6.
Bats and the virus hunters
‘The order Chiroptera (the “hand-wing” creatures) encompasses 1,116 species, which amounts to 25 percent of all the recognized species of mammals. To say again: one in every four species of mammal is a bat.’
DAVID QUAMMEN
SARS, SARS-CoV-2 and other SARS-like coronaviruses predominantly thrive in just one genus of bat, Rhinolophus, the horseshoe bats. These are a diverse group, with 106 species known so far. They are found only in the old world, having not reached the Americas, and are mostly tropical or subtropical in their range although two do live as far north as southern Britain. Noted for their manoeuvrability on their relatively short, broad wings, and their top-of-the-range, sophisticated echo-location equipment, they are among the most accomplished bats when it comes to flitting through trees and shrubs in the dead of night finding insects on the wing. Horseshoes are small or average-size bats, with large, broad, but pointed ears and rich, often reddish fur. They get their name from their most distinctive feature, a strange, fleshy sonar dish known as a nose-leaf on the end of the snout, the outer part of which is usually shaped like an upturned horseshoe. The name Rhinolophus translates as ‘nose leaf’. The nose-leaf serves to focus the high-pitched ultrasound beams the bats send out via their nostrils, while shielding their ears from the sound. Horseshoe bats generally like to roost in caves and some species are very gregarious, gathering in roosts of thousands of animals.
China is home to many horseshoe bat species: Rhinolophus ferrumequinum, the greater horseshoe bat, lives in central China (and across Eurasia), so it is found near Wuhan, but not further south. In southern China, near the borders with Laos, Vietnam and Thailand, at least nine species of horseshoe bat are common, some almost indistinguishable from one another. There is the intermediate (affinis), the Chinese rufous (sinicus), the big-eared (macrotis), the woolly (luctus), the king (rex), the Thai (siamensis), Osgood’s (osgoodi), Pearson’s (pearsonii) and the least (pusillus), plus there are another ten that are either very rare in China or not necessarily recognised as being separate species. So if you walk into a cave in Yunnan in south-west China, shine a light on the ceiling, and catch a glimpse of a bunch of horseshoe bats huddled there, they could be several different species together. The differences in their appearance and behaviour are sometimes slight.
Two greater horseshoe bats (Rhinolophus ferrumequinum). This species occurs in Europe, Northern Africa, Central Asia and Eastern Asia.
Rudmer Zwerver/Alamy Stock Photo
In the last few decades, no other group of animals has proved as prolific as bats at serving as the reservoir of new viruses that make their way to human populations. Hendra in Australia in 1994, Nipah in Malaysia in 1998, SARS in China in 2002–3, MERS in Saudi Arabia in 2012, Ebola in Sudan and Zaire in 1976, Guinea in 2013 and Congo more recently: all are deadly viruses that ultimately came from bats. There are probably several reasons that bats prove such a reservoir of zoonotic viruses. Bats are mammals, which means they are sufficiently related to other mammalian intermediate hosts and human beings that it is not a great leap for a bat-borne virus to find its way into people. In comparison, viruses that infect reptiles or fish or birds are living in very different bodies with very different cellular machinery from that in humans, making it less straightforward for a virus to cross host classes in the animal kingdom. Furthermore, bats have not been domesticated, are nocturnal, and they are usually to be found in dense roosts in remote caves. This means that although humans are sometimes exposed to bats through practices such as the guano trade, we are less likely to encounter their diseases.
Bats are highly diverse, though it is difficult to be sure how many bat species there are. ‘Lumpers’, who downgrade some species to subspecies, estimate around 900 species; ‘splitters’, who upgrade some subspecies to species, can get to nearly 1,400. That means that about one in four mammal species is a bat. Each species can have its own viruses, and many viruses evolve to become proficient at jumping between bat species and even to other animal species. For their small size, bats are surprisingly long-lived animals. A horseshoe bat has been found to live to the age of thirty and most survive for six or seven years – far longer than a mouse of the same size. It is possible the bat that was carrying the RaTG13 virus in the Mojiang mine in 2013 is still out there.
Like humans and farmed animals, bats sometimes live in dense populations. In some breeding colonies, there can be up to five hundred bat pups per square foot on the wall of a cave. At certain times of the year, one cave in Texas houses twenty million bats, a concentration of mammals paralleled only by people in cities. Another cave in Borneo is home to ten million bats. Moreover, different species roost together and share their viruses. Coronaviruses are good at recombining and shifting between host species. Also, bats are the only flying mammals. This means that, unlike mice, they travel long distances, meeting a lot of stranger bats as they do so, with the opportunity to pick up new viruses. All of this presents terrific opportunities for the spread and diversification of viruses. A tiger or a pangolin, living a solitary life and hardly ever meeting another of its species except to mate, just isn’t much of a prospect for an ambitious coronavirus.
Bats have existed for an estimated fifty million years and have evolved unique immune systems (with distinct properties from the human immune system) that more often enable them to show no sign of disease when infected by various viruses. Scientists have found that bat viruses that cause severe disease in humans often trigger an excessive immune response and inflammation in human hosts but do not stimulate the same overreactive response in bats. Dr Linfa Wang of Duke-NUS Medical School in Singapore has been arguing for years that one reason bats have disproportionately more virus diseases than other mammals is that they tolerate chronic viral infections better than other mammals. Many other scientists are now persuaded that he is right.
The reason, Dr Wang thinks, is that bats run their bodies at high temperatures while flying. A flying bat’s pulse might reach a thousand beats a minute and its blood temperature can exceed 100 degrees Fahrenheit. This requirement for ultra-high metabolic activity has led to faster oxygen metabolism, which can damage the DNA in the cell nuclei and sometimes cause DNA to leak into the rest of the cell. That would normally induce an immune response leading to inflammation and the production of interferons: proteins that cells make to communicate to other cells that they are under attack and to trigger a protective response. But in bats the system seems to be dampened so that this inflammation is avoided. As a consequence, viruses also do not provoke such a strong inflammatory response in bats. This may hold clues to how to treat people who are infected by viruses and it could even prolong our health span – the years of our life when we are in good health.
In 2018, Dr Peng Zhou, Dr Shi Zhengli and colleagues published the results of an experiment at the Wuhan Institute of Virology that aimed to understand how bats dampen their interferon response. Spleen cells taken from three bats of the species Rhinolophus sinicus, captured in the Taiyi cave in Xianning, about fifty miles south of Wuhan, were used to test the interferon response as compared with spleen cells from three mice. Sure enough, when the cells were stimulated with a molecule that is a product of DNA breakdown, the genes that produce interferons were more active in the mouse cells than in the bat cells. The scientists zeroed in on a particular mutation in the so-called STING gene found in most animals that modulates the interferon response, ensuring that their immune systems do not overreact and cause inflammation. The team concluded that ‘bats are more effective in peaceful co-existence with a large number of viruses’.
Incidentally, these experiments illustrate the fact that the WIV was doing experiments on bat cells in the laboratory. In the light of this, it is interesting to read of the risks of working with bat cells, as set out in a paper by an Australian team in 2018. They pointed out that such cells can harbour latent viruses ‘that can become reactivated during in vitro cultivation when the cells are outside the host and isolated from other components of the immune system that would otherwise control virus replication’. They caution that cell lines from bats should therefore be handled with much care. Nonetheless, different teams of scientists are beginning to create their own customised laboratory cell lines derived from wild animals in order to facilitate the collection and study of entirely novel viruses found in nature. What is in each laboratory’s virology toolkit will likely be a mystery as long as scientists continue not to publish the details of the animals they have captured and used to create so-called ‘immortal’ cells – cells that seem to be able to grow and divide endlessly in the laboratory. It appears that several such cell lines were established at the WIV likely from bats taken from the Jinning caves (Shitou and Yanzi) and the Mojiang mine.
The virus hunters
After the 2002–3 SARS epidemic, the WHO convened a scientific mission to investigate the origins of the first SARS virus in China. The team included Dr Linfa Wang, based in Australia at the time, who had previously studied Hendra and Nipah viruses that had originated in bats, and Dr Shi Zhengli from the WIV, together with international scientific colleagues. They eventually traced SARS-like viruses to bats in southern China. After locating caves in the hillsides where the bats roosted in good numbers, the team set mist nets over the entrance to catch the bats as they emerged at dusk. The nose and anus of each one would be swabbed to provide a sample. Next morning after first light the scientists would return and collect fresh droppings that had fallen onto tarpaulins they had stretched on the floor of the cave. As one of Dr Shi’s star doctoral students, Dr Ben Hu, recalled, Dr Shi often led these virus-hunting expeditions herself, trekking through the wilderness with her group, and was admired by her colleagues for her perseverance.
At first the scientists struggled to find evidence of bat infection in the caves, but when they started looking for antibodies to SARS instead of virus genetic material, they began to find strong indication of past infection in horseshoe bats. Seeking expertise in wildlife handling, Dr Wang and Dr Shi teamed up with Dr Peter Daszak, then of the Consortium for Conservation Medicine in New York. By 2005, the team had found a SARS-like virus in a faecal sample from a Rhinolophus bat, the genome of which proved to be approximately 92 per cent identical to the human SARS virus. The group went on to publish a review of bats and SARS, describing their discovery of several Rhinolophus bat species that were reservoirs of SARS-like viruses.
Over the next decade and more, many other influential papers from this research consortium describing novel viruses isolated from bats would follow. Thanks to this history of hunting down such viruses, Dr Wang earned the nickname Batman, while Dr Shi became known as the Bat Woman. While chasing the SARS-like viruses across China, they also forged friendships and collaborations with overseas scientists such as Dr Daszak and Dr Hume Field, who later became the president and the science and policy advisor respectively of the EcoHealth Alliance non-profit organisation. After their first discovery of SARS-like viruses in bats in southern China, Dr Daszak sought grants in the United States to support the work, starting a long and fruitful collaboration with Dr Shi.
Despite this early success, scientists had not found the bat virus that had given birth to the 2002–3 SARS epidemic. It remained a mystery as to how the killer virus had emerged in Guangdong. In the wake of SARS, governments around the world began to funnel money towards virologists and wildlife biologists in the hope of averting the next pandemic. The biggest of these projects, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) programme began in 2009. Intended to last for five years, it would be renewed in 2014 for another five. The EPT was divided into four strands: Predict, Identify, Respond, Prevent. The first of these, Predict, aimed to estimate the spillover potential of animal viruses, based on where each virus was found and the range of species it infected. Predict was led by the University of California at Davis One Health Institute, where the veterinary scientist Dr Jonna Mazet was the director of the programme, partnering with Metabiota, a viral database firm based in San Francisco, and the EcoHealth Alliance, as well as the Wildlife Conservation Society and the Smithsonian Institution.
The EcoHealth Alliance’s roots lie partly in the books of Gerald Durrell (1925–95), a naturalist who combined a career collecting animals for zoos with writing light-hearted books about his adventures. The books were so successful that he founded his own zoo and conservation charity, based on the island of Jersey in the English Channel. In 1971, Gerald Durrell’s charitable legacy, the Jersey Wildlife Preservation Trust, formed an American branch, which in 1999 became the Wildlife Trust. Shortly after this, Dr Peter Daszak joined the organisation. Dr Daszak had earned his PhD studying parasitic infectious diseases at the University of East London and then followed his wife to the United States. While waiting for a work visa, he volunteered at the US Centers for Disease Control and Prevention at the time of the Nipah outbreak, then joined the University of Georgia before in 2000 applying for a job at the Wildlife Trust. This work consisted of coordinating a project involving five universities studying diseases carried by wildlife, which became the Consortium for Conservation Medicine. The project grew to dominate the finances of the Wildlife Trust and in 2010 Dr Daszak became president of the organisation and it changed its name to the EcoHealth Alliance.
The task of preventing zoonoses was both urgent and noble, and it required expertise in wildlife as well as viruses. The new organisation secured a series of large grants, mainly through Predict, to lead work around the world on pandemic risks from new viruses found in wild animals. As the distributor of these grants to various academic institutions internationally, Dr Daszak gained considerable influence. By 2018, the EcoHealth Alliance had grown its income to almost $17 million a year, nearly all of it from government. In total, in its first decade of existence, the organisation received more than $120 million in US government grants. It takes some diligence to work out from the EcoHealth Alliance’s accounts that a lot of that money came from the Pentagon. One journalist, Sam Husseini, found his emails and voicemails ignored when requesting this information, despite the EcoHealth Alliance website’s own proclamation that ‘A copy of the EHA Grant Management Manual is available upon request to the EHA Chief Financial Officer’. Government databases eventually revealed to Husseini that from 2013 to 2020 the EcoHealth Alliance received $39 million from the Pentagon, mainly via the US Department of Defense’s Threat Reduction Agency. It received $20 million from the Department of Health and Human Services and more than $64 million from the USAID’s Predict.
Predict’s grants to the EcoHealth Alliance were to help it build local capabilities and test high-risk wildlife. ‘After scientists collect swabs or small amounts of blood, they analyze the samples in the lab to look for evidence of disease,’ the organisation explained. The money was spent partly on funding research by overseas partners, one of the most high-profile of which was the WIV. In the search for the origin of SARS, Dr Daszak and Dr Shi travelled throughout Yunnan and other parts of China collecting bats to be tested for viruses. He was a regular collaborator, co-author and funder of her work.
By 2011, Dr Shi and Dr Daszak had begun to focus on the caves of Yunnan. Slowly, the team zeroed in on the area and the species with the most SARS-like of the SARS-like viruses. Between April 2011 and September 2012, Dr Shi’s team took 117 anal swabs and faecal samples from bats in the Shitou cave near Kunming, more than a thousand kilometres to the west of Guangdong where palm civets and people had become infected by SARS virus. Twenty-seven of the samples tested positive for coronavirus, and at least seven strains of SARS-like viruses could be detected. The complete genomic sequences of two strains were obtained and they were named SARS-like coronavirus (SL-CoV) RsSHC014 and Rs3367. This time the key part of the spike protein – the receptor-binding domain – was similar to that in the SARS virus; it was the first time that scientists had discovered a wild bat SARS-like virus that could use the same ACE2 receptor that the 2003 SARS virus had utilised to infect its animal hosts. Overall, the virus sequences that the WIV had found were about 95 per cent identical to the SARS viruses that had been isolated from humans and civets during the SARS epidemic. They announced the discovery triumphantly in a paper in Nature on 30 October 2013, entitled ‘Isolation and Characterization of a Bat SARS-like Coronavirus That Uses the ACE2 Receptor’.
Not only had this expedition resulted in the identification of the closest match to the epidemic SARS virus, but the team also succeeded for the first time in ‘isolating’ a live virus from one of the samples. The phrase ‘isolating a virus’ has a specific meaning: to coax the virus into replicating in cells in the laboratory and thus produce new, infectious viruses for further study. It is a difficult task. RNA viruses are fragile and the virus particles and their genomes are usually too broken up to work with by the time they have been transported thousands of kilometres to the laboratory. Isolating a virus provides greater confidence that the genome assembled from fragments of sequences is accurate and represents a real virus. In this case, Dr Shi’s team retrieved a fully viable virus from a sample taken from a Chinese rufous horseshoe bat, Rhinolophus sinicus. They called this virus SL-CoV-WIV1, which stands for SARS-like coronavirus Wuhan Institute of Virology 1.
Successes in pathogen surveillance
In 2017 the virus hunting at the WIV scored a significant success: identifying the source of a new epidemic and proving the worth of their work to date. However, it did not concern beta-coronaviruses in people, but alpha-coronaviruses in pigs. Between 28 October 2016 and 2 May 2017, severe diarrhoea broke out on four pig farms in Guangdong. Piglets five days old or younger had up to 90 per cent mortality if they caught this disease, known as swine acute diarrhoea syndrome (SADS). In all, 24,693 pigs died. The WIV was called in to help investigate. About a year later, the usual team from Dr Shi’s laboratory, with Dr Peng Zhou as lead author, and Drs Peter Daszak, Linfa Wang and Shi Zhengli among the co-authors, announced that they had extracted more than fifteen million genetic reads from the intestines of one piglet. Among these, they found 4,225 that were from an alpha-coronavirus, which they deduced was the cause of the disease.
They then isolated thirty-three complete genomes of the coronavirus taken from pigs at all four farms and found that it was roughly 95 per cent the same as a coronavirus genome isolated from sinicus horseshoe bats in Hong Kong and Guangdong ten years before, known as HKU2. However, the spike protein was much less similar, 86 per cent, so they concluded that the bat virus was only a close cousin of the pig virus. They then returned to their freezers, much as they would do in 2020, and dug out the sequences from faecal swabs of bats caught at seven locations in Guangdong between 2013 and 2016. They found fifty-eight samples positive for SADS coronavirus, all from horseshoe bats, and among them were four genomes that very closely resembled that of SADS.
In the lab, the scientists tried to isolate the novel SADS virus using a variety of different cell types from different species: Vero (monkey kidney); home-grown R. sinicus cells from bat kidney, lung, brain and heart; and swine cells from the intestines, kidney and testes. The reason being that it is difficult to know how to grow novel viruses in the laboratory. Even when you know the host species that the virus was collected from, the virus may not grow well in cells from that same animal species in the lab. So some scientists inoculate different types of cells, derived from different host species, with the novel virus sample. Then the scientists take what grows in that first batch of cells and inoculate another batch of cells, hoping that the fittest of the virus particles will propagate. This process can be repeated as many times as needed and is called serial passaging. However, this approach can be risky when a sample contains multiple viruses, or multiple virus samples are combined before passaging. With different viruses growing together in an entirely new host environment, unique recombinants may emerge.
In the case of the SADS virus, it was only after five passages in Vero cells that the scientists finally observed cell death due to viral infection – in other words, effective virus replication and spreading among cells. The team then tested whether the viruses could infect human cells using the receptors of SARS, MERS or alpha-coronaviruses. It turns out that the SADS virus did not use any of these but was able to cause severe disease and mortality in challenge studies, in which healthy piglets were inoculated with the virus. The conclusion was that the virus, presumably from a horseshoe bat, had somehow directly infected the pigs on the four farms once or several times, and fortunately it did not look as if it would be very dangerous for people. As Dr Shi later pointed out, ‘This is the first documented spillover of a bat coronavirus that caused severe diseases in domestic animals.’
The SADS episode is one that the WIV-EcoHealth Alliance collaboration could rightly look back on as textbook: there is an outbreak of disease, the virus is identified, its natural reservoir (bats) is tracked down, and the risk from the virus to people is assessed – all made possible by years of sampling of bats in the wild, storing samples in the laboratory, and testing them against cells from different species, organs, presenting different virus entry receptors. The scientists wrote in their paper that their study demonstrated the ‘value of proactive viral discovery in wildlife, and targeted surveillance in response to an emerging infectious disease event’.
Sampling human beings for novel pathogens
As well as sampling bats and other animals, the WIV-EcoHealth Alliance team sampled people. They wanted to know whether people living near bat caves in which SARS-like viruses had been found were getting infected by these viruses. In other words, what was the risk of another SARS virus outbreak stemming from the bat caves in Yunnan? In October 2015, they took blood from 139 women and 79 men living in four villages within a few kilometres of two of the caves in Yunnan in which the scientists had been catching bats: Shitou and Yanzi caves near Jinning. Most of the subjects were farmers, most kept livestock or owned pets, and one had handled a dead bat. The area had not experienced any part of the SARS epidemic. As a control, the scientists also sampled the blood of 240 donors in Wuhan. The results were intriguing. Of the 218 villagers, six had detectable levels of antibodies to the nucleocapsid protein of a SARS-like virus named Rp3 (which had been determined to be a reliable method for detecting SARS-specific antibodies). By the same assay, none of the Wuhan controls proved positive for SARS antibodies. The scientists obtained oral and faecal swabs as well as more blood samples from the six individuals but could not detect any virus genetic material.
The six positive cases were typical villagers. In the year before the human samples had been collected, only one had travelled outside the province, only one had visited Kunming, and two had not left the village. They were all among the twenty people in the study who had noticed bats flying about their villages. None remembered developing any clinical symptoms in the previous year. The scientists concluded that ‘the 2.7 % seropositivity for the high risk group of residents living in close proximity to bat colonies suggests that spillover is a relatively rare event, however this depends on how long antibodies persist in people, since other individuals may have been exposed and antibodies waned’.
Over the next two years the team repeated the survey on a wider scale, throughout southern China, targeting people who regularly visited or worked around bat caves or who were involved in the wildlife trade, catching, rearing, transporting or selling animals. Of the 1,596 participants in the study, 265 had reported recent severe acute respiratory infections and/or influenza-like illness. However, only nine (of the 1,497 participants who provided samples) tested positive for SARS antibodies and none of the nine had reported experiencing any symptoms in the year preceding their interviews. Eight of them were farmers of crops with no unusual work connection to animals. The highest self-reported risk factor for having experienced these symptoms was the consumption of raw or undercooked meat from a carnivorous animal. There was no evidence of contact with bats influencing whether a person was more likely to have SARS antibodies.
Like the previous study, this one, published in September 2019, concluded that ‘bat coronavirus spillover is a rare event’. Once the Covid-19 pandemic began, however, Dr Daszak (a co-author on the two studies) took a rather different line, emphasising now how common the spillovers of bat coronaviruses were, rather than how rare. In April 2020, in an interview with Vox, he said that the maths was straightforward: ‘We also find tens of thousands of people in the wildlife trade, hunting and killing wildlife in China and Southeast Asia, and millions of people living in rural populations in Southeast Asia near bat caves.’ Extrapolating from the Yunnan study, he argued that between one million and seven million people were getting infected every year by bat viruses.
Youth in the wild
In parallel with the work of the WIV scientists, another Wuhan laboratory also got into bat virus hunting. At the Wuhan Center for Disease Control and Prevention, a laboratory less than three hundred metres from the Huanan seafood market, Dr Tian Junhua, an expert on pathogens carried by ticks and mosquitoes, began sampling bats in Hubei province. According to a profile in the Yangtze River Commercial Daily in 2017, Dr Tian graduated from Huazhong Agricultural University, majoring in plant protection in 2004, before joining the Department of Disinfection and Vector Control of the Wuhan CDC. He started work on cockroaches but later shifted to a bat sampling project. By 2019, he was managing director of the division for vector biology at the Wuhan CDC (in this case, vectors refer to disease-carrying insects).
In December that year, the China Association for Science and Technology released a video, unwittingly coinciding with early cases of Covid-19, as part of a series celebrating young scientists. Called ‘Youth in the Wild: Invisible Defender’, it is a slickly produced seven-minute film about the work of Dr Tian. He recounted his experiences in exploring caves in search of bats, often with his wife and colleague, saying that ‘the caves frequented by bats became our main battlefields’, and adding ‘bats usually live in caves humans can hardly reach. Only in these places can we find the most ideal virus vector samples.’
In the video Dr Tian said he had visited every corner of Hubei province over the past decade and had explored dozens of caves to study more than three hundred types of viruses. In the process, he claimed to have trapped nearly ten thousand bats. Dr Tian is a co-author with Dr Zhang Yongzhen in Shanghai on the Nature paper reporting the first genome sequence of SARS-CoV-2, in which Dr Tian is reported to have ‘performed the epidemiological investigation and sample collection’. Although his laboratory did not itself carry out genomic sequencing, there is no doubt that bat samples were brought to the Wuhan CDC. The withdrawn paper (speculating on possible lab origins of Covid-19) by two Wuhan scientists, Dr Botao Xiao and Lei Xiao, pointed out that a 2013 publication by the Wuhan CDC had described surgeries on bats to obtain tissue and organ samples for downstream pathogen detection.
Dr Tian’s extensive and diligent work apparently did not turn up SARS-like sequences in Hubei, of which Wuhan is the capital. No SARS-like virus utilising the ACE2 receptor has been found in the central province despite the thousands of bats that have been sampled there over the past decade. In fact, in 2019, when Dr Shi Zhengli and Dr Ben Hu, alongside other WIV scientists, published a paper reviewing their years of bat virus sampling across China, they stated that the 2003 human SARS virus may have originated from southern China, and that SARS-like viruses ‘clustered according to their geographical location of sampling, indicating that geographical range overlap between hosts is likely to play an important role in shaping the evolution of these viruses’. In other words, geography limits the overlap of viruses that encourages the diversification of SARS-like viruses. China is after all a very large country, with regions sometimes separated by expansive mountain ranges. Bats can travel long distances, but unlike birds they rarely undertake long seasonal migrations, preferring instead to hibernate during winter in colder climates. In July 2020, Dr Shi told Science magazine that her group had ‘done bat virus surveillance in Hubei Province for many years, but have not found that bats in Wuhan or even the wider Hubei Province carry any coronaviruses that are closely related to SARS-CoV-2. I don’t think the spillover from bats to humans occurred in Wuhan or in Hubei Province.’
For all of the WIV’s hard work in collecting SARS-like viruses from bats in Yunnan, none yet found could be the immediate ancestor of the 2002–3 SARS virus. In 2015, the researchers got a step closer, finding and isolating a virus they named WIV16 in the Shitou cave that was the closest match yet (96 per cent identical) to SARS in humans and civets. But, strangely, in one gene, ORF8, it was not the closest relative of SARS. It began to look as if the 2003 SARS virus was derived from ‘a complicated recombination and genetic evolution among different bat SL-CoVs’, as the WIV scientists put it.
The two Wuhan labs were not the only ones to sample horseshoe bats for coronaviruses in the 2010s, although they were by far the most active. From 2012 to 2015, a study led by Dr Zhang Yongzhen sampled 1,067 bats from twenty-one species at five sites throughout China, finding SARS-like coronaviruses in five species of horseshoe bat, with the most SARS-like ones being found in Guizhou, the province between Guangxi and Yunnan.
In eastern China, near the city of Zhoushan, in the province of Zhejiang, a team of biologists from the Third Military Medical University in Chongqing and the Research Institute for Medicine of Nanjing Command visited a mountain cave on four occasions between July 2015 and February 2017, catching 334 Chinese rufous horseshoe (R. sinicus) bats, a quarter of which tested positive for coronaviruses. They sequenced two SARS-like viruses, named ZXC21 and ZC45, which proved to be not very closely related to SARS, but would later prove to be more closely related to SARS-CoV-2. Indeed, with the exception of the 4991 fragment from Mojiang, these were the first SARS-CoV-2-like viruses published in the scientific literature before the emergence of Covid-19.
In the laboratory, they managed to isolate one of these SARS-like viruses, ZC45, by injecting fluids from virus-infected ground-up bat intestines into the brains of suckling rats. This demonstrated that such viruses were capable of infecting other mammals. Furthermore, despite the route by which the virus had been introduced into the bodies of the suckling rats, the highest viral loads were later found in the lungs rather than the brain or other organs. The same team had already shown that least horseshoe bats, Rhinolophus pusillus, and greater horseshoe bats, R. ferrumequinum, captured in buildings in south-east China, also sometimes carried SARS-like coronaviruses.
In a 2017 interview with Xinhua News Agency, Dr Tian of the Wuhan CDC recounted how he once forgot to wear protective clothing and ‘bat urine dripped from the top of his head like raindrops’. He returned home, took the initiative to isolate himself from his wife and children and quarantined himself ‘for half a month’. On several occasions he was spattered with bat blood on his skin while trapping the bats. Dr Tian’s account shows that, for all their precautions, virus-hunting scientists do run a risk of becoming a patient zero of a new epidemic. Photographs and accounts of people involved in the WIV-EcoHealth Alliance expeditions catching and handling bats without wearing full protective clothing have popped up online. In a Chinese television film of 2017 to showcase the work of Dr Shi in caves in Yunnan and labs in Wuhan, members of her team are shown handling bats with their bare hands, collecting bat faeces in caves while wearing shorts and short-sleeved shirts, working among flying bats without face coverings, and handling the animals indoors while not wearing masks. One researcher, Cui Jie, describes being bitten by a bat’s fangs through his gloves – it was ‘like being jabbed with a needle’.
In his book Spillover, David Quammen describes squirming deep into a narrow cave near Guilin in Guangdong province with Aleksei Chmura, Guangjian Zhu and Yang Jian, as part of an EcoHealth Alliance bat virus survey to catch bats in mist nets. ‘At this moment I became conscious of a dreary human concern: Though we were searching for SARS-like coronavirus in these animals, and sharing their air in a closely confined space, none of us was wearing a mask. Not even a surgical mask, let alone an N95. Um, why is that? I asked Aleksei. “I guess it’s like not wearing a seat belt,” he said.’
Tourists and cavers visit caves all over the world, wearing no special protective clothing, so it is harsh to pick on scientists for sometimes doing the same. At least scientists are aware of the risks and do often take precautions. But then they also run extra risks by catching and handling bats. The possibility that one of these researchers caught an infection from a bat, possibly mild and barely noticed, is not high, but nor is it zero. Dr Shi’s group at the WIV has handled several thousands of bats in less than a decade, throughout the caves and mines of southern China, deliberately going to known virus hotspots and harvesting viruses from the bats in them before taking them back to a large city. Dr Tian from the Wuhan Center for Disease Control and Prevention, across town, has handled nearly ten thousand bats.
Bats in the lab
Did the WIV ever keep bats in the laboratory in Wuhan? In April 2020, Dr Peter Daszak was clear that the answer was no: ‘The researchers don’t keep the bats, nor do they kill them. All bats are released back to their cave site after sampling. It’s a conservation measure and is much safer in terms of disease spread than killing them or trying to keep them in a lab.’ In December he repeated the claim: ‘This piece describes work I’m the lead on and labs I’ve collaborated w/ for 15 years. They DO NOT have live or dead bats in them.’
Yet in 2009 a colleague of Dr Shi’s gave an interview to Science Times and said: ‘The research team captured a few bats from the wild to be used as experimental animals. They need to be fed every day. This Spring Festival, the students went home for a holiday, and Dr Shi quietly took on the task of raising bats.’ And, as open-source intelligence analyst Charles Small discovered, in 2018, the WIV lodged a patent application for a new design of bat cages, including details of how the bats would be fed and encouraged to breed. The animals, it said, are ‘captured as needed, and . . . freed after taking [the] required sample or are temporarily raised [for] a period of time’. The patent was granted in January 2019. Of course, it is possible that the cages might have been used by the WIV not in Wuhan but at a site nearer to the caves where bats were captured. Yet it is worth noting that, by November 2019, the WIV had filed another eyebrow-raising patent for a device to quickly bind and disinfect finger wounds.
In June 2021, Billy Bostickson and a fellow Drastic member named Jesse found a video produced by the Chinese Academy of Sciences in 2018 to mark the inauguration of the highest-security laboratory at the WIV. Among other revelations, the video clearly showed a brief clip of bats clinging to wire mesh in a metal container not unlike those shown in the patent. Every indication from the context is that this is in the laboratory in Wuhan. A researcher is then shown feeding a mealworm to a bat, clearly inside a laboratory. In October 2020, the WIV had filed a patent on bat breeding, describing the capture of fifty bats for domestication purposes. When questioned about allegations that the WIV might have ‘bat rooms’, Dr Daszak replied on Twitter: ‘We didn’t ask them if they had bats. I wouldn’t be surprised if, like many other virology labs, they were trying to set up a bat colony. I know it’s happening in labs here and in other countries.’
The Global Virome Project
In September 2019, Predict came to an end after two budget cycles costing $207 million. Having collected more than 140,000 animal samples, identified 1,000 new viruses, trained 5,000 people in virus surveillance across thirty African and Asian countries, and funded sixty laboratories worldwide, the project’s supporters were dismayed. The head of the Emerging Pandemic Threats programme, Dennis Carroll, blamed the decision on the ‘ascension of risk-averse bureaucrats’. But much of the work continued under new headings, with the US Department of Defense funding some. Also, in 2018, an even more ambitious global project called the Global Virome Project (GVP) had been launched, an international effort to identify all of earth’s viruses with epidemic potential within a decade. ‘Predict showed us that we are ready to do this on a much larger scale,’ Dr Jonna Mazet, implementation director of the GVP leadership board, told an interviewer in March that year. The aim was to catalogue viruses, sequence their genomes and detail their characteristics so that humanity could be one step ahead: ‘We have to stop chasing the last virus that just attacked our community, and instead get prepared in advance,’ said Dr Mazet.
China was to play a leading role in the GVP. ‘China will help lead a project to identify unknown viruses from wildlife to better prepare humans for major epidemics – if not global pandemics,’ Dr George Gao of the Chinese CDC told the Lancet in 2019. Dr Daszak told the Guardian that under the GVP, ‘we are about to start initial work in China and Thailand by studying bats, rodents, primates and water birds there’. China’s national chapter of this project, called the China National Global Virome Initiative, was duly launched but has not yet reported on its progress.
The GVP received sharp criticism from fellow scientists. Three prominent virologists, Drs Edward Holmes, Andrew Rambaut and Kristian Andersen, published an article in Nature in mid-2018 in which they expressed strong doubts about whether the approach of virus hunting would achieve foreknowledge: ‘Advocates of prediction also argue that it will be possible to anticipate how likely a virus is to emerge in people on the basis of its sequence, and by using knowledge of how it interacts with cells (obtained, for instance, by studying the virus in human cell cultures). This is misguided.’ They argued that no matter how many viruses were found, predicting which one out of the estimated 1.6 million animal viruses – a number derived by extrapolating from the prevalence of viruses known in animals – might jump into people would remain impractical. ‘We urge those working on infectious disease to focus funds and efforts on a much simpler and more cost-effective way to mitigate outbreaks – proactive, real-time surveillance of human populations.’
Dr Daszak was undeterred. On 21 October 2018, after he spoke at a conference about more than four years of productive collaboration with Dr Shi, he could be forgiven a moment of pride. The species of bat that carried the progenitor virus of SARS had been identified, so had the region of China where the virus came from, and so had the mechanism by which it had probably evolved through recombination within a population of similar viruses co-infecting bats. The origin of the SADS coronavirus that afflicted pigs had also been quickly tracked down. As he reflected on the effort expended and the detective work done in reaching a persuasive conclusion, he tweeted about the success of their partnership: ‘5,370 bats sampled and released, 2 papers in Nature, one in Cell, 15 others published and more on the way.’ By late 2019, the WIV’s records reflected similarly huge numbers of samples – in total, descriptions of more than 22,000 samples and specimens stored on a database, at least 15,000 of them relating to bats.
Equally impressive was the laboratory work downstream of the virus hunting to sequence genomes, synthesise viruses, manipulate their genomes and test their virulence. A year after his conference speech, around the time the pandemic was starting in Wuhan, on 21 November 2019, Dr Daszak had an exchange on Twitter with the virologist Dr Andrew Rambaut who again voiced the concern widely shared among scientists that all this monitoring of bats in caves might not have improved our ability to prevent pandemics. ‘The more we look the more new viruses we find,’ wrote Dr Rambaut. ‘The problem is that we have no way of knowing which may be important or which may emerge. There is basically nothing we can do with that information to prevent or mitigate epidemics.’ Dr Daszak shot back: ‘Not true – we’ve made great progress with bat SARS-related CoVs, ID’ing >50 novel strains, sequencing spike protein genes, ID’ing ones that bind to human cells, using recombinant viruses/humanised mice to see SARS-like signs, and showing some don’t respond to [antibodies], vaccines . . .’ Adding that ‘it’s proof-of-concept in a v. important viral family with pandemic potential’.
By July 2020, Dr Daszak had told the Economist that approximately sixteen thousand bats had been sampled and around a hundred new SARS-like viruses discovered.