Wuhan-based virologist Shi Zhengli has established dozens of deadly SARS-like viruses in bat caves, and she advises there are an ext out there


The mysterious patience samples arrived at the Wuhan academy of Virology in ~ 7 P.M. ~ above December 30, 2019. Moments later on Shi Zhengli’s mobile rang. That was her boss, the institute’s director.

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The Wuhan facility for an illness Control and also Prevention had actually detected a novel coronavirus in 2 hospital patients through atypical pneumonia, and it wanted Shi’s renowned activities to investigate. If the finding to be confirmed, the brand-new pathogen could pose a serious public health and wellness threat—because the belonged come the same household of viruses together the one that caused severe acute respiratory syndrome (SARS), a an illness that plagued 8,100 people and also killed almost 800 that them in between 2002 and also 2003. “Drop everything you are doing and resolve it now,” she recalls the director saying.

Shi, a virologist who is often referred to as China’s “bat woman” by her colleagues because of she virus-hunting explorations in bat caves over the previous 16 years, walked out of the conference she was attending in Shanghai and hopped top top the following train back to Wuhan. “I wonder if obtained it wrong,” she says. “I had never meant this sort of thing to occur in Wuhan, in main China.” Her research studies had displayed that the southern, subtropical districts of Guangdong, Guangxi and Yunnan have the best risk of coronaviruses jumping to human beings from animals—particularly bats, a well-known reservoir. If coronaviruses were the culprit, she remembers thinking, “Could they have come from ours lab?”

While Shi’s team in ~ the Wuhan institute, an affiliate the the Chinese Academy the Sciences, raced to uncover the identification of the contagion—over the adhering to week they associated the illness to the novel coronavirus that end up being known as SARS-CoV-2—the an illness spread like wildfire. Through April 20 an ext than 84,000 human being in China had been infected. Around 80percent that them stayed in the district of Hubei, of i beg your pardon Wuhan is the capital, and more than 4,600 had actually died. Outside of China, around 2.4 million people across 210 or therefore countries and territories had recorded the virus, and more than 169,000 had actually perished native the condition it caused, COVID-19.

Scientists have actually long warned the the price of appearance of new infectious conditions is accelerating—especially in developing countries wherein high densities the people and animals progressively mingle and also move about. “It’s incredibly vital to decide the source of infection and also the chain of cross-species transmission,” says disease ecologist Peter Daszak, president of EcoHealth Alliance, a new York City–based non-profit research organization that works with with researchers, such as Shi, in 30 countries in Asia, Africa and also the Middle eastern to discover new viruses in wildlife. An equally essential task, the adds, is come hunt down various other pathogens come “prevent similar incidents from happening again.”

OUTSIDE A BAT cavern in China"s Guangxi province in 2004, Shi Zhengli releases a fruit bat after taking a blood sample. Credit: Shuyi Zhang


To Shi, her an initial virus-discovery expedition felt favor a vacation. On a breezy, sunny spring day in 2004, she join an worldwide team of researchers to collect samples native bat nests in caves close to Nanning, the resources of Guangxi. Her inaugural cavern was usual of the region: large, well-off in limestone columns and—as a well-known tourist destination—easily accessible. “It was spellbinding,” Shi recalls. Milky-white stalactites hung indigenous the ceiling choose icicles, glistening with moisture.

But the holidaylike environment soon dissipated. Many bats—including several insect-eating species of horseshoe bats the are numerous in southern Asia—roost in deep, narrow caves ~ above steep terrain. Often guided by advice from neighborhood villagers, Shi and also her colleagues had to hike for hours to potential sites and inch v tight absent crevasses on their stomachs. And also the flying mammals deserve to be elusive. In one frustrating week, the team explored an ext than 30 caves and also saw just a dozen bats.

These explorations were part of the effort to capture the culprit in the SARS outbreak, the first major epidemic of the 21st century. A Hong Kong team had reported that wildlife traders in Guangdong first caught the SARS coronavirus indigenous civets, mongooselike mammals the are indigenous to tropical and also subtropical Asia and Africa.

Before SARS, the world had only an inkling that coronaviruses—so named due to the fact that their spiky surface resembles a crown as soon as seen under a microscope, says Linfa Wang, that directs the emerging contagious diseases regimen at Singapore’s Duke-NUS clinical School. Coronaviruses were mostly well-known for causing common colds. “The SARS outbreak to be a game changer,” Wang says. It was the an initial emergence the a deadly coronavirus through pandemic potential. The incident helped to jump-start a global search for pet viruses that might find their way into humans. Shi was very early recruit of the effort, and both Daszak and also Wang have been her irreversible collaborators.

With the SARS virus, just just how the civets acquired it stayed a mystery. Two previous incidents were telling: Australia’s 1994 Hendra virus infections, in i m sorry the contagion jumped from equines to humans, and also Malaysia’s 1998 Nipah virus outbreak, in i beg your pardon it relocated from pigs come people. Wang uncovered that both diseases were caused by pathogens the originated in fruit-eating bats. Horses and also pigs were merely the intermediary hosts. Bats in the Guangdong market additionally contained traces of the SARS virus, yet many researchers dismissed this together contamination. Wang, however, assumed bats might be the source.

In those first virus-hunting months in 2004, at any time Shi’s team located a bat cave, that would placed a net at the opening prior to dusk and also then wait for the nocturnal creatures to undertaking out to feed because that the night. As soon as the bats were trapped, the researchers took blood and also saliva samples, and also fecal swabs, frequently working into the little hours. After capturing up on some sleep, lock would go back to the cave in the morning to collect urine and also fecal pellets.

But sample ~ sample turned up no trace of hereditary material native coronaviruses. It was a hefty blow. “Eight month of difficult work appeared to have gone down the drain,” Shi says. “We thought perhaps bats had actually nothing to carry out with SARS.” The scientists were about to provide up once a research team in a surrounding lab handed them a diagnostic kit for trial and error antibodies created by civilization with SARS.

There to be no guarantee the the check would occupational for bat antibodies, but Shi offered it a walk anyway. “What did we need to lose?” she says. The outcomes exceeded her expectations. Samples from three horseshoe bat species contained antitoxin to the SARS virus. “It was a transforming point because that the project,” Shi says. The researcher learned that the presence of the coronavirus in bats to be ephemeral and also seasonal—but an antibody reaction might last native weeks to years. The diagnostic kit, therefore, offered a an important pointer regarding how to hunt under viral genomic sequences.

Shi’s team provided the antibody test to narrow under the list of locations and bat species to pursue in the search for genomic clues. ~ roaming mountainous terrain in most of China’s dozens that provinces, the researchers turned their attention to one spot: Shitou Cave, top top the suburbs of Kunming, the funding of Yunnan, where they conducted intense sampling during different seasons over 5 consecutive years.

The efforts paid off. The pathogen hunters uncovered hundreds of bat-borne coronaviruses through incredible genetic diversity. “The bulk of them space harmless,” Shi says. But dozens belong to the same group as SARS. They have the right to infect human lung cells in a petri dish and cause SARS-like illness in mice.

In Shitou Cave—where painstaking scrutiny has yielded a natural hereditary library that bat-borne viruses—the team found a coronavirus strain that came from horseshoe bats through a genomic sequence practically 97percent the same to the one discovered in civets in Guangdong. The finding concluded a decade-long find for the natural reservoir that the SARS coronavirus.

ON THE very same 2004 trip, a team of researcher prepare bat blood samples that they will display screen for viruses and other pathogens. Credit: Shuyi Zhang

A dangerous MIX

In countless bat houses Shi has actually sampled, consisting of Shitou Cave, “constant mixing of various viruses creates a good opportunity for dangerous brand-new pathogens to emerge,” claims Ralph Baric, a virologist at the university of phibìc Carolina at Chapel Hill. In the vicinity of such viral melting pots, Shi says, “you don’t need to be a wildlife trader to be infected.”

Near Shitou Cave, for example, countless villages sprawl among the lush hillsides in a region known for its roses, oranges, walnuts and also hawthorn berries. In October 2015 Shi’s team gathered blood samples from more than 200 residents in 4 of those villages. It found that six people, or practically 3percent, brought antibodies versus SARS-like coronaviruses native bats—even though none that them had actually handled wildlife or report SARS-like or other pneumonialike symptoms. Only one had traveled outside of Yunnan prior to the sampling, and all stated they had actually seen bats flying in your village.

Three years previously Shi’s team had actually been dubbed in to inspection the virus file of a mine tower in Yunnan’s such as mountain Mojiang County—famous because that its fermented Pu’er tea—where 6 miners experienced from pneumonialike diseases and two died. After ~ sampling the cave for a year, the researchers discovered a varied group the coronaviruses in six bat species. In many cases, multiple viral strains had actually infected a single animal, turning it right into a flying manufacturing facility for brand-new viruses.

“The mine column stunk prefer hell,” says Shi, who, prefer her colleagues, went in attract a security mask and also clothing. “Bat guano, covered in fungus, littered the cave.” return the fungus turned out to be the pathogen that had sickened the miners, she says it would have actually been only a issue of time before they captured the coronaviruses if the mine had not to be promptly shut.

With growing human populations progressively encroaching top top wildlife habitats, through unprecedented transforms in floor use, v wildlife and livestock transported across countries and their products about the world, and with sharp rises in both domestic and also international travel, pandemics of brand-new diseases space a mathematical close to certainty. This had actually been keeping Shi and many various other researchers awake at night long prior to the secret samples landing at the Wuhan institute of Virology on the ominous evening critical December.

More than a year earlier Shi’s team published two substantial reviews around coronaviruses in Viruses and Nature reviews Microbiology. Illustration evidence indigenous her very own studies—many of i m sorry were published in top academic journals—and from others, Shi and her co-authors warned the the danger of future outbreaks that bat-borne coronaviruses.


On the train earlier to Wuhan top top December 30 last year, Shi and her colleagues debated ways to immediately start experimentation the patients’ samples. In the adhering to weeks—the many intense and also the many stressful time of her life—China’s bat woman felt she was fighting a battle in her worst nightmare, also though it was one she had actually been preparing because that over the past 16 years. Making use of a an approach called polymerase chain reaction, which can detect a virus by amplifying its genetic material, the team discovered that samples from five of seven patients had hereditary sequences present in all coronaviruses.

Shi instructed her group to repeat the exam and, in ~ the same time, sent out the samples to an additional facility to sequence the complete viral genomes. At the same time she frantically went v her very own lab’s documents from the past couple of years to check for any type of mishandling of speculative materials, especially throughout disposal. Shi breathed a sigh that relief once the results came back: nobody of the sequences suitable those of the viruses her team had actually sampled native bat caves. “That really took a fill off my mind,” she says. “I had actually not slept a wink fordays.”

By January 7 the Wuhan team had established that the new virus had indeed caused the an illness those patients suffered—a conclusion based on results native analyses making use of polymerase chain reaction, full genome sequencing, antibody tests of blood samples and also the virus’s capacity to infect person lung cell in a petri dish. The genomic succession of the virus, ultimately named SARS-CoV-2, to be 96percent identical to the of a coronavirus the researchers had identified in horseshoe bats in Yunnan. Their results appeared in a file published digital on February3 in Nature. “It’s decision clear the bats, when again, are the natural reservoir,” says Daszak, that was not associated in the study.

Since then, researchers have published more than 4,500 genomic assignment of the virus, reflecting that samples roughly the world show up to “share a usual ancestor,” Baric says. The data also point to a solitary introduction right into humans followed by sustained human-to-human transmission, researcher say.

Given the the virus seems fairly stable initially and also that numerous infected individuals appear to have actually mild symptoms, scientists suspect that the virus might have actually been about for mainly or also months prior to severe situations raised the alarm. “There could have been mini outbreaks, yet the viruses either burned out or maintained low-level transmission before causing havoc,” Baric says. Many animal-borne viruses reemerge periodically, that adds, so “the Wuhan outbreak is by no method incidental.”

IN YUNNAN PROVINCE, CHINA, scientists from EcoHealth Alliance, an international team that searches for illness that can jump from animals to people, hunt because that pathogens in a bat cave. Credit: EcoHealth Alliance


To many, the region’s burgeoning wildlife markets—which sell a wide selection of animals such as bats, civets, pangolins, badgers and crocodiles—are perfect viral melting pots. Back humans can have recorded the deadly virus indigenous bats straight (according to number of studies, including those by Shi and her colleagues), independent groups have said that pangolins may have actually been an intermediate host. This teams have reportedly uncovered SARS-CoV-2-like coronaviruses in pangolins the were seized in antismuggling work in southerly China.

On February 24 China announced a long-term ban top top wildlife consumption and trade except for research, medicinal or display purposes—which will certainly stamp the end an sector worth $76billion and put approximately 14million human being out of jobs, according to a 2017 report i was delegated by the Chinese Academy the Engineering. Some welcome the initiative, whereas others, such as Daszak, concern that without efforts to change people’s traditional beliefs or to administer alternative livelihoods, a blanket ban may simply push the business underground. This can make condition detection even more challenging. “Eating wildlife has been part of the social tradition” in China for hundreds of years, Daszak says. “It won’t adjust overnight.”

In any type of case, Shi says, “wildlife trade and also consumption space only component of problem.” In so late 2016 pigs across four farms in Qingyuan ar in Guangdong—60 miles from the website where the SARS outbreak originated—suffered from acute vomiting and also diarrhea, and almost 25,000 of the animals died. Regional veterinarians can not detect any type of known pathogen and referred to as Shi for help. The cause of the illness—swine acute diarrhea syndrome (SADS)—turned out to it is in a virus whose genomic sequence to be 98percent identical to that of a coronavirus uncovered in horseshoe bats in a surrounding cave.

“This is a serious cause for concern,” says Gregory Gray, an infectious disease epidemiologist at duke University. Pigs and humans have very similar immune systems, making it simple for viruses to cross in between the two species. Moreover, a team in ~ Zhejiang university in the Chinese city the Hangzhou found that the SADS virus could infect cell from numerous organisms in a petri dish, consisting of rodents, chickens, nonhuman primates and humans. Given the scale of swine farming in many countries, such together China and the U.S., Gray says, looking for novel coronaviruses in pigs should be a peak priority.

The present outbreak adheres to several others during the past three decades that have been brought about by six different bat-borne viruses: Hendra, Nipah, Marburg, SARS-CoV, MERS-CoV (Middle eastern respiratory syndrome) and Ebola. Yet “the animals room not the problem,” Wang says. In fact, bats encourage biodiversity and also ecosystem wellness by eating insects and pollinating plants. “The difficulty arises as soon as we acquire in contact with them,” that says.


When ns spoke come Shi in late February—two months right into the epidemic and one month ~ the government applied severe movement constraints in Wuhan, a megacity the 11million—she said, laughing, that life felt virtually normal. “Maybe we are obtaining used to it. The worst work are absolutely over.” The academy staffers had a unique pass to travel from house to their lab, however they can not go almost everywhere else. They had to subsist on prompt noodles during their long hours at work because the institute’s canteen to be closed.

New revelations around the coronavirus maintained coming to light. The researcher discovered, for instance, the the microorganism enters human lung cells by making use of a receptor referred to as angiotensin-converting enzyme2, and they and also other groups have due to the fact that been screening for drugs that have the right to block it. Researchers are additionally racing to build vaccines. In the lengthy run, the Wuhan team to plan to develop broad-spectrum vaccines and drugs versus coronaviruses deemed risky to humans. “The Wuhan outbreak is a wake-up call,” Shi says.

Many researchers say the world should move beyond merely responding come deadly pathogens when they arise. “The best means forward is prevention,” Daszak says. Because 70percent the emerging transmittable diseases of pet origins come indigenous wildlife, a height priority need to be identifying them and also developing better diagnostic tests, the adds. Doing so would essentially mean continuing on a much bigger scale what researcher such as Daszak and Shi had actually been doing prior to their capital ended this year.

Such initiatives should emphasis on high-risk viral groups in mammals prone to coronavirus infections, such as bats, rodents, badgers, civets, pangolins and nonhuman primates, Daszak says. That adds that emerging countries in the tropics, where wildlife diversity is greatest, have to be the front line of this battle versus viruses.

Daszak and also his colleagues have analyzed approximately 500 human transmittable diseases indigenous the previous century. They uncovered that the emergence of brand-new pathogens tends to happen in places where a dense population has been changing the landscape—by building roads and mines, cutting down forests and also intensifying agriculture. “China is not the just hotspot,” he says, noting the other significant emerging economies, such as India, Nigeria and also Brazil, are likewise at an excellent risk.

Once potential pathogens room mapped out, scientists and also public health officials have the right to regularly check for feasible infections by evaluating blood and also swab samples native livestock, native wild pets that room farmed and traded, and from high-risk human populations such together farmers, miners, villagers who live near bats, and people that hunt or manage wildlife, Gray says. This approach, recognized as “One Health,” intends to incorporate the health and wellness management the wildlife, livestock and also people. “Only then deserve to we catch break out before that turns into an epidemic,” that says, including that the strategy might potentially conserve the thousands of billions the dollars such an epidemic have the right to cost.

Back in Wuhan, whereby the lockdown was finally lifted on April8, China’s bat woman is no in a celebratory mood. She is distressed because stories indigenous the internet and significant media have repeated a tenuous pointer that SARS-CoV-2 by chance leaked from her lab—despite the fact that its hereditary sequence does not match any type of her lab had previously studied. Other scientists are fast to dismiss the allegation. “Shi leader a world-class laboratory of the greatest standards,” Daszak says.

Despite the disturbance, Shi is identified to proceed her work. “The mission should go on,” she says. “What we have uncovered is simply the guideline of one iceberg.” She is plan to lead a national project to systematically sample viruses in bat caves, v much more comprehensive scope and intensity than previous attempts. Daszak’s team has approximated that there are more than 5,000 coronavirus strains wait to be found in bats globally.

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“Bat-borne coronaviruses will cause more outbreaks,” Shi claims with a tone of brooding certainty. “We must discover them prior to they uncover us.” 

Read an ext about the coronavirus outbreak from Scientific Americanhere. And read coverage indigenous our global network of magazines here.