Lurking in the Shadows

Bats harbor diverse pathogens, including Ebola, Marburg, SARS, and MERS viruses. Understanding why could help researchers stymie deadly emerging diseases.

Bob Grant
Bob Grant
Dec 1, 2014


In a dusty, subterranean room beneath a crumbling sand building a few miles north of Naqi, Saudi Arabia, EcoHealth Alliance veterinary epidemiologist Jon Epstein finally found what he was looking for: bats. It was early October 2012; he’d travelled to the country with a team of scientists at the request of the Saudi Ministry of Health. A researcher in Jedda had isolated RNA from a strange virus found in the mucus coughed up by a 60-year-old Saudi businessman who’d recently suffered acute pneumonia and renal failure. The man, whose main place of business was located in Naqi, died 11 days after being admitted into the hospital in mid-June.

Epstein and Columbia University epidemiologist Ian Lipkin had been scouring the man’s homes and businesses around the desert town of Bishah in search of the source of the deadly virus. They were intent on sampling bats because a...

So when Epstein and Lipkin were summoned to Saudi Arabia to hunt down the new coronavirus, which would become known as the Middle East respiratory syndrome coronavirus (MERS-CoV), the obvious place to look for the emerging threat was in bats. “Our main goal was to meet with [the] ministry of health, go out to the homes of the patient, and see if he had contact with animals,” says Epstein. “Those are moments when there’s an urgency to understand where diseases are coming from.”

In the forgotten basement of the sand building, the researchers found a colony of 400 to 500 lesser mouse-tailed bats (Rhinopoma hardwickii). “That was our first breakthrough moment,” Epstein recalls. The researchers captured about 60 bats, took blood and urine samples, fecal pellets, and throat swabs, then released the animals unharmed.

I’m confident that MERS does originate in bats. It really appears that this family of viruses has bats as their natural reservoir.—Jon Epstein, EcoHealth Alliance

Buoyed by their discovery of roosting bats in the area, the researchers turned their sights on Bishah, where they found more bat colonies in the town’s abandoned buildings. They returned in April 2013 to collect more evidence, and after catching and working up more than a thousand bats from seven different species, they found a viral RNA fragment in a fecal sample from an Egyptian tomb bat (Taphozous perforatus) that matched the MERS-CoV sequence isolated from the man who had died of the disease months earlier.2 Although the bat sample yielded only a short stretch of RNA, and scientists are still seeking confirmation with a longer sequence, Epstein says that the initial discovery was important in establishing bats’ role in the MERS epidemic. “I consider this a really strong clue,” he says. “I’m confident that [MERS] does originate in bats. It really appears that this family of viruses has bats as their natural reservoir.” It is not yet clear if bats are directly transmitting MERS to humans or if they play some more nuanced role in the cycle of infection—for example, through interactions with camels, which are also suspected to carry the MERS virus—but Epstein and others are gathering evidence to resolve the picture.

Healthy cauldrons of disease

Mexican free-tailed bats (Tadarida brasiliensis)© POELKING, F./CORBISMERS, with a fatality rate of around 65 percent, is only one of the deadly diseases that bats have been blamed for transmitting to humans. Researchers have confirmed that the Marburg virus, which causes the particularly gruesome Marburg hemorrhagic fever that killed about 125 people in the Democratic Republic of Congo between 1998 and 2000, resides in the widely distributed African fruit bat (Rousettus aegyptiacus), which likely spread the disease to miners working in the country.3,4 Ebola, which has infected more than 10,000 and killed nearly 5,000 people during the current outbreak in West Africa, may also have its roots in bats. Amazingly, in most cases, the bats themselves don’t seem to get sick from Ebola, which kills from 25 percent to 90 percent of its human victims, depending on viral strain and treatment availability.

Lesser mouse-tailed bat (Rhinopoma hardwickii) © B.G. THOMSON/SCIENCE SOURCESo, while epidemiologists and health-care workers scramble to help communities being ravaged by emerging disease in the Middle East and Africa, researchers around the world are studying bats’ unique ability to harbor viruses—especially zoonotic viruses that readily cross species boundaries to infect other animals, including humans. Some attribute the high viral diversity associated with bats to the animals’ unique behavior and ecology. And at least one scientist holds that the secret to bats’ virus-hosting capacity lies deep within their cellular machinery.

Recently, Epstein and collaborators, working in Bangladesh, uncovered dozens of viruses that were previously unknown to science circulating in Indian flying foxes (Pteropus giganteus), a bat species known to carry the deadly zoonotic Nipah virus, a member of the paramyxovirus family.5 And Colleen Webb, an evolutionary ecologist at Colorado State University, determined with collaborators that bats harbor more zoonotic viruses per species than rodents, which carry nasty bugs such as hantavirus and lymphocytic choriomeningitis virus.' “That’s really the first paper that provides some quantitative evidence that bats are special,” Webb says.

Even to the casual observer, bats are distinctive animals. They are the only mammals that are capable of sustained flight; some species possess bizarre facial features to aid in the echolocation they use for hunting and navigation; and they often live in massive colonies comprising hundreds of thousands of individuals.

A closer look at bat biology and ecology reveals other traits that set the animals apart. To fuel their daily flight and long migrations, bats have extremely high metabolic rates, which make their bodies frequently mimic a fever-like state. And bats have remarkably long life spans for their body size, giving them plenty of time to be exposed to environmental pathogens. They also roost in large groups that often contain multiple species in tight quarters, setting the stage for pathogen transmission to occur readily and often. “We know that there are these ecological traits that they have that make them theoretically very good at being pathogen reservoirs and spreading diseases,” says Clif McKee, a Colorado State University grad student who studies bacterial pathogens harbored by bats.

Bats’ long evolutionary history may also be at play. Having evolved sometime between 100 million and 66 million years ago, when fearsome dinosaurs ruled the land and pterosaurs patrolled the skies, bats have been battling viral infection and transmission for millennia. “What we’re finding is that bats have had a relatively long-term association with these viruses,” says Epstein. “They come to an understanding over time.” In other words, viruses may have become less threatening but ever-present and easily transmissible commensals of bats.

There’s still a staggering amount of things that we don’t know about bats.—Paul Cryan, US Geological Survey

Answering questions about bat-virus interactions is challenging because bats are extremely difficult research subjects. (See “Experiments on the Wing,” here.) The flying mammals are notoriously hard to keep in captivity, and scientists know surprisingly little about their biology. “Bats are mysterious, and it’s an extremely diverse group of wild animals,” says Paul Cryan, a US Geological Survey bat ecologist who has collaborated with Webb on several bat studies. “There’s still a staggering amount of things that we don’t know about bats.” Given that these animals carry pathogens that have collectively killed thousands of people, that’s a scary thought.

“It wasn’t until very recently that a lot of the interest in viral disease in bats sprung up,” adds Cryan. “The floodgates are now open.”

Learning to fly

Indian flying foxes (Pteropus giganteus)© FLETCHER & BAYLIS/SCIENCE SOURCEThe most obvious distinction between bats and other mammals—flight—may hold clues to why bats are so adept at ferrying dangerous pathogens. Evolving the ability to propel their bodies through the air, it seems, has had a strong impact on bat physiology and immunity.

“Flight is very much like fever,” says Tom O’Shea, a US Geological Survey bat biologist in Fort Collins, Colorado. The body temperature of a bat is consistently above normal, which “creates a very different environment in the whole body of a bat compared to any other animal.” From the perspective of viruses, this persistent fever state keeps replication at a lower level than occurs in susceptible animals; the virus never overruns the bat’s immune system.

Researchers have also turned up evidence that bats may have less-reactive innate immunity than other mammals. Lin-fa Wang of the Duke–National University of Singapore Graduate Medical School and his collaborators recently sequenced the genomes of two distantly related bats—a fruit bat called the black flying fox (Pteropus alecto) and the insectivorous mouse-eared bat (Myotis davidii)—and found positively selected genes in DNA damage-repair pathways in both species.7 Wang says that this adaptation was likely spurred, in part, by the energetic and metabolic demands of flight, which can cause DNA damage through the release of reactive oxygen, nitrogen, and carbonyl species. Bats also live 3 to 10 times longer than other mammals of a similar size, giving their genes more time to accumulate mutations. “We believe that [bats] are better at DNA repair because that’s required for their ability to live longer and to fly without too much DNA damage,” Wang says. “Flight drove that evolution.”

Chinese horseshoe bat (Rhinolophus sinicus)© MERLIN D. TUTTLE/SCIENCE SOURCEIn the past decade, scientists have uncovered how such changes in their DNA repair pathways can, in turn, affect bats’ innate immune response, possibly allowing the animals to survive with viruses and other resident pathogens.8 In the two bat species’ genomes, Wang and his team also found positively selected genes in the nuclear factor κB (NF-κB) pathway, which plays roles in transcriptional control, cellular stress responses, and immunity. And the evolutionary timing of these changes, traced using molecular-clock calculations, is telling, says O’Shea. “The genetic adaptations in the innate immune system of bats seem to have changed at about the same time that bats evolved flight.”

Murky territory

Colorized transmission electron micrograph of the Middle East respiratory syndrome coronavirus (MERS-CoV)© SCIENCE SOURCEThere are some researchers who are not yet convinced that bats are special with regard to their relationships with zoonotic viruses and other pathogens. “I think the jury is still out on that,” says Peter Daszak, a disease ecologist and president of EcoHealth Alliance, a nonprofit research consortium and conservation group that aims to protect wildlife while safeguarding humans from the emergence of zoonotic disease.

Daszak maintains that while science may show that bats have unique traits that increase their capacity to harbor pathogens, the real reason why bat viruses seem to be spilling over into human populations with increasing regularity is the relationship and proximity between bats and people. “It’s only now, when we’re really starting to encroach in tropical areas, that we’re really coming into contact with bats,” he says. “One possible scenario might be that bats are no more special at harboring viruses than are rodents, but we’ve already come into contact with all the rodent viruses.”

“When we hassle bats or encroach on their habitats, disease is more likely to spill over to us,” Cryan agrees. He adds that there is a danger in broadly painting bats as pathogen ferries on the wing. Despite all the bad press, bats do, after all, provide a multitude of ecosystem services, from pollination and seed dispersal to insect control and plant fertilizer (bats produce scads of nutrient-rich guano), and they constitute an important source of dietary protein in many cultures around the world.9 Many bat researchers are mindful of the possibility that increased interest in the relationship between viruses and bats could translate into vigilantism against what might be perceived as dangerous animals.

“These are wild animals, and just because they might somehow deal with disease in a special way doesn’t mean they’re bad or evil,” says Cryan. “Bats seem to be able to live with viruses that we consider to be extremely lethal to humans. The advances to human medicine [from studying bats] could be huge, yet those will never happen if the knee-jerk reaction of ‘Kill them all’ manages to prevail.” 

Correction (December 2): Jon Epstein's affiliation was incorrect in the original version of this story. It has been corrected to reflect the fact that he is a veterinary epidemiologist at EcoHealth Alliance. The Scientist regrets the error.

Clarification (December 4): The original version of this story may have given the impression that MERS is transmitted to humans by bats. In fact, the route that the virus has taken to infect humans is not yet clear to researchers, who have gathered substantial evidence that camels in the Middle East also harbor the pathogen that causes MERS. The story has been changed slightly in an attempt to convey this. The Scientist regrets any confusion on this point.



  1. X.Y. Ge et al., “Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor,” Nature, 503:535-38, 2013.
  2. Z.A. Memish et al., “Middle East respiratory syndrome coronavirus in bats, Saudi Arabia,” Emerg Infect Dis, 19:1819-23, 2013.
  3. D.G. Bausch et al., “Marburg hemorrhagic fever associated with multiple genetic lineages of virus,” N Engl J Med, 355:909-19, 2006.
  4. J.S. Towner et al., “Isolation of genetically diverse Marburg viruses from Egyptian fruit bats,” PLOS Pathog, 5:e1000536, 2009.
  5. S.J. Anthony et al., “A strategy to estimate unknown viral diversity in mammals,” M Bio, 4:e00598-13, 2013.
  6. A.D. Luis et al., “A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special?” Proc Biol Sci, 280:20122753, 2013.
  7. G. Zhang et al., “Comparative analysis of bat genomes provides insight into the evolution of flight and immunity,” Science, 339:456-60, 2013.
  8. G. Chatzinikolaou et al., “DNA damage and innate immunity: links and trade-offs,” Trends in Immunology, 35:429-35, 2014.
  9. T.H. Kunz et al., “Ecosystem services provided by bats,” Ann NY Acad Sci, 1223:1-38, 2011.


• Flight: Likely in response to the metabolic demands of flight, bats have evolved heightened DNA damage-repair pathways and a high body temperature that mimics a fever state, imparting higher resistance to pathogens.

• Long-lived: With life spans that are 3 to 10 times longer than other mammals of similar size, bats may encounter more pathogens throughout their lives.

• Hibernation: The aggregation of many different bat species in hibernacula during colder months can facilitate the spread of pathogens.

• Colonial: Even during their waking months, some bat species live in remarkably large groups, again facilitating pathogen transmission.

• Evolutionary history: Bats evolved between 100 million and 66 million years ago. They may have established a truce with many bacteria and viruses over the millennia.


Fruit bats roosting in Kumasi, GhanaCOURTESY OF DAVE HAYMANA scientist striving to know more about a virus or bacterium isolated from bats would likely rely on the traditional methodology of injecting the pathogen into rodent models in the lab to study its pathophysiology and the host’s immune response. But bats appear to have anything but traditional immune systems, putting investigators studying emerging tropical diseases at a disadvantage. “Lab virologists typically don’t have access to the natural host,” says University of Cambridge infectious disease epidemiologist James Wood.

To gain real insights into both the pathogens that infect bats and how the flying mammals cope with such infections, researchers must study—you guessed it—bats. But studying wild bats presents its own challenges: bats tend to live in such massive colonies, and their ranges tend to be so large, that recapturing a particular bat—to check on the persistence of a virus, for example—is virtually impossible.

That’s why, in 2009, Wood and his then–PhD student Dave Hayman decided to start raising a captive colony of bats in Ghana. Along with collaborators, the researchers captured a dozen straw-colored fruit bats (Eidolon helvum), a species widely distributed throughout sub-Saharan Africa. (See photograph at left.) After succeeding in keeping the animals alive for about six months in a roughly 6,000-cubic-meter, double-roofed aviary on the outskirts of Ghana’s capital city, Accra, the team added about three dozen more bats to the colony, now a 100-bat-strong, self-sustaining population. “The beauty of establishing a captive colony is that . . . you know that an individual is exposed to the infections in that colony,” says Hayman, now a disease ecologist at Massey University in New Zealand.

The colony, one of only a few around the world, gives Hayman and his colleagues a unique window onto the bat immune system and the coevolution of bats and their pathogens. “[We’re] trying to understand what we see in the wild, which is a constant, high prevalence of infection,” says Hayman. So far, the researchers who study the captive bats in Ghana have focused on pathogens that were present in the animals when they were captured in the wild and pathogens to which the animals carried antibodies at the time of their capture. These include the Lagos bat virus, henipavirus, and bacteria from the genus Bartonella, to name a few. The team has learned, for example, that henipavirus, a genus that contains the deadly Hendra and Nipah viruses, is capable of persisting in the bat population, with antibody titers ebbing and flowing in female bats through cycles of pregnancy and lactation (J Anim Ecol, 83: 415–28, 2014). Yet the bats don’t seem to die from the viruses, which have spilled over to infect humans and horses in Australia.

We’re trying to understand what we see in the wild, which is a constant, high prevalence of infection.—Dave Hay­man,
Massey University

The team has also discovered that young animals born into the captive bat colony harbor henipaviruses. Researchers used to think that henipavirus infections were immunizing, in the way that flu or measles viruses can be in humans, with virus-specific antibodies able to defend against subsequent attack. In such situations, the persistence of the virus within a population can only be achieved through the introduction of new individuals that have not yet been infected. But the pres­ence of the virus in young bats suggests that the adults are continuously harboring low levels of the pathogen in their cells. While the animals are not sick, they can still pass the virus around. “This work has caused us to rethink the mechanisms of persis­tence of that whole family of viruses within populations of bats,” says Wood.

Eventually the researchers would like to house subgroups of bats in separate enclosures, where the team could expose a subgroup to a new pathogen and follow the dynamics of the disease, Wood says. “We have some facilities in which we could do infection experiments or small-scale transmission experiments in bats.”

“The ultimate aim is to do population-level transmission studies,” Hayman adds. Such research can yield the type of understanding that will help scientists go beyond simply cataloging the different emerging zoonotic diseases that are crossing species boundaries to infect humans, and begin to acquire a functional knowledge of the biology and ecology of bats and the myriad pathogens they host.