Bats, snakes or pangolins? Inside the hunt for the animal behind the coronavirus outbreak

Three-quarters of new or emerging human diseases originate in animals, but pinpointing the source of Covid-19 could help us combat future outbreaks

  

By SABRINA WEISS

Sunday 16 February 2020

wired

Getty Images / WIRED

In 2013, scientists captured a wild horseshoe bat in a remote cave in Yunnan province, 1,700km southwest of Wuhan. It was carrying a virus strain almost identical to the form of coronavirus that has infected over 65,000 people since December 2019. The cave, the location of which is kept secret, was found after an intense search across southern China for the origin of the 2003 Sars epidemic.

Now an even more urgent hunt is underway – this time to find the animal source of Sars-CoV-2, the virus that causes Covid-19, the disease that has killed almost 1,400 people in mainland China and three beyond its borders. Bats, snakes and now pangolins have all been suggested as hosts of the virus that later made its way into humans, but we still don’t know how exactly the virus jumped from animals to humans. But understanding which animal the virus came from could have a profound impact on how we manage future outbreaks.

The search for the source of Sars – which killed more than 770 people two decades ago – has given us a head start for the current hunt. Wearing hazmat suits and equipped with mist nets, a team from the Wuhan Institute of Virology, together with the ecologist and president of EcoHealth Alliance Peter Daszak, ventured into limestone caves to collect faeces and blood samples from thousands of roosting bats before testing them for novel coronaviruses in the lab. “At the time, we were looking for Sars-related viruses, and this one was 20 per cent different,” says Daszak. “We thought it’s interesting, but not high-risk. So we didn’t do anything about it and put it in the freezer.” The group has found around 500 bat-borne viruses in China over the last 16 years, but only flagged those that most resembled Sars to the authorities – a lack of funding meant they couldn’t further investigate the virus strain now known to be 96 per cent genetically similar to the virus that causes Covid-19.

Could further research on the strain have prevented or minimised the impact of the current outbreak? Possibly. It certainly allowed them to quickly trace the new virus, which emerged in a seafood market in Wuhan, back to bats. Scientists in China sequenced the full genome of Sars-CoV-2 and made it freely available online on January 10, less than two weeks after public health officials reported it to the World Health Organisation (WHO). This immediately started a race among biotechnology companies to research and create diagnostic test kits, antiviral drugs and vaccines.

Three out of four new or emerging diseases in humans are transmitted by wildlife or livestock, according to estimates published by the US Centers for Disease Control and Prevention (CDC), so it’s not surprising that people were quick to point accusing fingers at animals when Covid-19 emerged.

Although bats have evolved to tolerate viruses and are believed to host most coronaviruses, it’s likely they didn’t pass Sars-CoV-2 directly to humans. Bats are the only mammal with the ability to fly and transmit viruses far and wide, and they are traditionally hunted for their meat in China and other parts of Southeast Asia. Because of the bats’ strong immune system, researchers think that viruses replicate faster and then easily kill the human or animal hosts they move into. Having said that, the scientists who took samples from the seafood market in Wuhan did not find many bats. “It’s very likely that there is an intermediate host that has been contaminated,” said Sylvie Briand, WHO’s head of global infectious hazard preparedness at a conference in Geneva on February 11, which hosted 200 experts on coronaviruses and emerging diseases.

Whilst dealing with the outbreak and containing its global spread remains the top priority, tracking the path of the virus is crucial for preventing further exposure and outbreaks in the future, says Jonathan Ball, professor of molecular virology at the University of Nottingham, who specialises in emerging viruses. “You want to rule out whether or not there could be continual animal to human spillover events. So you would want to get an idea of how prevalent that virus is.”

That’s a massive feat of detective work. Researchers need to find out exactly which animals were present in the seafood market, where wild animals such as snakes, rats and porcupines were kept alive in cages while waiting to be sold illegally. Thirty-three of the 585 samples collected from surfaces and cages tested positive for Sars-CoV-2 and the majority were found around stalls that traded wildlife. However, the market – which was closed on January 1, 2020 – has been disinfected since and cleared from any environmental contamination. To complicate things even further, some of the first people to have been infected with Sars-CoV-2 had no connection with the market, which suggests they may have been exposed to infected animals or people elsewhere.

Daszak, who was invited to Geneva to share his experiences with retracing animal sources of coronaviruses, says questioning wildlife traders in markets doesn’t necessarily provide a simple answer. “The wildlife trade changed after Sars, it became local hunters in rural China supplying directly to restaurants,” he says, adding that Sars-like coronaviruses have spread to people living near bat colonies and contaminated livestock since the initial outbreak. In 2016 and 2017, a coronavirus originating from horseshoe bats killed 25,000 piglets at four Chinese farms.

In the search for the source of the Covid-19 outbreak, travel restrictions in China have meant many people are only just returning from the extended lunar new year holiday. “Hopefully work will begin soon on trying to trace back that animal origin,” says Daszak. “Right now the big priority is to deal with the outbreak, which is gradually coming under control.”

The similar genome sequences between Sars-Cov-2 and "RaTG13" (the bat coronavirus that was sampled in the Yunnan province in 2013) suggest the original virus was able to subsist for a long period in bats without harming them. Coronaviruses rarely evolve to jump directly from bats to humans, so virologists are still racing to find the missing piece of the puzzle: which animal served as an intermediate host between bats and humans. Civet cats are thought to be an intermediate host of Sars and camels an intermediate host of Middle East Respiratory Syndrome (Mers) – another disease caused by a coronavirus that was first identified in Saudia Arabia in 2012.

Coronaviruses are transmitted through droplets of bodily fluids, such as saliva and mucus, as well as faeces – or guano, as the accumulated excrements of bats are called – which can come in contact with another animal’s mouth. For example, they may enter livestock farms and nibble on fruit, dropping their contaminated leftovers to the ground. This then allows the virus to transmit to farmed animals like pigs or civets, which are then eaten by humans. The first humans to have been infected with Mers owned and lived closely with their companion camels that had contracted the virus from bats.

In the search for the Covid-19 culprits, snakes were suggested in January but quickly dismissed by virologists because there is currently no evidence of coronaviruses infecting animals other than mammals and birds. The latest candidate is the heavily-trafficked and critically endangered pangolin, a scaly, insect-eating mammal whose meat is considered a delicacy. In traditional Chinese medicine, the coveted scales are believed to help mothers with lactation and cure all kinds of diseases ranging from asthma to cancer.

Due to the seriousness of the novel coronavirus outbreak, scientists across the world have been publicly sharing gene sequences and reports, bypassing the scientific peer-review process and skipping traditional journals. Last week, two researchers from South China Agricultural University claimed to have found a coronavirus in pangolins that is a 99 per cent genetic match to Sars-CoV-2. The pair didn’t provide details on their study, but their claims were then backed up by another preliminary report released on February 13 by researchers at the Baylor College of Medicine in Texas.

Ian Lipkin, an epidemiologist from Columbia University who recently returned from China and is in self-imposed quarantine, assisted the WHO and China during the Sars outbreak and currently advises Saudi Arabia about Mers, which continues to occasionally break out in Saudi Arabia. “When these animals [bats and pangolins] are placed into juxtaposition in markets there is an opportunity for them to exchange viruses.” His research showed that Mers viruses had been circulating in camels and infecting people for at least two decades without anyone noticing or diagnosing it. “As the viruses move between two species, they may further adapt and become more capable of causing infections in humans,” he says.

The reports on pangolins as a source of Covid-19 remain inconclusive and it could yet be shown that they are simply another link in the chain of contamination having been infected with the same virus as humans. What the findings might mean for the illegal trade in pangolins is also unclear. The elusive, nocturnal animals have virtually been “eaten to extinction” in China and are likely being smuggled in alive from Malaysia. The illegal trade in pangolins is incredibly lucrative and on the rise – wildlife traffickers who used to cash in on elephant ivory until China banned its domestic trade in 2017, are increasingly turning to pangolins to maintain their profits.

It is not the first time China introduced a temporary ban on wildlife markets in the wake of an epidemic. In 2003, it banned the transport, breeding and sale of civets and other wildlife, but lifted it again after six months once the SARS epidemic faded.

Due to the country’s long history of wildlife consumption, Vincent Nijman, a professor of anthropology and wildlife trade researcher at Oxford Brookes University thinks closing the markets permanently is unrealistic. It would put livelihoods at stake, and as a result, push the trade underground where many endangered animals like pangolins are already sold illegally. Introducing and enforcing stricter hygiene rules in so-called wet markets – where fresh meat, fish and produce is sold – and breeding facilities would be a better starting point and avoid close contact between the different animals, he says.

Understanding and publicly communicating how viruses like Sars-CoV-2 spread among humans will have a much greater impact. “I would be surprised if more than a handful of these patients have ever seen a live pangolin,” says Nijman, adding that most people don’t visit wildlife markets and would simply dismiss the science and go on with their lives. “People get the virus from other people and that will be the overall experience of the population.”

For virus hunters like Lipkin, however, the current outbreak is a stark reminder that bats, pangolins and other animals could be the source of future infectious diseases as cities and towns encroach on their habitats. “Whether they come through bushmeat hunters or people encountering animals in markets, the principle is the same. Wildlife should stay in the wild.”