Emerging Killer Bat Virus Keeps Spilling Over to Horses

An emerging bat-borne viral disease—one that can be fatal to humans—keeps spilling over into horses, and now scientists have documented how climatic changes and habitat loss are driving this process.

The study, published on Wednesday in the journal Nature, could have significant implications for our understanding of virus spillover as well as the prevention of future pandemics.

Zoonotic spillover is a process in which pathogens are transmitted from animals to humans, often via an intermediate host. This process has resulted in the emergence and spread of several dangerous diseases among humans, including Ebola and SARS. Many scientists believe COVID also originated in animals—although some have argued that the virus may have come from a lab leak.

Among these zoonotic pathogens is the Hendra virus—an emerging disease that primarily infects Australian flying foxes, which are a group of large fruit bats. Given their robust immune defenses, bats are an incubator of numerous viruses. Pathogens originating in these animals have become an increasing public health concern.

A flying fox bat and two horses
A split image showing an Australian flying fox fruit bat and a pair of horses. Flying foxes are hosts of the Hendra viruses, which can be transmitted to horses—and subsequently humans—causing an often-deadly disease. iStock

What Is the Hendra Virus?

Hendra virus does not seem to cause notable signs of illness in infected bats but it can be transmitted to horses—the intermediate host—causing a highly lethal disease. The virus was identified in the mid-1990s after it caused the deaths of several horses in Australia. It has since been responsible for numerous outbreaks among these animals, leading to the deaths of over 100 horses.

The virus is also capable of spilling over from horses to humans, in which case it can cause a severe or fatal infection. Only a small number of people have been infected with Hendra virus to date but four out of the seven infected people—most of whom were veterinary professionals—died, figures from Australian health authorities show.

Professor Raina Plowright of the department of public and ecosystem health at Cornell University's College of Veterinary Medicine, and one of the authors of the Nature study, told Newsweek: "Hendra virus has a 57 percent fatality rate in humans and has had a devastating impact on those who have been infected, and their families, and on the veterinary and equine industries in areas where the virus spills over."

"However, Hendra virus does not spread efficiently among people, and is unlikely to cause a large outbreak or pandemic," she added.

Previous correlational studies have indicated that virus spillover from animals to humans may be linked to land use changes or other anthropogenic activities. But it has been challenging for scientists to identify how exactly these pathogens spill over into human populations and, in some cases, result in pandemics.

Identifying Virus Spillover

The latest study conducted by Plowright and colleagues goes some way to addressing this issue by providing a detailed analysis of the mechanisms driving the spillover process.

For their research, the scientists collected and collated data over nearly three decades to describe how flying foxes in subtropical Australia were responding to the loss of their habitat and climatic changes. They found that changes in climate and land use may be driving the spillover of the virus from bats to horses.

"Many studies have correlated disease emergence with environmental change but few studies have collected empirical data over decades and across many scales to actually show how environmental change causes disease emergence," Plowright said. "This study demonstrates how the loss of habitat interacts with climate to drive pathogens into human populations. This has been a key knowledge gap."

The idea for the research came after Plowright and her collaborator on the study, Peggy Eby, noticed a connection between starving bats and the Hendra virus.

Eby—a researcher with the School of Biological, Earth, and Environmental Sciences at the University of New South Wales and the Centre for Planetary Health and Food Security at Griffith University, both in Australia—had observed that bats were staring during a big cluster of spillover events in 2011. Meanwhile, Plowright had identified high levels of the Hendra virus in bats that were starving after a cyclone in the Northern Territory of Australia.

"These conversations led to a 10-year collaboration to understand this connection," Plowright said. "Eby had collected huge amounts of data across subtropical Australia. She had been documenting the behavior and population structure of bats over three decades. I had been studying the virus in bats. When we started to put the datasets together, the story just grew and grew and grew."

For the study, the researchers analyzed 25 years of data from 1996-2020 on land use change, bat behavior, and Hendra virus spillover.

"We developed over a dozen datasets to describe the location and size of bat populations, the types of landscapes the bats foraged in, the climate, when there were food shortages, bat reproductive rates, intakes of bats into rehabilitation care, pulses of flowering in native forests, the loss of the forests that provide nectar in winter, and when the remaining winter forests produced pulses of flowers and nectar," Plowright said.

Artist's illustration of a henipavirus
An artist's illustration of a henipavirus. This group of viruses includes Hendra. iStock

How Land Use and Climatic Changes Affects Bats

The scientists first noticed that spillover was coming from small populations of bats that had just formed in agricultural areas. They then found that these new populations formed after starvation events that were almost always preceded by moderate to extreme El Niño events—an irregular periodic climate pattern, characterized by the warming of surface waters in the eastern tropical Pacific Ocean, which can affect weather around the world.

Plowright and Eby continued to analyze the trends they were observing but realized that they needed sophisticated statistical techniques to understand how everything fits together.

The scientists brought in other collaborators to develop "Bayesian network models"—a machine-learning method that can identify how different variables are connected.

"In a simple sense, the network framework can identify connections between a set of variables," Andrew Hoegh, another author of the study, with the Department of Mathematical Sciences at Montana State University, told Newsweek. "Unlike most statistical models, a network model can identify multiple levels of connection."

The researchers then used the Bayesian network models to test different hypotheses on how the environment, bats, and spillover were connected. The analysis showed that land use and climatic changes drove bats to live in agricultural and urban areas. (Many flying fox species are in decline due to habitat loss resulting from the clearing of forests for agriculture, among other factors.)

The models confirmed that climatic factors such as strong El Niño events drove food shortages for bats and that during these shortages, big nomadic populations split up into many smaller ones, roosting in places where humans live—such as agricultural and urban areas—which provide access to food.

Historically, the smaller, broken-up populations would only persist as long as the food shortage. Thus, the bats would become nomadic again when nectar became available. But over time, more bats stayed in human areas, increasing the chances of spillover as they came into greater contact with horses. Physiological and immunological responses to food shortages also increased the excretion of pathogens, contributing to the phenomenon, the researchers said.

"Our models showed that then, when another food shortage happened, we would see clusters of spillover events from these bats," Plowright said.

Why Restoring Bat Habitats Is Crucial

The researchers also found that the loss of the bats' natural habitats drove them to roost closer to areas where humans live, which also increased the risk of Hendra spillover into horses.

"The models showed that the highest risk of spillover was from bats in agricultural areas after a food shortage when no winter habitat produced food—nectar," Plowright said. "However, when the remaining winter habitat produced nectar, bats fused back into large nomadic populations and fed in (their) native habitat. When this happened, the probability of spillover from any roost in the subtropics was nearly zero."

"Critically, once we understood how the loss of habitat and climate drove the emergence of this pathogen, and once we had the data to show that flowering winter habitat mitigates spillover, we could see a way to prevent spillover," she said.

The potential solution to stop spillover is to restore the winter habitat of the bats and preserve what is left, the researchers found.

"We show that to prevent pandemics, we need to preserve and restore the habitat of the reservoir hosts of the pandemic-potential pathogens, especially in the face of increasing climate variability," Plowright said.

High biodiversity hotspots with rapid environmental change in Asia, Africa, and South and Central America are the places where pandemics are likely to start but there is a lack of detailed data on these regions.

An Australian grey-headed flying fox
An Australian grey-headed flying fox in flight. Flying foxes do not seem to show any apparent signs of illness when infected with Hendra virus. iStock

"Our study shows how to start to understand pandemic risk and pandemic prevention in the places where we currently know nothing," Plowright said.

While the Hendra virus is not likely to become a pandemic, viruses like it circulate in bats throughout places in the world where environments are rapidly changing. Hendra is part of a group of viruses, called henipaviruses, which includes known viruses like the Nipah virus that spill over in Bangladesh and India, with fatality rates of 50-100 percent in people.

"The unknown henipaviruses are even more concerning," Plowright said. "Variants of henipaviruses can be found in bats from eastern Australia to West Africa—across the entire Old World tropics. Only a handful of these viruses have been characterized. We know almost nothing about these henipavirus variants—could there be a variant with characteristics that allow efficient spread in humans? Is there another henipavirus in bats—somewhere in Asia or Africa—with a fatality rate like Hendra or Nipah virus and the ability to transmit efficiently among people?"

"There is the chance that these undetected and uncharacterized viruses could pose a pandemic threat," Plowright said. "Spillover of such a virus would lead to a global catastrophe and would be much more severe than anything we experienced with COVID."

Showing how the destruction of habitat in the context of a more variable climate might unleash these viruses is an "important step in figuring out how to prevent another global disaster" like COVID-19, the researchers said.

"This study shows that we should investigate how the hosts of these viruses—bats or otherwise—are responding to the loss of their habitat and changing climate," Plowright said. "Even if we can't decipher the detailed mechanisms like we could in Australia, the Hendra virus study shows that habitat loss can lead to increasing contact of wild animals with humans, and increasing viral excretion from those animals."

"We can address those issues by preserving intact habitat and reducing fragmentation of that habitat—for example, by reducing forest clearing and road building—so that animals can safely move and feed and do all the things they need to do to survive in their environment without having to depend on food or shelter in areas where there are humans. If we can reduce the overlap of animals and people, and reduce the stress experienced by those animals, we can reduce the probability of viral spillover from those animals."

Tristan Burgess, an assistant professor of wildlife health and epidemiology with the Center for Wildlife Studies, who was not involved in the research, told Newsweek the study was "well-designed and executed," weaving together multiple data sources in order to improve our understanding of disease spillover from correlations to the underlying mechanisms.

"This is very difficult to do, but also very useful," he said. "This paper paints a very compelling picture of the way in which drivers such as land use change and habitat loss affect ecosystems and animal health in ways that increase spillover risk."

Robert Garry, a professor of microbiology and immunology at Tulane University School of Medicine, told Newsweek the study was "very interesting" and that the results are likely generalizable to other potential viruses that can spillover from animals to humans, as occurred with SARS-CoV-2.

"As the planet continues to warm the range of animals such as bats, rodents and other animals will change," he said. "Humans are also increasing clearing forest living in areas with greater exposure to wild animals. The numbers of the spillover events are likely to increase.

"To be better prepared we need to more closely monitor the animal-human interface. This study with its superb insight into animal ecology and behaviors shows how this can be done."

Update 11/16/22, 12:40 a.m. ET: This article was updated to include additional comments from Tristan Burgess and Robert Garry.


Eby, P. et al. Pathogen spillover driven by rapid changes in bat ecology. Nature https://doi.org/10.1038/s41586-022-05506-2 (2022)