Hunting for Ebola among the bats of the Congo

It's a new moon, and the jungle is as dark as the deep sea. Four men sit on plastic chairs, waiting. Despite the heat, they wear long-sleeved shirts, gloves, and respirators. Above them in the darkness, a huge net hangs unseen between the trees. They are fishermen of the sky, awaiting their prey.

The men are listening for the short, hoarse barking of the hammer-headed fruit bat. Every night, dozens of males of that species congregate in this patch of rainforest in the northern part of the Republic of the Congo, vying for females with their calls. With a wingspan of up to 1 meter, they are Africa's biggest bats. And they could be the answer to one of virology's dark mysteries: Where does the deadly Ebola virus lurk?

The question has obsessed researchers for more than 40 years. In 1976, the virus emerged suddenly from the jungle a few hundred kilometers northwest of here close to the Ebola River. The then-unknown pathogen tore through a small mission hospital in Yambuku, in what is now the Democratic Republic of the Congo (DRC), and surrounding villages. Victims suffered at first from sore throat, fever, headache, and abdominal pain. Then they began bleeding from the eyes, nose, and other orifices. They died within days. The virus infected 318 people, killing 90% of those before vanishing.

Since then, the virus—now named for the river where it appeared—has re-emerged unpredictably, mostly in Central Africa but sometimes farther afield, causing small but deadly outbreaks in a village or two. Then, in late 2013, Ebola surfaced in Guinea and spread to the densely packed capital, Conakry. The epidemic quickly engulfed neighboring Liberia and Sierra Leone. More than 11,000 people died in the three West African countries, in the largest recorded outbreak.

Researchers have learned a lot about Ebola. Under tight security in biosafety labs around the world, scientists have characterized the virus's proteins and sequenced its genome. They have collected blood samples and clinical data from hundreds of patients. During the West African outbreak, researchers tested several drugs, none of which worked well, and a vaccine, which did. But the virus's natural history is a mystery, says virologist Vincent Munster, sitting outside his tent in the darkening jungle. "We know everything about its replication cycle but fricking nothing about where it comes from and how it causes outbreaks."

At a rainforest camp, a team of researchers works deep into the night to snare and sample fruit bats.

K. KUPFERSCHMIDT/SCIENCE

Ebola is a zoonosis—an animal disease that can jump to humans. The virus kills several species, including antelopes, chimpanzees, and gorillas. But some other animal must be able to host the virus without dying from it, and bats are the chief suspect. Scientists have traced Marburg virus, Ebola's close cousin, to bats and found antibodies to the Ebola virus in several bat species—evidence of past infection. But no one has isolated live virus from bats, and no one knows how Ebola might jump from bats to other mammals, including people—or why that fateful leap is so unpredictable in time and geography.

Munster, 44, usually works a continent away in a high-security lab run by the National Institute of Allergy and Infectious Diseases in Hamilton, Montana, where he studies Ebola and other dangerous pathogens. Earlier in his career, at the Erasmus Medical Center in Rotterdam, the Netherlands, Munster took part in the controversial "gain of function" experiments that engineered the lethal H5N1 bird flu virus to spread more readily among mammals—including, presumably, people. These days, however, Munster talks less about viral genes and proteins than about virus ecology: the web of interactions that allows a zoonotic virus to travel between species. Logging, hunting, and other human encroachment on pristine environments all play a role, bringing people into contact with the microbes that lurk there. Once a new infectious agent jumps to humans, Munster says, the forces of globalization, urbanization, and mobility can spread it faster than ever.

That's why Munster has come to catch bats in this piece of Congo jungle. More than half of all outbreaks of Ebola Zaire, the deadliest variety of Ebola virus, have occurred here or in the neighboring DRC. "This is the biggest Ebola hot spot in the world," Munster says. In fact, on 11 May, the DRC's Ministry of Health notified the World Health Organization of a new outbreak of the virus in that country, with 37 suspected cases in seven villages so far, and several deaths. Munster is planning to travel to the area to help investigate the outbreak's origin.

To be sure, other researchers have looked for Ebola in the forest here, sampling many animals in multiple locations. Munster, however, has returned to the same spot again and again—eight times in 6 years—to sample the same bat species. This time, he and his colleagues plan to catch about 100 bats in 2 weeks. He hopes to do more than just find active Ebola virus. By comparing results over time, he hopes to see an emerging pattern that might explain when the animals are most likely to carry and transmit the virus.

Dangerous crossings

The Ebola virus infects multiple mammal species but kills most of them. Bats are thought to be its reservoir, where it waits harmlessly until conditions favor its emergence. Researchers are tracing the paths along which it might then spread

Contact with feces of infected animal Ingest fruit partially eaten by infected animal Contact with living infected entity Meat of infected animal consumed Contact with infected medical equipment Contact with dead infected body Modes of transmission Confirmed pathways Intraspecies transmission Unknown host? ?
V. ALTOUNIAN/SCIENCE

Suddenly, a slight fluttering in the darkness. "Light!" someone yells, and the men's headlamps flare up and pan like search-lights across the huge net, 9 meters by 18 meters. High up, a fruit bat is trapped. The men lower the net, and Alain Ondzie, a Congolese veterinarian working for the Wildlife Conservation Society (WCS), approaches the trapped animal. Ondzie is a large man with calm, slow movements. While the bat screams and thrashes, Ondzie grips the animal, frees it from the net, and puts it in a gray bag. Another man carries the bag a few hundred meters and ties it to a rope strung between two trees. As the night goes on, the rope fills with bagged bats. Occasionally one of the animals twitches, setting off a macabre dance of thrashing bags, like a laundry line of nightmares. The Ebola virus might be hiding in one of them.

Munster's team hopes to build on work by Eric Leroy of the International Center for Medical Research in Franceville, Gabon, and his team. In 2002 and 2003, in Gabon and the Republic of the Congo, they captured and screened more than 1000 bats, birds, and rodents for traces of Ebola. They found antibodies and viral RNA fragments in three species of bats, including hammer-headed fruit bats. But they failed to isolate the virus itself, so other species might be more important in transmitting it. "Despite scattered evidence from years of study, we're still searching for the ‘smoking gun’ that identifies the most important reservoir host species of Ebola," says Kevin Olival, a researcher at the EcoHealth Alliance in New York City.

If bats are the reservoir, many questions remain. Why is the virus so hard to find? Do the animals get infected young and carry the virus for only a short time, in the bat equivalent of childhood measles? Or is it simply a rare infection afflicting only a few animals? If so, which ones are at risk, and when are they most likely to be full of the virus? "If you really want to understand emergence of these viruses, how they transmit, and what species are involved, you need to do longitudinal sampling," Olival says. That means coming back again and again to catch bats.

At 2 a.m., Munster and epidemiologist Sarah Olson start their workday. Her job begins where Ondzie's ends. She's clad in scrubs and a protective suit and wears a visor, a respirator, and leather gloves on top of two layers of plastic gloves. She unties a bag and carries it to a tent serving as a makeshift laboratory. Munster, similarly clad minus the leather gloves, is waiting. A bare bulb illuminates the tent, an island of light in the dark forest, powered by a loud generator. The back wall is made of banana leaves.

Grasping the bat's head between her thumb and index finger, Olson exposes its lower body. Munster massages its bladder until urine dribbles into a plastic vial. Then Olson unpacks the whole animal, and Munster examines and measures it while another researcher takes notes. "Hypsignathus monstrosus," Munster says, though the only thing monstrous about the hammer-headed fruit bat is its scientific name. The huge head with its big, yellow eyes, cleft chin, and curled lower lip evokes pity rather than fear. "Endearingly ugly," Olson calls it.

As night goes on, the makeshift lab fills with urine and blood samples from hammer-headed fruit bats. Researchers are garbed and masked for protection against what they hope to find: live Ebola virus. Change in viral levels over time might reveal when and how the bats infect other mammals—and ultimately humans.

K. KUPFERSCHMIDT/SCIENCE

Olson, like Ondzie, works for WCS, where she studies how Ebola affects chimpanzees and gorillas. How the virus might travel from bats to primates is anyone's guess. But it is as dangerous to those primates as it is to humans, if not more so, which is why WCS is a partner in Munster's quest. "Ebola is the biggest threat to gorillas apart from poaching," primatologist Emma Stokes of WCS said a few days earlier at the WCS office in Brazzaville. By some estimates, Ebola killed about half the gorillas in the Republic of the Congo between 2005 and 2012. That's a huge blow to the species because some 60% of the world's gorillas live in the northern part of the country, where the team is working.

The gorillas and other primates, in turn, pose a threat to humans, who often contract the virus by handling the dead animals or eating bushmeat. That's why another part of Ondzie's job is to visit local communities to urge people not to touch dead animals in the forest but instead to call WCS.

Just 2 days earlier, such a call alerted the team to a chimpanzee carcass in the forest. It was covered in maggots, Munster says—"just a huge, pulsating mess." Ebola may be scarce in living animals, but carcasses like that one practically explode with virus. "We've done those studies," Munster says. "Every cell, every orifice of that carcass is loaded with Ebola." To minimize the risk to researchers, Munster helped develop a protocol for collecting samples from dead animals: swabbing the outside instead of using sharp instruments to collect blood or tissue.

The first bat examined tonight is alive and apparently well. "Good body condition," Munster says. "Head length, 42 millimeters. Body, 97. Lower arm, 95." He swabs the mouth, nostrils, and anus. Suddenly the animal flinches, and a claw scrapes across Munster's plastic glove. Even though no tear is visible, he discards his outer gloves and dons a new pair.

Then comes the most dangerous part: While Olson holds the animal, Munster plunges a needle into a vein in the wing and slowly draws blood. "You have to be extremely careful," he says. "We're talking about Ebola, after all."

Before Munster lets the sampled bat go, he injects it with a tiny ID chip. This allows the researchers to identify animals that they have recaptured.

K. KUPFERSCHMIDT/SCIENCE

Munster knows how to handle deadly viruses. He was in Monrovia during the 2013–15 Ebola outbreak, testing hundreds of samples. Far too many were positive for the virus. "We underestimated the virus," he says. He is determined not to make that mistake again. The Republic of the Congo is changing rapidly. The researchers' tents are perhaps 100 meters from a road that transects the country, stretching 800 kilometers south to Brazzaville. When Munster first came here a few years ago, the road was red dirt. Now, it's smooth asphalt. If the virus emerges from the forest again, it could be in Brazzaville tomorrow, he says—and in Boston, Bombay, or Berlin the day after.

One by one, the team examines the 13 animals and releases them. At about 5 a.m., the cries of the hammer-headed fruit bats subside. The last bag is opened, and the researchers swab the last animal. They store the night's crop of samples in liquid nitrogen. Because shipping material that might contain the Ebola virus is a bureaucratic nightmare, the samples might not arrive in the United States for months.

Once the samples arrive, they will be split, with one part tested for Ebola RNA in Munster's Montana laboratory. If it proves positive, the researchers will mix another portion of the sample with cultured bat and monkey cells to test for active virus. "You just add a bit from that sample to your cells and wait [to see] whether you get virus replication," Munster says. If enough samples test positive, his team might be able to build a model of how virus levels fluctuate in the bat population. That kind of monitoring helped scientists understand the factors that trigger flu viruses to jump from animals to humans—and it may one day lead to a similar understanding for Ebola.

But that is the future. Now, it's time for an early breakfast and a bit of sleep. With the sampling done, Olson hangs the last fruit bat upside-down from a rope. The animal hesitates for a few seconds, as if deciding whether to share one last secret with the researchers. Then it spreads its wings and flies into the jungle, where dawn is breaking.