinese officials, vendors, and buyers should have been more cautious about the handling of animals in the wet market. And certainly, no matter where SARS‑CoV‑2 came from, the studies that have emerged out of the Huanan Seafood Market fiasco suggest that greater regulation enforcement is necessary to maintain public safety.

Still, none of this goes to say that wet markets are inherently “bad” places. Markets such as Huanan Seafood have been the beating heart of Asian cities for centuries, supplying residents with fresh food and cherished pets and providing a moving town square for friends to meet and exchange the latest news or gossip. These sites are deeply embedded in Chinese history and culture, and even though modern life has given us access to refrigeration and safe food-transportation networks, many people prefer to buy live or freshly slaughtered animals. In my opinion, we must find ways to minimize the risks of zoonoses without disrupting cherished traditions and customs.

In December 2019, business was progressing as usual at the Huanan Seafood Market. Despite some of the public-safety risks I have already mentioned, there was nothing to indicate that any animals were suffering from a new or unusual virus, even as reports of infected humans were beginning to emerge elsewhere in the city. It didn’t take long, though, for officials to grow suspicious and turn their attention to the market.

This made sense since civet cats sold in wet markets had been responsible for the rapid spread of SARS‑1, and camel markets had been the culprits behind the MERS coronavirus. On January 1, 2020, after performing extensive environmental sampling and spraying the facilities with a bleach solution, the Chinese authorities closed the market. In the media, the wet market quickly emerged as the de facto ground zero of the coronavirus outbreak. It all seemed to make sense that the source of the virus could very well be the Huanan Seafood Market. It was, indeed, my first assumption.

Market Theory Begins to Wear Thin

It soon became clear, however, that the most “logical” explanation for the origin of SARS‑CoV‑2 may not have been the correct one. An early clue that the market was not the source was the finding that although 66 percent of the early COVID-19 patients worked or shopped at the market, none of the live-animal vendors were infected with SARS‑CoV‑2.

Within mere months, experts suspected that the market was a red herring. Dr. George Gao, the Oxford- and Harvard-trained virologist and then-head of the Chinese CDC, said on May 23, 2020, “We first believed the virus originated in the seafood market, but now it looks like the market is just another victim.”

Although all agree that the host of the SARS‑CoV‑2 ancestor virus was bats, multiple investigations before and after the outbreak revealed that no bats were sold in the wet market, and bat was not a food source in Wuhan. Further, bats in Wuhan typically begin their winter hibernation in September each year. While it was possible that the virus spread through an intermediate host (as did the SARS‑1 virus, which jumped from a bat to a civet cat and then to humans), despite 1,380 specimens collected in the market, no evidence of virus genetic material or animal antibodies to the vrus has been found to suggest any intermediate host or that any animal other than humans had been infected.

Wuhan CDC

24 Jiang Han Bei Lu, Jiang’An Wuhan Metro Line 2: Hankou Railway Station

All the focus on the Huanan Seafood Market as the likely source had temporarily obscured the fact that it was not the only possible disease vector located in that bustling neighborhood. Not far away stood two laboratories researching bat viruses; one was about 300 meters from the site of the Huanan Seafood Market, the Wuhan CDC.

In February 2020, a research paper supported by the National Natural Science Foundation of China suggested that the Wuhan CDC, which regularly extracted tissue samples for DNA and RNA extraction and sequencing from caged-specimen bats, was a more likely source for the virus than the wet market. Almost immediately, the paper was taken down, likely upon the orders of the Chinese government. Nevertheless, as anyone who has posted awkward photos on social media knows, it’s a fruitless task to try to erase anything from the internet.

Thankfully, that means that even after the paper was scrubbed, I was still able to locate these researchers’ claims online. Their paper pointed out several crucial details. First, the likeliest source of the coronavirus appeared to be a particular species of bats named Rhinolophus affinis, which live in the caves of Yunnan Province, more than 1,118 miles from the seafood market. To put it in perspective, that’s almost the distance between Washington, DC, and the Everglades National Park in Florida.

One study of the feeding habitat range of the Rhinolophus indicates that it travels only about 1.2 miles from its roost, which leaves an extremely low probability that the bats had flown all the way from a cave in Yunnan to the market in Wuhan.

It also appears that at least some of the technicians at the Wuhan CDC had been long aware of the potential risks of bringing virus samples from undeveloped caves in remote areas of China back to headquarters in the heart of Wuhan. For example, a promotional video released by the Wuhan CDC on December 10, 2019, shows scientists collecting viruses from isolated bat caves. Tian Junhua, an Associate Chief Technician from the Department of Disinfection and Pest Control at the Wuhan CDC, narrates the video, explaining, “In the past ten-plus years, we have visited every corner of Hubei Province. We explored dozens of undeveloped caves and studied more than three hundred types of virus vectors. But I do hope these virus samples will only be preserved for scientific research and will never be used in real life” (emphasis added).

He warned that collecting viruses from bat caves can be extremely dangerous “because when you find the viruses, you are also most easily exposed to the viruses.” What is striking about the video is that, despite these clear indications of risk for the scientists collecting the specimens, many of the pictures show they are not wearing masks or gloves. One would have thought that for a promotional video they would have been on their best behavior.

In any case, the video ends on an optimistic note: “Nearly two thousand types of viruses have been discovered by Chinese CDC authorities over the last twelve years. Only 2,284 types of viruses had been discovered worldwide over the two hundred years prior to China’s discovery. China has taken the lead in the world in the field of basic research.” Junhua’s statement indicated his awareness that China’s extraordinary collection effort also meant that potentially up to two thousand viruses had been given the opportunity to encounter many more humans in a laboratory in the middle of a city of eleven million, next to a subway line that carried one million people a day.

It’s obvious that the Wuhan CDC lab not only could have had access to the bat coronaviruses that were the SARS‑CoV‑2 precursor, but that it had been culturing, growing, and harvesting those viruses, and it would have only taken one event to have enabled SARS‑CoV‑2 to escape into the populace.

Further, the outbreak happened to coincide with a planned relocation of the CDC’s lab. In anticipation of a move within Wuhan, the Wuhan CDC had submitted a waste-disposal procurement request on June 27, 2019, asking for help to dispose of two tons of medical waste that had piled up from 1994 to 2019.

This effectively places the CDC and all its medical waste a short walk from the Wuhan subway system. Could a leak during the removal and disposal of that much medical waste have been the process that kicked off the pandemic? The WHO report suggested as much when it noted: “The Wuhan CDC laboratory moved on 2nd December 2019 to a new location near the Huanan market. Such moves can be disruptive for the operations of any laboratory.”

Even so, the CDC still is not the likeliest source, as it was not the lab doing synthetic biology to create “human made” viruses. Only one lab in Wuhan had both collected new viruses from distant caves in China, Southeast Asia, and as far away as Africa, and engineered new features into the genetic code of these natural viruses, making novel viruses that had never existed in the 310 million years since the first virus, the nudivirus, first infected early insects.

That lab was the Wuhan Institute of Virology.

The Wuhan Institute of Virology

44 Xiao Hong Shan, Wuchang District Wuhan Metro Line 2: Hongshan Square Station

The story of the Wuhan Institute of Virology began in an unlikely place at an unlikely time: eighteenth-century Britain.

In 1796, the English physician Edward Jenner caught wind of some Gloucestershire folklore. Milkmaids, laborers tasked with milking cows, were notoriously immune to smallpox. Because of their work, they were frequently in close contact with cows and a mild disease called cowpox, which was not fatal and left only a single pustule on their hands. Locals had begun to inoculate themselves with cowpox as a means of warding off the more deadly smallpox disease.

Jenner, intrigued by the science behind this folk remedy, collected a specimen from the hand of Sarah Nelmes, a young milkmaid, and injected it into the arm of eight-year-old James Phipps. He monitored Phipps and, in 1797, submitted a paper to The Royal Society of London for Improving Natural Knowledge describing the experiment. He claimed that the method could provide immunity to smallpox. The society told Jenner that he required more proof, so he continued his experiments, even going so far as to use his own son in the trials. In 1798, he published the results and called the method “vaccination,” a term taken from the Latin word vacca, which means cow.

Jenner was widely ridiculed, but over time, the success of his ideas won out. Nevertheless, no one knew why the method worked until several generations later, in the mid-nineteenth century, when a French chemist and biologist named Louis Pasteur built on Jenner’s ideas and proved that tiny microorganisms called germs were responsible for infectious diseases such as smallpox. He tested his germ theory of disease using anthrax, an infectious zoonosis. Using a microscope and blood samples, Pasteur discovered microorganisms that he argued were responsible for the infectious diseases. Using a weakened sample of the organism, he experimented with inoculation and was able to prove that the anthrax bacteria was absent in the inoculated subject. To honor Jenner’s work, Pasteur called his own process “vaccination,” and it became the generic term for the technique.

In 1887, the Pasteur Institute was founded in Paris. It was dedicated to the study of microorganisms, diseases, and vaccines. That was an especially valiant mission at the time—infectious diseases were then the number one cause of death for anyone under the age of ten. In most cases, patients were left helpless, with no means of prevention or cure. Humans were subject to the whim of nature. For more than a century, the institute has been making discoveries that have allowed the world to control diseases such as diphtheria, tetanus, tuberculosis, influenza, yellow fever, and poliomyelitis.

The Pasteur Institute inspired other infectious-disease research institutions across the globe. In 1956, the Wuhan Microbiology Laboratory was founded under the Chinese Academy of Science. Following the mission of the Pasteur Institute, the Wuhan lab’s work focused on taking specimens from sick patients, collecting microbes, looking at them under the microscope, and creating vaccines for those illnesses. The name changed several times during the following decades, before eventually landing on the Wuhan Institute of Virology in 1978.

For the majority of the twentieth century, however, the lab continued to follow this traditional research agenda.

As time passed, though, that decades-old agenda had become humdrum. By the 1970s, many in the medical profession, including my own medical-school professors, actually had the arrogance to believe that we had put infectious diseases behind us. I remember witnessing that hubris when an instructor referred to the Spanish-influenza epidemic of 1918 and told my class, “This is for historical purposes only because this will never happen again.” Little did we know infectious-disease treatment and vaccines were coming into their full importance at the same time that new, deadly viruses such as Ebola and AIDS were emerging. As if to directly contradict my teachers, Ebola showed up in 1976 in the present-day Democratic Republic of the Congo and South Sudan. A June 1981 report from the U.S. CDC on five young men with an unusual infection, Pneumocystis pneumonia, would be the introduction of the HIV virus and the disease AIDS to the world. AIDS would be the disease tied to Anthony Fauci’s rise to the head of the National Institutes of Allergy and Infectious Diseases in 1988, a position he held until his retirement in 2022. It was clear by the end of the twentieth century that the truth of the ever-present danger of new infectious diseases had replaced the earlier misplaced confidence of the medical community that these diseases were a thing of the past.

The coronavirus SARS—severe acute respiratory syndrome—was the first major zoonosis of the twenty-first century. Humans were already dealing with four coronaviruses, all of which were mild infections and made up about 15 percent of all common colds. SARS was different, however, because it was the first lethal one—it killed 13 percent of its victims. Plus, it was airborne and spread easily. So, when SARS broke out in southern China’s Guangdong Province in 2002, the scientists at the WIV charged down to the area to investigate. The WIV, alongside the U.S. CDC, played an instrumental role in determining that the virus, formally SARS-CoV-1, had passed from civet cats to humans. Even with what are now considered primitive genetic tools, it took only five months to proclaim the civet cat as the intermediate host. Note, at the time of this writing, there is still no credible evidence for an intermediate host for SARS‑CoV‑2.

By February 2003, the virus had spread beyond Guangdong’s borders. Kwan Sui-chu, a seventy-eight-year-old Canadian woman, carried the virus to Toronto; three young women took the disease to Singapore; and Johnny Chen, a Chinese American businessman, carried the infection to Vietnam, where he was admitted to the French Hospital of Hanoi on February 26.

Italian microbiologist Carlo Urbani was called to examine Chen, and Urbani realized that Chen didn’t merely have a bad case of the flu. Urbani was an experienced tropical disease expert and had received the 1999 Nobel Peace Prize as part of his work with Médecins sans frontières (Doctors Without Borders). Urbani sounded the global alarm, notifying the WHO that this was a new and highly contagious disease. He also managed to convince the Vietnamese Health Ministry to isolate patients and screen travelers, which helped slow the epidemic’s spread.

On March 11, on his way to a conference in Bangkok, Urbani felt feverish and realized he had contracted the disease while treating patients in Hanoi. Several weeks later, he took his last rites from a Catholic priest, asked that his lung tissue be donated for scientific research, and died.

Six weeks later, on April 25, 2003, twenty-two scientists from the U.S. CDC in Atlanta, Georgia, filed for and later received a patent application claiming ownership of the virus that killed Dr. Urbani.

SARS-CoV-1 was only the fifth known human coronavirus in the world, and it was unexpectedly deadly. According to the WHO, SARS was the first severe and readily transmissible new disease of the twenty-first century. The world had not been prepared, but thankfully, scientists were quick to act and limit the spread. By July 2003, the virus’s threat had been mitigated. In total, SARS-CoV-1 infected around 8,000 people, with 774 deaths. Yet, even though the epidemic was over, the disruption had just begun. The entire world of virology was upended by SARS-CoV-1.

NIAID Chief Anthony Fauci, flush with $1.7 billion in new cash from Congress to fund biodefense research, convened the Blue Ribbon Panel on Bioterrorism, which managed to link the viral diseases AIDS, Ebola, and SARS-CoV-1 with the attacks on September 11, 2001, and the anthrax letter attacks later that fall. All of this became the foundation for the creation of one of the largest federal bureaucracies ever, linking the research activities of NIAID to the Department of Defense in an effort to develop biodefense-research capabilities against future theoretical bioweapons.

By 2005, SARS‑1 had motivated an international collaboration involving Dr. Peter Daszak, a British-born zoologist then at the Consortium for Conservation Medicine in New York City; University of North Carolina-based virologist Dr. Ralph Baric, whose experiments using synthetic biology to create human-made viruses led him to become the world’s leading expert in the field; Dr. Linfa Wang, who was at the Commonwealth Scientific and Industrial Research Organization Livestock Industries, Australian Animal Health Laboratory, Geelong, Australia and played a key role in the discovery of the deadly Hendra virus, which jumped from horses to humans in 1994; and Dr. Zhengli Shi, a Wuhan native and a senior scientist at the WIV.

The first paper by Daszak, Wang, and Shi described how they had collected specimens from 408 bats from four locations in China and processed those specimens at the WIV. Their research found that 28 to 71 percent of the bat specimens collected had evidence of prior coronavirus infections. Their paper, in October 2005, nearly three years after the SARS‑1 epidemic emerged, asserted that they had gathered enough genetic sequences from these viruses to determine that, although the virus passed from civet cats directly to humans, bats were the likely reservoir host of the SARS‑1 virus.

Their collaborative SARS investigation and subsequent paper led to a fifteen-year-long loose alliance of research by Wang, Shi, and Daszak, with occasional contributions from Baric, whose focus at the time was fixed on the creation and study of synthetic viruses made in his lab. Still, the collaboration led to a collection of thousands of viruses from some of the most remote areas of Southeast Asia, undergoing experiments that used ever more powerful synthetic engineering tools.

With bats now identified as the source of SARS, what we do know for certain is that at least one person on that team was dedicated to finding the next lethal virus before it found us: Dr. Zhengli Shi.

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