Delayed Wuhan Report Adds Crucial Detail to Covid Origin Puzzle

The origin story of Covid-19 remains a mystery mired in contentious geopolitical debate. But a research paper that languished in publishing limbo for a year and a half contains meticulously collected data and photographic evidence supporting scientists’ initial hypothesis—that the outbreak stemmed from infected wild animals—which prevailed until speculation that SARS-CoV-2 escaped from a nearby lab gained traction. 

According to the report, which was published in June in the online journal Scientific Reports, minks, civets, raccoon dogs, and other mammals known to harbor coronaviruses were sold in plain sight for years in shops across the city, including the now infamous Huanan wet market, to which many of the earliest Covid cases were traced. The data in the report was collected over 30 months by Xiao Xiao, a virologist whose roles straddled epidemiology and animal research at the government-funded Key Laboratory of Southwest China Wildlife Resources Conservation and at Hubei University of Traditional Chinese Medicine.  

In May 2017, Xiao began surveying 17 shops at four Wuhan markets selling live wild animals. He was trying to find the source of a tick-borne, Lyme-like disease that had spread in Hubei province years earlier. He kept up monthly visits until November 2019, when the discovery of mysterious pneumonia cases that heralded the start of the Covid pandemic brought his visits to an abrupt end.

As the virus started to explode, Xiao recognized the potential significance of his data. In January of 2020, he collaborated with Zhou Zhaomin, a researcher at a wildlife resources laboratory affiliated with China’s Ministry of Education, and three seasoned scientists from the University of Oxford’s Wildlife Conservation Research Unit, on a manuscript that was submitted to a journal the following month. (They declined to name the publication). “We’d imagined that the journal we sent it to would say, ‘Fantastic! Of course we want these data out as quickly as we can. The World Health Organization would be absolutely thrilled to receive this information,’” says Chris Newman, a British ecologist who is one of the paper’s co-authors. But it was rejected. “They did not think it would have widespread appeal,” says Newman.

Had the study been made public right away, the search for the origins of the virus might have taken a very different course. Not only did the study contain conclusive evidence that live animals were being sold for human consumption at the epicenter of the outbreak, but Newman says he assumes Xiao collected blood-sucking ticks from the wild animals he studiously cataloged. The blood meals of frozen tick samples could be examined for traces of the coronavirus, which would be extremely helpful in identifying infected species prior to December 2019. Xiao didn’t respond to emails requesting comment. 

In the first months of the epidemic, local researchers asserted that the new coronavirus resembled a spillover from animals, reminiscent of the emergence of the virus that caused severe acute respiratory syndrome (SARS) in wet markets in Guangdong almost 20 years ago. They also readily acknowledged the presence of “a variety of live wild animals” at Wuhan markets.

The Huanan market was shuttered in the early hours of Jan. 1, 2020, and its 678 stalls emptied and sanitized. In the middle of the month CNN broadcast unverified footage reportedly recorded in early December showing caged deer, marmots, and raccoon dogs there. Photographs of a menu board advertising the price and availability of exotic animals circulated online.

Disease detectives arriving from Beijing on the first day of 2020 ordered environmental samples to be collected from drains and other surfaces at the market. Some 585 specimens were tested, of which 33 turned out to be positive for SARS-CoV-2. “All current evidence points to wild animals sold illegally,” China Center for Disease Control Director George Gao and colleagues wrote in the agency’s weekly bulletin in late January. All but two of the positive specimens came from a cavernous and poorly-ventilated section of the market’s western wing, where many shops sold animals.

“We have found out which stalls on the seafood market in Wuhan had the virus,” Tan Wenjie, a researcher at China CDC’s viral disease control and prevention institute, was quoted telling the state-owned China Daily newspaper days later. “It is an important discovery, and we will investigate which animal was the source.”

China temporarily banned the wildlife trade. The decision became permanent a month later and widened to prohibit human consumption of terrestrial wild animals. 

A WHO-China joint mission to Wuhan to examine China’s response to the outbreak in February 2020 reported that an effort was under way to collect detailed records on the source and type of wildlife species sold at the Huanan market and the destination of those animals after the market was closed. But there’s no public record of that ever happening.

“Unfortunately, the apparent lack of direct animal sampling in the market may mean that it will be difficult, perhaps even impossible, to accurately identify any animal reservoir at this location,” Zhang Yongzhen and Edward Holmes, the scientists who published the first genetic sequence of SARS-CoV-2, wrote in a commentary published in the journal Cell in March 2020.

As other nations began blaming the Chinese Communist Party for the pandemic, the government grew defensive. It may have been embarrassed that its citizens were still eating wild animals bought in wet markets—a well-known path for zoonotic disease transmission that China tried unsuccessfully to outlaw almost 20 years ago.

Australia in April 2020 called for a global inquiry into the origins of the pandemic, including China’s handling of the initial outbreak. Days later, then-U.S. Secretary of State Mike Pompeo used part of his Earth Day message to call on China to close its wet markets to “reduce risks to human health inside and outside of China.”

In response, Geng Shuang, a spokesman for China’s Foreign Ministry, denied “wildlife wet markets” existed in the country. Government researchers now dismiss the market hypothesis completely. “SARS-CoV-2 could not have possibly evolved in an animal market in a big city and even less likely in a laboratory,” said a paper released in July, written by 22 researchers from mostly government-funded laboratories attached to the Chinese Academy of Sciences.

A more recent paper by government-affiliated scientists contends that the virus may have been imported from multiple locations worldwide, including parts of Europe where mink are raised in areas inhabited also by horseshoe bats known to harbor coronaviruses. “The official narrative changed not because the evidence changed,” says Robert Garry, a professor of microbiology and immunology at Tulane University’s School of Medicine in New Orleans. “A spillover from a wet market was what caused SARS, and, embarrassingly for China, those wet markets were never shut down.” Garry is the co-author of one of the earliest papers on the origins of Covid but wasn’t involved in the research on Wuhan’s markets.

Since he was not connected to a law enforcement agency, Xiao was granted “unique and complete access to trading practices,” he and his colleagues wrote. Seven of the shops he surveyed were in the Huanan market, which has been linked to two of the earliest documented cases of Covid-19. On each visit, Xiao asked vendors what species they had sold over the preceding month, documenting both their numbers and prices.

Xiao checked the animals for injuries and disease, noting that almost a third bore trapping and shooting wounds consistent with being caught in the wild, and that none of the shops displayed an origin or quarantine certificate, making the commerce “fundamentally illegal,” according to the study. 

His animal logs included masked palm civets and raccoon dogs—both involved in the 2003 SARS outbreak—and other species susceptible to coronavirus infections, such as bamboo rats, minks, and hog badgers. Of the 38 species Xiao documented, 31 were protected.

Anyone caught violating China’s wild animal conservation law faces fines and up to 15 years of imprisonment. But enforcement was lax, as evidenced by the fact that many of the Wuhan shops displayed their wares openly, “caged, stacked and in poor condition,” Xiao observed in the report. Xiao estimated that 47,381 wild animals were sold in Wuhan over the survey period. These were luxury food items priced at up to $25 a kilogram ($11 per pound)—or more than four times costlier than pork, China’s main meat staple.

The initial manuscript was revised twice following feedback by a reviewer, and after more than six months of exchanges, was rejected.

The researchers revised the manuscript a third time and included data on China’s pangolin trade networks (an earlier study, later contested, had implicated pangolins in the virus’s spread to humans). In October 2020 they sent it to Scientific Reports.

Springer Nature, the publisher of Scientific Reports, forwarded a copy swiftly to the WHO as part of an agreement with the agency, says Ed Gerstner, Springer Nature’s director of journals, policy, and strategy. But the publisher emailed the paper, titled “Pangolin Trading in China: Wuhan’s Alibi in the Origin of Covid-19,” to a generic address at the WHO that functions as an inbox for unpublished research where it languished amid tens of thousands of submissions flooding the agency.

Springer Nature also sent a copy to Maria Van Kerkhove, the organization’s technical lead for Covid-19. Van Kerkhove says there were so many submissions related to the pandemic that she didn’t look at it right away, and she regrets there was no direct follow-up from the journal or by the authors. “It’s a shame this important information was not shared directly with the mission team while the team was in Wuhan and visited the markets,” she said in an email. “This paper would certainly have added great value.”

Newman says his Chinese co-authors never told him why they didn’t take their data directly to the WHO, but it’s possible they were more comfortable writing a report on market surveys for publishing in a journal, he says. 

The China-based researchers would have had reason to be cautious. In February 2020, the China CDC prohibited scientists working on Covid-related research from sharing their data and required them to receive permission before conducting any studies or publishing the results. Days later, a special panel convened by China’s top executive body to oversee coronavirus research took control of all publication work related to the pandemic for “coordinated deployment.”

An international group of experts convened by the WHO to research the origins of Covid traveled to Wuhan earlier this year—a trip that might have yielded different results if the scientists had known about Xiao’s work.

By the time the team visited the Huanan market in the afternoon of Jan. 31—more than a year after its closure—little remained to assist the kind of epidemiological sleuthing that led SARS investigators to Himalayan palm civets, raccoon dogs, and Chinese ferret-badgers sold in live-animal markets in Guangdong almost two decades ago.

The researchers noted a mixed smell of animals and disinfectant in some areas of the market, but they were told by the market’s manager that they were probably smelling the lingering stench of rotten meat and sewage, according to the official joint WHO-China report released in March 2021.  

Chinese officials briefing the visitors told them 10 Huanan shops had been found to be selling frozen “domesticated” wild animals, including bamboo rats—some sourced from Yunnan province, where scientists found a coronavirus that most closely matches SARS-CoV-2 in horseshoe bats. But no live animals had been seen before the market was closed, the official said.

The researchers saw nothing to dispute that. They were invited to quiz two Wuhan residents whom they were told had shopped there regularly for 20 and 30 years and who, according to the report, said they “had never witnessed any live animals being sold.”

Earlier the same day, the international research team visited Wuhan’s larger Baishazhou market, where Xiao had regularly surveyed two sellers of live wild animals. Yet when the researchers were there they were told that only frozen food, ingredients, and kitchenware were on offer. Liang Wannian, an epidemiologist who led the Chinese experts collaborating with the WHO-convened team, says his group had no knowledge of Xiao’s data either. 

Among the earliest clusters of infections recorded in Wuhan, one involved three Covid cases among staff working at a stall in Huanan. One of the employees, a 32-year-old who fell ill on Dec. 19, traded goods back and forth between the Huanan and Baishazhou markets.

A confirmed case linking two markets that sold wild animals is “very intriguing,” says Stephen Goldstein, a research associate in evolutionary virology at the University of Utah in Salt Lake City. But tracing any contact the employee might have had with infected wildlife is impossible now that the animals are long gone. As for the existence of a flourishing live wild animal business, “It seems to me, at a minimum, that local or regional authorities kept that information quiet deliberately,” he says. “It’s incredible to me that people theorize about one type of cover-up, but an obvious cover-up is staring them right in the face.”

U.S. intelligence agencies will report their own findings on Covid’s origins later this month. But with only circumstantial evidence remaining, the world may now never know what caused the outbreak. “It is unclear why earlier initiatives within China to locate source animals for SARS-CoV-2 were curtailed, and now appear unfortunately to have stopped,” says Tulane’s Garry. “Instead, the focus is on highly implausible origin scenarios. If we continue to place politics over science, humanity will again be unprepared for the next emergence of a pandemic virus.” 

Read next: The Last—And Only—Foreign Scientist in the Wuhan Lab Speaks Out

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