Searching for the next Ebola in the Congo Basin

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 have crossed 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.”

“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. 

“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.”