By Sarah Ryan

Bats and humans depend on the caves that pockmark the Mount Elgon caldera in eastern Uganda, making it the perfect field site to study human-bat interactions and emerging viral pathogens.

This spring, an international team of scientists began a five-year research project in the area. Funded by the Defense Threat Reduction Agency, a Department of Defense agency tasked with identifying and mitigating emerging threats to global health, the research will help both countries understand and mitigate disease transmission from bats to humans and humans to bats.

Principal investigator and CSU virologist Dr. Rebekah Kading is building on a decade of experience in Uganda. “From a biodiversity perspective and an infectious disease perspective there’s a lot going on there,” Kading said. “People enter the caves to collect guano and salt crystals. They shelter in them with their cattle during rainstorms. They visit them for ceremonial purposes. It’s very tied with their communities and their resource needs, so it’s a really interesting place to study the interactions of humans, wildlife, and livestock and the transmission of infectious agents.”

Monitoring viruses, preventing outbreaks

After a year-long pandemic delay, Kading, veterinary postdoctoral fellow Dr. Anna Fagre, and postdoctoral researcher Dr. Emma Harris joined their Ugandan colleagues in May to capture, tag, and sample wild bats. They use passive integrated transponders—the wildlife equivalent of microchips for pets—to tag the bats. The PIT tags allow the team to identify individual bats and monitor virus infection and shedding over time.

“There’s some evidence that there are differences in viral shedding patterns according to the breeding and birthing seasons. We’re going to capture that information from these bat populations to get a seasonal assessment of the virus prevalence in these caves,” Kading said.

three scientists catch bats in mist net
Dr. Robert Kityo and his team from Makerere University set up mist nets inside a cave. The nets are strategically placed to intercept bats on expected flight paths, where they will be immediately extracted by researchers. Photo by Rebekah Kading

They sampled six species during the rainy season, when all of the female bats were pregnant. The team will return  during the dry season with wildlife veterinarian Dr. Kevin Castle to begin GPS tracking to collect data on the regional movement of the bats. Eventually, they’ll be able to develop risk scenarios that predict what viruses are circulating when and where so local communities can gauge their risk.

The team collected Rhinolophus and Hipposideros bats, which have an evolutionary relationship with beta coronaviruses, so they will be able to monitor for spillback of SARS-CoV-2 into the bat populations.

“The new post-pandemic perspective is that cross-species transmission is not unidirectional. If these bats are susceptible to this group of viruses, then we want to test for it because of human traffic in the caves,” Kading said.

The caves are considered community property because they provide valuable resources, such as shelter, guano, salt, and crystals. They are also used for tourism. Next year, the team will survey local communities to understand their knowledge, attitudes, and perceptions of bats and human-bat interactions. They will also collaborate with village health care workers who are the first people on the ground to see and respond to infectious diseases.

“With SARS-COV-2, it’s arguably more important now than ever before to understand these interactions and how to mitigate risk of disease transmission while ultimately still protecting the conservation of the bats and maintaining the integrity of their habitat as much as possible,” Fagre said.

bat research at Mt. Elgon cave
Local children observed the team at work. “The way that people interact with the cave systems in Uganda is completely different from in the Unites States where caves are used recreationally,” Emma Harris said. In Uganda, caves are community property and provide many valuable resources, including shelter, guano, salt crystals, and ceremonial purposes. Photo by Rebekah Kading

Understanding and protecting keystone species

Kading is mindful that their work could have unintended consequences on the bats. “People observe us going into the caves with Tyvek suits and respirators to protect ourselves from infectious agents, but we don’t want to instill fear in them,” Kading said. “That might have negative consequences on the conservation of the bats, and so engagement is critical. We have lots of conversations about how to live safely with bats.”

scientist in cave processes bats
Dr. Anna Fagre works with a colony of captive fruit bats, but she has dreamed of capturing her first free-ranging bat for years. “There was something different about holding the bat and knowing that this was its first interaction with a human,” Fagre said. Photo by Rebekah Kading

Kading’s team depends on a Ugandan team led by Dr. Robert Kityo, a natural history biologist at Makerere University and the author of the East African Bat Atlas. While Kading focuses on biosurveillance and virus discovery, Kityo focuses on bat ecology and conservation. 

Bats provide many ecosystem services as predators, prey, pollinators, and seed dispersers. As ecotourism and other economic pressures increase human-bat interactions, it becomes even more urgent to understand and protect bats and their habitats. 

“We want to know what species of bats are in which caves? What lives in there with them? What are they eating? Who is going into the caves? What are their interactions with the bats? What is the relationship between bat habitats and local communities?” Kityo said. 

Acoustic monitoring is essential to identifying species and understanding population distribution and movement. Kityo’s team and the Uganda Wildlife Authority aim to create a comprehensive library of bats and bat calls in Uganda. There are 110 known bat species in Uganda, but new species continue to emerge. Kityo’s team leads the bat capture and tagging efforts, and they also record bat calls in and around the caves. 

“We know quite a bit, but there is a lot to uncover. We might record a call that we don’t know, and that’s a reason to keep searching,” Kityo said. “Tourism is not just about the Big 5. It is about all of the biodiversity. Tourism around bats in Uganda is not big yet, but I hope it will thrive.”

Rebekah Kading is the lead investigator for “Ecology, Epidemiology, and Biosurveillance for emerging viral pathogens of Uganda bats.” The project is funded by the Defense Threat Reduction Agency. Partner intuitions include Colorado State University, Uganda Virus Research Institute, Makerere University, the United States Centers for Disease Control and Prevention, and Uganda Wildlife Authority.