Dec. 15, 2017

KIBALE NATIONAL PARK, Uganda - One morning seven years ago, Tony Goldberg was working in the tropical forests of Uganda’s Kibale National Park, when a colleague arrived at his research station with two students in tow. They were searching for bats.

Goldberg, a University of Wisconsin-Madison professor of epidemiology, had been visiting the station for several years, long enough to have noticed the jet-black figures that fluttered away from the kitchen building whenever he disturbed their daytime sleep.

Sure enough, with a few swooshes from a net, his colleague, Ugandan researcher Robert Kityo, trapped several bats. But as Goldberg watched one of them, he saw something strange crawl out of its fur.

“It was really big,” he recalled. “It looked like a spider, long legs, fat body, blackish-gray color.”

It was a bat fly. “I hadn’t even known there was such a thing,” Goldberg said. “I asked Robert if he wouldn’t mind taking samples of the flies. Maybe they’d come in handy in the future.”

In fact, the discovery would show why Goldberg and other researchers return to Kibale year after year, seeking knowledge that will help science fight the rising tide of zoonotic diseases, those that pass from animals to people.

Using tweezers, Kityo removed several of the odd-looking flies; they were eyeless and wingless. The group also took samples from the bats: blood and swabs from their mouths and urinary and genital organs. All were placed in a freezer at the station.

And there they stayed. For six years.

In 2016, during a kind of scientific spring-cleaning at the station he calls “Mango Palace,” Goldberg came upon a freezer bag labeled “Kityo bat samples.” The samples were well preserved, and when he examined their genetic code he got a surprise.

The bat’s genetic code didn’t match that of any other bat on file in research databases.

Nor did the bat fly’s genetic code match that of any known bat fly.

Then there was perhaps the most compelling discovery, a virus lurking inside the bat fly — it too was unlike any other he’d seen.

“There is no evidence that this virus is harmful to people,” Goldberg said. “But it’s related to viruses that are known to cause diseases in people.”

Dubbed Kanyawara virus after the location of Goldberg’s research station, the potentially new pathogen belongs to the rhabdovirus family. Other members of the family include species that cause rabies and the fish disease viral hemorrhagic septicemia.

Genetic information from the bat, the bat fly and the virus still must be compared with data from samples in museum collections. But it is entirely possible that not far from the building where Goldberg slept, lay three previously undiscovered species: bat, bat fly and virus.

“A transcendent moment nears upon the world for a microbial perfect storm,” the nonprofit Institute of Medicine warned in 2003. “Unlike the meteorological perfect storm — happening just once in a century — the microbial perfect storm will be a recurrent event.”

The report on infectious diseases listed numerous factors edging the world toward this “perfect storm”: changing climate; the fast pace of global travel; increased trade in food and livestock; greater human migration due to war and poverty; and surging land development resulting in more frequent contact between humans and animals.

Today those pressures show no signs of abating. Since 2009, the global health landscape has been reshaped by the H1N1 swine flu pandemic, major outbreaks of the Ebola and Zika viruses, and the mass migration of 5 million refugees from the Syrian War. 

For the last three decades, emerging infectious diseases have continued to rise; more than 70% of them zoonotic.

At present, there are about 4,400 known viruses, including some 220 that can infect humans. Three to four human viruses are discovered each year. 

But those numbers are dwarfed by the estimated 320,000 mammalian viruses that have yet to be discovered, according to a 2013 paper in the American Society for Microbiology journal mBio. The paper’s authors focused on a single species, the Indian Flying Fox, conducting tests and estimating that it hosted about 58 viruses, a number they then multiplied by the total number of mammalian species.  

The authors estimated it would cost about $6 billion to find all of these unknown viruses, though much of the expense would be required to track down the rarest ones. For about $1.4 billion, the authors wrote, scientists could find about 85% of the undiscovered ones.

“Many of these viruses may end up never crossing over into humans,” said Charles Chiu, an associate professor of infectious diseases at the University of California, San Francisco, who has done fieldwork in Mexico, Brazil and the Democratic Republic of the Congo. “But there’s always the worry that there are additional viruses that have the capacity to jump.” 

Such threats to human health often emerge from places where humans and animals are in contact. They come from crowded Third World slums where impoverished families live side by side with the animals they keep. 

They also come from rural areas where contact is less frequent, where wildlife may harbor pathogens for years before the microorganisms jump to humans and take off. An example is Zika virus. Discovered in a Ugandan forest in 1947, the virus barely appeared on the medical radar until February 2015 when it swept through Brazil, causing babies to be born with underdeveloped brains and other birth defects.

There is an additional layer of complexity in this hunt. Many viruses have different versions, or strains. Each strain is distinguished by its own genetic and clinical characteristics. One version of a virus may be harmless to humans, another deadly.

Identifying the different strains can tell scientists how the virus evolved and how the lethal versions emerged. Also, weak strains may be used to develop vaccines, which cause little or no harm, but train our immune system to deal with the full strength virus.

The ultimate goal of identifying viruses and their strains is to spot potential threats early, before they ignite in a heavily populated area, before they cross continents via global trade and travel.

So, where does a scientist go to find new viruses, or new strains?

“In the future, diseases are going to emerge from remote areas into remote populations more often. And the reason we know that to be true is because the frequency of emerging diseases is increasing over time,” explained Peter Daszak, president of the EcoHealth Alliance, a U.S.-based organization that researches matters of global health, conservation and international development.

“The risk of emergence is increasing exponentially, the risk of becoming pandemic is increasing exponentially, and the cost to our global economy is increasing.”   

As the human population grows, people are venturing into remote jungles and forests with greater frequency seeking food, timber, land for crops, even attractions for tourism. “Scientists look for new pathogens in rural areas,” said Chiu, “because you’re right at the human-animal interface.”

That’s why scientists come to places like Manú National Park in southern Peru; Los Tuxtlas Biosphere Reserve in the Mexican state of Veracruz; and the island of Borneo in between Malaysia and Indonesia. 

 And Kibale. 

Goldberg returns to the park in southern Uganda year after year because it stands at a crossroads of biodiversity. Kibale’s 300 square miles bring together the biologies of East Africa (the great savanna systems and the patchy forests of the Serengeti) and Central Africa (the dark, humid lowland rainforests).

Some nights, the air around Mango Palace is alive with the distant trumpeting of elephants and the sounds of nearby villagers banging pots to scare them away from their crops.

The park is home to 70 mammal species, from bush pigs and forest antelopes to red colobus monkeys and a dozen other species of primates. Kibale also draws 375 species of birds. 

Then there are the hitchhikers that birds and mammals bring with them: their parasites, bacteria and viruses. Some of these animal pathogens can jump to humans, but the reverse can happen as well. Animals sometimes fall ill and die from human pathogens.

Such are the possibilities on display at Kibale.

“It’s a mixing zone,” Goldberg said, “and one of the best-studied areas … It’s a living laboratory where I go to test fundamental ideas about how ecology affects viral transmission.”

The questions he asks include how viruses percolate in populations — sometimes for decades — before suddenly spreading quickly and extensively.

“We believe there are pre-emergent pathogens in the world,” he said. Pre-emergent pathogens are disease-causing microorganisms that are currently rare but have a high potential for epidemic spread. 

Goldberg wonders, too, about the role animal behavior plays in the spread of disease. We know animals spread viruses through fighting, biting and sex. Rabies is the classic example of a virus spread through aggressive behavior.

But trips to Kibale often yield surprises, humbling reminders that we have much to learn about animals and the diseases they carry.        

January 2017. A strange respiratory disease was spreading through the chimpanzees in Kibale. 

Researchers wondered if the disease was something new — the kind of discovery that lures Goldberg back to the spartan research station a mile above sea level. In past years, he and his colleagues discovered a new bat disease and new strains of simian hemorrhagic fever, a disease that strikes Asian macaques and is almost always fatal.

When the respiratory illness emerged in early 2017, an outbreak of skin disease was already underway among the park’s red colobus monkeys, eroding the faces of the infected until it was possible to see inside their sinuses.

As researchers tracked the respiratory disease, an extraordinary scene played out, involving one of the female chimpanzees, Rwanda. She had been coughing for days, possibly from the respiratory illness. Then, in full view of fieldworkers, a group of six male chimpanzees savagely beat her.

Chimpanzee society can be harsh. Males bite, grab, beat and stomp each other in fights over territory. Some males will kill the infant of a female if they believe a rival to be the father. But it is unusual for male chimpanzees to gang up on a female from their own social group. 

In this case, most of the males departed after the attack, leaving the female barely alive. A lone male remained behind guarding her body for hours before she died.

That researchers were present when the attack occurred was no accident. Scientists have been following the same chimpanzee communities at Kibale for decades, naming the individuals and cataloging their behavior in detail.

From close observation, they knew the approximate chronology of Rwanda’s death. She began coughing around Jan. 3., was attacked Jan. 11 and remained motionless all day on Jan. 12, the day researchers believe she died. The presence of carrion flies signaled death. On the morning of Jan. 13, observers examined her body. The flies were right.

The fieldworkers who witnessed the attack and Rwanda’s subsequent death were required to follow a cardinal rule of primate research: They could watch, but they could not intervene.

“You can’t watch dispassionately,” Goldberg said. “You get really involved in the lives of these animals, but you have to hold back.”

Only officials of the Ugandan Wildlife Authority may intervene, and then only under certain conditions — for example, if a chimpanzee is caught in a snare.

However, researchers can perform an autopsy after a chimpanzee has died, and that is what Goldberg and his Ugandan colleagues did with Rwanda. Not surprisingly they found that she died from the beating. She had also been suffering from severe chronic pleurisy pneumonia; it was unclear if she had the mysterious respiratory disease.

In the months following the autopsy, the case churned through Goldberg’s mind.

“As far as Rwanda goes,” he said almost a year later, “I've been second guessing myself. Because of the coughing, we were looking hard for lung disease. But, she wasn't as fresh as we would have liked.

“So, it could have been post-mortem changes, rather than pneumonia. The only thing we know for sure is that the males beat her hard and then she died a day later.”  

Researchers at Kibale knew of one other possible factor: Rwanda had given birth to several babies that did not survive. Maybe it was this inability to enlarge her community with new offspring that angered the males.

The incident and its elusive meaning underscored one of the frustrations for scientists investigating diseases in Kibale and similar places. Answers often take years.

Just this month, Goldberg and his colleagues published their investigation into a respiratory illness that afflicted one of Kibale’s chimpanzee communities in February 2013. Their paper, published in the journal Emerging Infectious Diseases, reported a remarkable culprit for the illness that killed five of the community’s 56 chimpanzees; a human “common cold” virus known as rhinovirus C.

“Prior to this discovery, we did not know that rhinovirus C could infect anything other than humans, let alone potentially cause a lethal infection,” Goldberg said. “That was surprising.”

One reason investigations often take years is that while some labs in Uganda are extremely adept at molecular biology, few routinely do the kind of broad analysis necessary for “virus-hunting” research. Moreover, the process of gaining approval to ship samples out of African countries and into the U.S. is lengthy and time-consuming.

Goldberg has been trying to develop ways for researchers to conduct analysis in the field so that it will no longer be necessary to go through the lengthy permitting process.

For now, the 2017 investigation is on hold. Goldberg said he may perform additional testing when he returns to Uganda in March. 

“It’s really frustrating,” he said. “From a selfish perspective, I really can’t stand not knowing. But there’s also a decent chance that if we did know, we could help the chimps in real time.”

For the scientists at Kibale and elsewhere, the search for new viruses has its perils.

When studying bats, researchers must often squeeze into hollow trees and stare up maybe 30 to 40 feet to locate the colony’s roost. They must cover their mouths and noses with airtight face masks and avoid breathing in spores from a fungus that grows on bat guano. 

One family of scientists who peered inside a bat tree without masks, Goldberg said, came down with histoplasmosis, a severe, sometimes deadly respiratory disease also found in the U.S., and sometimes known as cave disease.  

So, on a day last January, a colleague of Goldberg’s, Swaibu Katusabe, strapped on a mask before slipping inside a tree thick with bats. Inside the tree he placed a canister — actually a used paper towel holder — containing an electronic air sampler with a filter small enough to trap viruses. 
 
Katusabe has been studying a coronavirus found in all of the Kibale bats. He took control air samples from other nearby areas to determine whether the virus is present all over the forest and not just in bats. Coronaviruses belong to the viral family responsible for the common cold, pneumonia and the sometimes fatal illness Severe Acute Respiratory Syndrome (SARS).

Goldberg peaked inside the tree his colleague had just sampled and said, “I can hear them.” Shining a flashlight up the tree, he saw eyes twinkling in the darkness and the gray outline of fist-sized shapes.

“We can study these diseases because of conservation,” he said, emerging from the tree. “But we don’t want people to think these bats and monkeys are horrible bags of germs.”

Certain bats eat the insects that infest local crops. Others are important in the dispersal of seeds, or pollination of flowers.  

Still, some studies suggest that bats carry more than 60 diseases that can spread to humans.

It’s not known precisely why bats carry so many diseases, though their nature suggests some possible explanations. They have been around for at least 52 million years and include more than 1,200 species.

They interact with both humans and livestock. They live in large colonies and their ability to fly allows them to cover greater distances and therefore spread diseases more widely than other mammals.

There is also the fact that human settlements keep drawing closer to the forests where many bats live, increasing the likelihood of human-bat contact.

Diseases may be following another route on their way between animals and humans. 

David Hyeroba, another member of Goldberg’s team, has been studying the dogs that live in villages at the edge of the park. The relationship between the dogs and the humans they live with differs greatly from that in the U.S.

In the villages around Kibale, dogs are adopted by families, largely for protection. They roam freely day and night. At times, baboons and other wildlife attack the dogs, and villagers have told Goldberg that on other occasions the dogs chase and catch monkeys.

Two of the most common causes of death for the dogs near Kibale are infectious diseases and baboon attacks. A third is death by human hand — often a farmer who has caught a dog killing his chickens or goats.

In theory, the dogs may spread diseases when they return from the forest simply by licking people’s hands, though it’s not known if diseases have spread this way.

There is precedent, however, for a dog disease jumping to other animals. In 1994, the Serengeti’s lion population was decimated by canine distemper; one-third of the lions died, about 1,000 animals.

In fact, canine distemper may be one of the most prolific diseases when it comes to jumping from one animal to another. The long list of animals known to have been infected by canine distemper includes rhesus monkeys, pandas, American black bears, South American jaguars and even seals. 

Humans have also caught canine distemper, a disease closely related to measles, though people rarely show any symptoms.

The jumping of diseases from species to species, known as spillover, is more likely to happen in places that have a great diversity of species, such as Kibale. Some researchers believe this process can occur slowly and tentatively, a phenomenon known as viral chatter. In such cases, a virus or pathogen doesn’t rush all at once into a new species, but makes forays here and there, possibly mixing with pathogens already in the new species and mutating.

“The fear is that something completely new will come into people and no one will have immunity to deal with it,” Goldberg said.  

That’s one reason why he and his colleague are seeking to determine whether dogs may be ferrying diseases from forests to human communities. Hyeroba has been asking villagers to enroll their dogs in a study. He hopes to register 200 to 300 dogs, each of which would be fitted with a microchip, allowing Hyeroba to track their movements for a year or so.

In return, Hyeroba examines the dogs for the villagers and provides on-the-spot diagnoses and treatment if needed.

So each month Hyeroba makes his way along rutted dirt roads, the Rwenzori Mountains in the distance, checking up on each of the dogs. He asks three questions of the owners: Are the dogs still in the same home? Are they healthy? And, if they are sick, what happened to them?

One morning he arrived at the home of 71-year-old Kimara Solomon, who keeps a small scattering of pigs and goats, and grows bananas, sweet potatoes and pineapples. He said he keeps three dogs for protection from thieves and is glad to be part of the study.

One of the three was ill on this particular morning. The dog in question was emaciated, its fur disheveled, its skin marred by several wounds, a sign it may have had run-ins with the park’s wildlife. Hyeroba tried to examine the injured dog, but it would not allow him close enough. 

Instead, he worked gently with the other two dogs, placing muzzles over their jaws in order to take their temperatures.  

“You treat the dogs, even if they are sick,” Solomon said, praising his veterinary skills. 

Hyeroba told Solomon he would be back. He would need to examine the injured dog. 

The Earth is awash in undiscovered viruses, bacteria and parasites.
 
Not only in the remote corners of Africa and Asia. Here in Wisconsin, too.

Goldberg seeks new pathogens at the research station in Uganda because it is “a hot spot” of biodiversity, a place where the great variety of species is likely to translate into a great variety of pathogens.  

He also carries on the search in his home state, where he hikes, canoes and fly-fishes. Here, as in Uganda, human actions are influencing the spread of zoonotic diseases. 

Pathogens, Goldberg has learned, emerge in the most ordinary and the most surprising of places.

In the summer of 2012, he discovered a new species of tick — in his nostril. Although he made that discovery in his Madison home, he had just returned from Uganda where he almost certainly acquired the tick.

In 2014, Goldberg and his colleagues published a paper explaining what had caused the mysterious death of Mahal, the popular orangutan at the Milwaukee County Zoo. The culprit was a new species of tapeworm.

And in 2016, while investigating a fish die-off on a lake in northeastern Wisconsin, he and other researchers discovered a previously unknown virus, which they named largemouth bass reovirus. The reovirus family includes species that infect plants, animals and humans.

“There are plenty of new viruses to be discovered in Wisconsin,” Goldberg said.

One of the best known was discovered in 1965, after the death of a 4-year-old in the western part of the state. Today the virus spread by the tree-hole mosquito bears the name of the county where the child died.

La Crosse encephalitis.