Searching for the next Ebola in the Congo Basin

KISANGANI, Democratic Republic of Congo — At a crowded stall hidden deep in the the city’s central market, a group of women hover over charred pieces of meat. They call out to the passing shoppers: $4 for an antelope, $6 for the thigh of a bush pig. For $10, you can purchase an entire monkey. Officially, the sale of bush meat is illegal, and when the market chief walks by, the women quickly shove their wares into tattered plastic bags hidden behind the concrete slab tables.

“I sell everything,” says Motumbe Marie Biako, who has been a vendor at this particular stall for the last 10 years. “Usually I have monkey, wild pig, antelope, python. Even bat. But I’m not selling bat today.”

The sale of bush meat, she laments, has slowed. Not because it’s illegal to purchase, but because a constant stream of programming on the local radio station has convinced Biako’s customers that they are better off eating more typical dinner fare, like chicken or beef.

“People are saying, ‘Ebola, Ebola,’” she sighs. “I’m eating it. My family has been eating it for generations. How come I don’t have Ebola?” According to Biako, monkey is the sweetest meat, and if Ebola gets her, it won’t be from eating a primate.

The Congo Basin is the world’s second-largest tropical rain forest, after the Amazon. The forest is also home to more than 270 species of mammals, including endangered gorillas and the elusive forest giraffe, the okapi. It’s a mecca for biodiversity, a giant lung for the earth and an important resource for the 40 million people who live along its borders. But the Congo Basin is also home to millions of viruses, many of which have yet to be identified. And the deeper that people encroach into the forest, the greater the likelihood that those viruses will make the jump to humans from other animals.

Most of the global epidemics the world has faced in the past few decades have originated in forest ecosystems. The Congo Basin alone has been the source of a remarkable number of pandemic threats. AIDS is believed to havecrossed from chimpanzees to humans sometime in the late 1920s in what is now known as the Democratic Republic of Congo. The first cases of Ebola, now believed to have originated from fruit bats, were also recorded in the DRC in 1976. Scientists estimate that 60 percent of emerging infectious diseases come from animals, and the vast majority of those are from wildlife.

“All viruses are dangerous,” explains Dr. Jean-Jacques Muyembe Tamfum, better known as Dr. Ebola for his extensive experience working with the disease. He runs the Institut National de Recherche Biomédicale (INRB), headquartered in the capital, of Kinshasa. “Of the viruses we know, Ebola is the most dangerous. It’s a Level 4 virus. But we don’t know what else is out there.”

According to Tamfum and many other public-health experts, the key to fighting pandemics is early detection. To that end, the United States Agency for International Development (USAID) has just completed a five-year program, its first one for monitoring viruses before they become a threat to people. Known as Predict, the project brings together a consortium of scientists and virus experts to collect samples from the field. Leaders of the project hope to build a global virus library to aid in early detection.

“In the last five years, we have detected over 800 viruses globally,” says Jonna Mazet, the global director of Predict. “Five hundred and forty of these viruses have never been seen before. We don’t know if they are all pathogens, but some of them certainly are.” A pathogen is any infectious agent that can produce illness in its host. It’s often a virus, but can also be bacteria, fungus or other microorganism. Viruses can be particularly problematic pathogens because they are able to mutate quickly and are not easily treated.

Today scientists are exploring the world’s virus hot spots, including the Amazon Basin, the Congo Basin and Southeast Asia in search of these new pathogens. Samples of blood, urine and other bodily fluids are collected from animals that are most likely to come in contact with humans; rats, bats and primates account for the majority of the specimens. “We’re interested in surveillance of viruses that are most likely to be transmitted,” explains Mazet. Transitions occur primarily from eating infected animals or being in contact with their blood or urine. “So for example, we might take a sample rodent urine and feces, because they are likely to be found in the home of a human. But we wouldn’t take a sample of rodent blood, because people don’t eat rodents, by and large.” They also sample primate brains and blood because of contact with hunters and take samples of bush meat from public markets. But “we don’t kill any animals,” she adds. “We work with the sample we can get.”

Gorilla doctors take samples

Dr. Eddy Kambale doesn’t break a sweat as he crests the last hill in a three-hour hike through Virunga National Park. Kambale is the head veterinarian in Congo for Gorilla Doctors, a nonprofit organization that monitors the health and well-being of the world’s last remaining mountain gorillas. Today he is checking up on an injured silverback, the head of the Munyaga family.

“You can see he has a skin flap hanging low from above his eye,” says Kambale, as he snaps some photos. His team has recently treated the injured animal with antibiotics. “We only intervene when absolutely necessary. In this case, we were able to administer antibiotics and painkillers without approaching the animal.”

But sometimes Kambale and his team have to take a more direct role when treating the apes, and it’s during these interventions that samples are collected for virus testing. Gorillas share 95 percent of their genetic code with humans, making it particularly easy for viruses to jump between the two. “We have the gorillas, and we have our gorilla trackers,” Kambale explains, referring to the rangers whose job it is to monitor the creatures and protect them from disease and poachers. “The trackers, they go to see the gorillas. Then they come home. They have goats, chickens and other animals at their homes that they interact with.” According to Kambale, this provides the perfect storm in which diseases can jump. 

Kambale says that the bush meat trade is closely monitoried in Virunga, so there is little opportunity for the human population that lives on the edge of the forest to consume contaminated meat. But this is not the case in the rest of the country. Earlier this year, he was sent to the neighboring WaliKale territory to sample primate meat in the market. Samples from the 43 animals were processed and shipped to Kinshasa for further analysis. In the past, bush meat vendors were reluctant to have their meat sampled, but that's changing. "The Ebola outbreak is making our job easier," says Kambale. "People understand the risk is real, and they don't want to get sick. When we sample, we also educate. People are listening now."

A new virus emerges

The DRC has seen seven Ebola outbreaks in the last 38 years — more than any other country in the world. When Ebola emerged in Ikanamongo village, in Équateur province, medical workers were mobilized to promptly identify the virus.

“Samples were sent to INRB in Kinshasa,” explains Corina Monagin, an emerging-infectious-disease expert. Monagin works with Metabiota, a private company that contracts with governments and health agencies to investigate infectious-disease threats, including the Predict program. Working with the INRB in Kinshasa, the company has created a world-class laboratory to analyze specimens of never-before-seen viruses. “Many of the Congolese experts were already in West Africa,” adds Monagin, “assisting with the outbreak there. Predict stepped up to help with diagnostics.” Several samples collected from sick patients tested positive for Ebola and were subsequently analyzed by the World Health Organization, leading to the official declaration of an Ebola outbreak. The diagnoses triggered a number of protocols that allowed health officials to contain the Ebola outbreak in the Congo quickly.

To discover emerging pathogens, scientists must follow strict protocols designed to keep them safe and to challenge any assumptions they may have about identifying the virus. A pathogen that may initially appear familiar can later reveal itself to be unknown and deadly. This is what happened in 2009, when a new virus was discovered deep in the Congo forest. Three people in the isolated village of Mangala suddenly became ill with what appeared to be hemorrhagic fever. Their temperatures spiked and they started to vomit blood. Two of the patients died within three days.

“We followed our protocols and tested for a Filoviridae virus,” recalls Dr. Damien Joly, referring to the family of viruses that Ebola is classified under. Joly is the director of epidemiology and information management at Metabiota and develops databases that contain the genetic sequences for all the emerging viruses scientists are discovering. “The samples kept coming back negative for Ebola. We were stumped.” Investigators decided to use deep sequencing, a process in which all the nucleotides that make up a DNA sample are spelled out individually without reference to any other DNA of known pathogens. It gives scientists the virus’ complete genome and allows them to place it within the family tree of known viruses for identification.

“It turned out to be a rhabdovirus, which is the family that rabies belongs to,” explains Joly. The virus was named Bas-Congo virus, after the province it hailed from. To date, there have been no further outbreaks anywhere in the world. “It’s the first rhabdovirus that we have ever seen that causes hemorrhagic fever,” says Joly. “To be able to identify it so quickly was a big success.” A serological test was subsequently developed to identify how many people had been exposed, in order to manage and quarantine the outbreak. Only three individuals contracted the virus: two teenagers and one health care worker, all living within 55 yards of one another in the same village. The genome revealed that its closest viral relatives were found in insects, though it’s still not clear exactly which animal was the initial host. It’s clues like this that pathogen experts rely on to get to the bottom of emerging viruses, before they become deadly outbreaks.

The pathogens of the past that have been devastating to humans, Joly explains, often were respiratory and airborne. So testing is frequently focused on influenza and filoviruses (the viral family Ebola belongs to). But it’s important not to make assumptions: SARS turned out to be part of the coronavirus family, previously believed relatively harmless to humans. The current outbreak of Middle East respiratory syndrome, or MERS, virus is also a coronavirus. 

A library of viruses

The kind of deep genetic sequencing that made identifying the Bas-Congo virus possible requires libraries of information to compare the viruses’ DNA sequences. Scientists are now working to make this information publicly available. “As soon as the government allows us to release data, we put it out there,” says Joly. When a sample is collected, it is placed in liquid nitrogen for transport to the lab at the INRB. There, scientists analyze samples in bio-secure laboratories.

The INRB is housed in a Soviet-era building in the center of Kinshasa. Since 1984, it has been the country’s main hub for analyzing viruses and diagnosing Ebola outbreaks. “We are in the Congo, but this is a world-class facility,” says Dr. Stomy Karhemere, the INRB deputy director. “As Congolese, we’re proud of that.”

The INRB, which has some of the world’s most experienced Ebola doctors, is trying to assist with the current Ebola outbreak in West Africa. Senior staff traveled to Liberia to help advise the government there on how to contain and treat the virus. INRB staffers are training health care workers on the best practices for treating patients suffering from Ebola, with the hope that some of them will assist with the outbreak in West Africa.

On the streets of Kinshasa, people monitor the news for updates on Ebola and other mysterious illnesses that could prove deadly. The population is used to malaria, typhoid fever and even the occasional Ebola outbreak, but deep in the forest. What scares them is the idea that a virus like Ebola might mutate into something even more deadly.

“We’re city people,” says Henrie Mulonda, a government employee out shopping for groceries with his daughter. “But many of us came from villages. We have relatives who still live near the forest. They get sick and sometimes no one knows the cause.” His daughter picks up some mangoes to put into their shopping bag, while Mulonda negotiates the price for meat. When asked if he ever eats bush meat, he replies, “I prefer chicken.”

To date, Predict has collected more than 350,000 specimens from roughly 55,000 animals in 20 countries. Along with the samples, information is collected about each animal, such as the details of human contact, if any. All the information is entered into the Global Animal Information Network. “It’s a big database,” says Joly. “Coming up with a way to manage data in a global project, with all the ways scientists might want to use them in different contexts, has been quite a challenge. It needs to work everywhere from rural Laos to the DRC.”

Most of the samples are also registered on GenBank, an open-access database of DNA sequences created by the National Institutes of Health in the United States, which is open and available for anyone to view. Predict has also created an interactive map on which the public can look for up-to-date information on the program’s activities. During the recent outbreak of Ebola in Congo, the lab was able to release the genetic sequence to the public. “We could quickly show that the Congo Ebola strain really was a separate outbreak,” Joly says. “This is good for public health.”

As Predict has ended its first five-year cycle, USAID has put out a call for proposals under the second phase of its Emerging Pandemic Threats program. In the future, the focus will be on strengthening the capacity of local labs to identify and respond to emerging pathogens. The latest economic figures from the World Bank suggest that the current Ebola outbreak in West Africa could cost more than $30 billion by the end of 2015.

In the midst of the world's largest Ebola outbreak, monitoring emerging pathogens seems more important than ever. But those on the front lines of virus discovery are quick to point out that the best defense might be to leave the forest alone. 

“The same virus that can live peacefully in the forest can destroy a human community,” says Karhemere. “So deforestation — people moving into the forest — it isn’t helping.” When asked if the solution might be to remove the forest altogether, Karhemere laughs. “You cannot cut the forest and say you are free from viruses. The viruses will live. What we need to do is learn how to live with the forest. That includes the viruses that call it home.”

Elaisha Stokes is a 2014 International Women’s Media Foundation reporting fellow in the Democratic Republic of Congo.