Habitat loss and food shortages have pushed bats into closer proximity to horses and humans, fueling Hendra virus spillover, a new study suggests.
In September 1994, a mysterious interspecies outbreak erupted in Hendra, a suburb of Brisbane, Australia. First, a pregnant mare fell ill and died. Soon, more horses were sick, spiking fevers and expelling a foamy discharge from their snouts. Two middle-aged men — a stablehand and a horse trainer who had reportedly tried to hand-feed the dying mare — developed flulike symptoms, too. Although the stablehand recovered, the trainer ultimately died, as did more than a dozen horses.
Scientists eventually traced the outbreak to a virus carried by fruit bats, also known as flying foxes. The bats shed the pathogen, which was named the Hendra virus, in their feces and saliva, spreading it to horses, which can then pass it on to humans. In the years since, there have been dozens of additional outbreaks in horses, and several more cases in humans.
A new study, based on 25 years of data from Australia, suggests that environmental changes have been driving these spillovers by radically altering the ecology of black flying foxes. Deforestation, coupled with climate-linked food shortages, has driven the bats into human-dominated habitats like farms, where food is readily available but may be of poorer quality, scientists reported in Nature on Wednesday.
In many of these new roost locations, the bats are not only in closer contact with horses but may also shed higher levels of the virus, perhaps because of nutritional stress, according to a second study conducted by many of the same researchers and published in Ecology Letters last month.
“We’re transforming the planet in this way where we’re driving animals to be really at the brink — at the edge of their capacity to cope,” said Raina Plowright, an infectious disease ecologist at Cornell University and senior author of both studies. “And this is creating stresses that are also more likely to drive pathogens into human populations.”
The idea that deforestation can increase the risk of disease spillover is not a new one, and scientists have repeatedly documented connections between forest fragmentation and outbreaks of diseases as varied as Ebola, malaria and Lyme.
But the new research is an extraordinarily detailed case study, experts said, unpacking precisely how environmental changes can drive disease risk — and how and where experts might be able to intervene.
“It’s just an enormously impressive undertaking,” said Dr. Aaron Bernstein, the interim director of the Center for Climate, Health and the Global Environment at the Harvard T.H. Chan School of Public Health, who was not involved in the research. “These scientists have essentially traced the dots across a bunch of the factors that we know can drive emerging infections.”
He added, “I think it points to how critically important it is to focus on prevention upstream to really prevent spillover.”
Nomads no more
The new study is the result of a decade-long collaboration between Dr. Plowright and Peggy Eby, a wildlife ecologist with an adjunct position at the University of New South Wales who has spent 30 years studying the flying foxes that live in a subtropical region of Eastern Australia. They worked with an interdisciplinary group of colleagues to analyze a wide range of ecological data — including on bat roosts, bat fitness, climate, nectar shortages, habitat loss and viral spillover into horses — collected in the region between 1996 and 2020.
Historically, the local black flying foxes, which feed heavily on the nectar of eucalyptus flowers, have lived in enormous nomadic groups, winging their way through native forests in search of trees in bloom. Although the flowers are abundant in summer, during the winter and spring, the supply is much more limited. And every few years, a fluctuation in the climate, such as a strong El Niño event, disrupts winter or spring blooming, creating food shortages.
Typically, the bats have coped by splitting into smaller groups and setting up temporary roosts near more readily available food sources, such as farms or urban gardens. When the nectar shortages eased, the bats would find their way back to the forest. “As soon as the nectar started to flow again, they’d re-fuse into big aggregations and start becoming nomadic and feed in native forests again,” Dr. Plowright said.
This pattern held during the early years of the study period, from 1996 to about 2002, the researchers reported. And during these years, there were no Hendra spillovers detected in the region.
But around 2003, the pattern changed, the scientists found. When major food shortages struck, new groups of bats would still splinter off from their compatriots and set up shop near farms and cities. But now, the bats made these new habitats permanent, abandoning their nomadic forest lifestyles.
Between 2003 and 2020, the total number of roosts in the region tripled, while the size of each bat group declined. In addition, the roosts grew closer together, and the bats foraged in smaller areas.
The researchers theorized that this behavioral change stemmed from the fact that the forests the bats had relied upon, especially for the scarce supply of nectar in winter, were rapidly disappearing. In southeastern Queensland, nearly one-third of the bats’ winter foraging habitat disappeared between 1996 and 2018, they found.
“We think what’s happened is that it doesn’t make any sense anymore for these animals to maintain these big nomadic populations,” Dr. Plowright said. “It’s too hard to find food.”
Instead, she said, the bats may find it easier to survive by settling near the ready supply of lower-quality food that farms and gardens provide. “You don’t have to spend a lot of energy to find it,” she said. “It’s easier to eke out a living. You live next door to McDonald’s.”
In their second study, Dr. Plowright, Dr. Eby and their colleagues reported that bats living in these novel habitats also excreted more virus in winter than those that remained in the forest, perhaps because they were not well-nourished enough to maintain a robust immune response. (Viral shedding also tended to be higher in both bat populations after food shortages.)
Together, these findings suggest that more bats are now shedding more virus while living in closer proximity to horses, increasing the frequency of Hendra transmission. Between 2003 and 2020, there were at least 40 bat-to-horse spillover events in the region, the scientists found. These events were especially common in agricultural areas in the winters following food shortages.
Cara Brook, a disease ecologist at the University of Chicago, praised the study. “It’s just an exceptional piece of work,” she said. “We actually have a rigorous, quantitative example of how land-use change impacts habitat for a wildlife species and accelerates zoonotic risk. And I think I think that’s really important for conservation arguments.”
Similar dynamics might be at play in other ecosystems, she added: “There are wild bat populations that are reservoirs for emerging diseases all over the world.”
The study also points to possible solutions. In some years, the remaining eucalyptus trees did burst into bloom in winter, luring more than 100,000 flying foxes back to the forest. These increasingly rare winter “flowering pulses” reduced the risk of Hendra virus spillovers, the scientists found.
In this particular ecosystem, Dr. Plowright said, replanting winter-blooming species might help draw bats away from farms, protecting horses — and humans — from the virus.
“The Hendra virus case study,” Dr. Eby said in an email, “shows that with the collaborative efforts of wildlife ecologists, disease ecologists, data scientists and veterinary health specialists, it is possible to add spillover mitigation to the tools available to us for reducing pandemic risk.”