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Remote Research, Remotely

Eberly researchers use satellites to monitor bat habitat and study virus spillover events during a global pandemic
10 November 2021

Over the last year and a half, the word remote has come to dominate a large portion of our collective consciousness. We’ve had to work remotely, learn remotely, and even socialize remotely. But before the pandemic, because of the nature of their research, remote was already a part of the daily lexicon of some Penn State Eberly College of Science researchers.

Many types of research can only be done remotely, or, at the very least, greatly benefit from it. There’s a famous story of a team of archaeologists searching the dense jungles of Central America for a Mayan ruin that they knew from records must be there. With help from satellite imaging, which could bore down through the nearly impenetrable vegetation and see what was beneath, they learned that the large stone structure was mere meters away from where they fruitlessly searched on the ground. As another example, astronomers, because of the nature of their study subjects, and our disappointing lack of light-speed travel technology, must do nearly everything from a distance. Even for chemists, physicists, statisticians, and biologists, for whom our usual image is of them hunkered over a lab bench or computer, or maybe in the field, up close with their research, this isn’t always the case.

One researcher in the college who takes advantage of remote technology for her research is Assistant Professor of Biology Nita Bharti. She studies the interactions of social and biological processes that underlie human health in relation to infectious disease. Her expertise has been crucial to the University and the greater community during the COVID-19 pandemic in a number of capacities. Bharti, who is the Lloyd Huck Early Career Professor in Biology, is one of the faces of the “Ask CIDD” video series, which was developed by Penn State’s Center for Infectious Disease Dynamics (CIDD) and provided guidance on many commonly asked questions during the pandemic.

Aerial image of Bungawalbin National Park in New South Wales, Australia
Aerial image of Bungawalbin National Park in New South Wales, Australia. This National Park contains important winter diet species for flying foxes and was unfortunately affected by the 2019/2020 fires. Credit: Kelsee Baranowski

Disease Research at a Distance

In one facet of Bharti’s remote research, she uses satellite images of nighttime lights to track the movement of people in remote areas of the globe. This allows her team to better understand disease transmission as, for example, people gather seasonally. She can then use the information to aid in the development of strategies to effectively deliver vaccines and other preventative health care. In another project, she used data from traffic cameras to study how lockdown measures during the COVID-19 pandemic affected movement and transmission.

Bharti is also part of another large, interdisciplinary project where she uses remote technology to study virus spillover events and the emergence of novel diseases. Because of COVID-19, we have all been forced into a crash course in spillover events—when a pathogen jumps from one host species into another—and just how important they can be for global human health.

“Understanding the underlying mechanisms that give rise to virus spillover is a critical step forward in global health today,” said Bharti. “Spillover events have been increasing in frequency and global distribution every year. But, as with COVID, science has been a step behind the pathogens and we’ve tended to focus on documenting spillover events and mitigating outbreaks after they happen. In an effort to get ahead of them, our project aims to decipher the ecological processes and molecular interactions that create spillovers and cause outbreaks.”

Grey-headed flying fox at the Tolga Bat Hospital
Grey-headed flying fox at the Tolga Bat Hospital.

Credit: Nita Bharti

The spillover event that Bharti studies involves habitat loss in Australia that is forcing closer contact between the reservoir species, which carries the virus, and humans and their domestic animals. You may not be surprised to learn that the reservoir species is a bat, although in this case the bats are huge—but somehow also cute and cuddly—fruit bats, often called flying foxes. The virus—Hendra virus—may be less familiar, but it is deadly to humans. It was first documented in 1994 when an outbreak killed over a dozen horses and their owner in Australia. It is closely related to Nipah virus—these bat-borne pathogens are collectively known as henipaviruses—outbreaks of which have resulted in hundreds of deaths in Malaysia, Bangladesh, and India, and it is now endemic there.

Unlike Nipah virus, Hendra virus has not yet shown human-to-human transmission, which gives researchers like Bharti and her team an opportunity to study the mechanisms, or step-by-step process of spillover, and potentially get ahead of future spillover events. Remote technology helps Bharti and her team track and understand habitat loss with the goal of protecting critical habitat areas and developing strategies to either restore it or at least reduce the impacts of loss. Bharti’s graduate student Kelsee Baranowski spearheads this part of the project. What they learn will hopefully be generally applicable to other novel spillover systems, such that we can prevent future outbreaks instead of responding to them.

From PlantVillage to Hendra Virus

Kelsee Baranowski
Kelsee Baranowski. Credit: Nate Follmer

The stereotype of a graduate student in the sciences is of someone who spends most of their day in a lab. Baranowski, who is a third-year doctoral student, is no exception to this general rule even though the source of much of her data is remote, but her path to graduate school was not necessarily stereotypical.

Baranowski first came to Penn State as undergraduate student majoring in biology, with a minor in statistics. That was 10 years ago, and she is still here, going strong. As an undergrad, she began to work on a research project with David Hughes, professor of entomology and of biology. Hughes is Dorothy Foehr Huck and J. Lloyd Huck Chair in Global Food Security and founded a program called PlantVillage, a web-based platform to help small farmers around the world access information on plant diseases and pests from experts. Baranowski started working on the project by documenting common local plant diseases.

“I got really, really interested in the global impacts of this project and the potential to help so many people, so I was happy to stay after graduating and work as a research technician in David’s lab,” said Baranowski. “I helped manage the PlantVillage project, collected images of plant diseases, and eventually became the chief image curator. I led the creation of a huge image database of global plant diseases so that those images could be used to train machine-learning algorithms to recognize the disease and help small farmers around the world to identify plant diseases just with their camera phone.”

Although Baranowski had considered graduate school as an undergraduate, her work with PlantVillage was important and gratifying, so she thought it might be a longish-term position. That all changed when Bharti came into the lab to borrow a drone, which PlantVillage was using to remotely capture images of entire fields to get field-wide analyses of crop diseases.

When Bharti explained that she wanted the drone for a trip to Australia for a project involving Hendra virus, Baranowski’s interest was immediately piqued. Baranowski had previously attended a CIDD seminar on Hendra viruses and was fascinated by the complexities of spillover. The two struck up a conversation that eventually led to the topic of career goals.

“She basically convinced me right then and there to go to grad school,” said Baranowski. “It was one week before the grad school application deadline. I hadn’t taken the GRE or asked for reference letters, so I thought I would just wait and apply for the following year, but Nita convinced me to just go for it. And without even really realizing what had just happened, my whole life changed in that meeting.”

Map of the state of Queensland (in grey), with the range of all four Australian flying foxes outlined in black, and the loss of winter diet species from pre-European colonization (~1750 to 2019) shown by the red polygons
Map of the state of Queensland (in grey), with the range of all four Australian flying foxes outlined in black, and the loss of winter diet species from pre-European colonization (~1750 to 2019) shown by the red polygons, representing a loss of ~45% of their historic winter habitat. Credit: Kelsee Baranowski

Flying Fox Habitat from Afar

Kelsee Baranowski flying a Mavic 2 Pro Drone over a flowering Eucalyptus tree in Bungawalbin National Park
Kelsee Baranowski flying a Mavic 2 Pro Droneover a flowering Eucalyptus

tree in Bungawalbin National Park. Credit: Peggy Eby

For her graduate work, Baranowski is interested in how land-use change, deforestation, and habitat loss impact the movement of bats that carry Hendra virus in eastern Australia and, in turn, how that influences spillover events.

Large segments of Australia are inhospitable for bats, so their natural range includes forested areas along the coast, which also tend to be the most attractive areas for humans. It is thought that since European colonization of Australia in the mid-18th century, about half of the bat habitat has been taken over by humans. Because of this, many of the bats, which are typically nomadic and fly up and down the coast in the pursuit of seasonal food sources, have settled into more permanent roosts near towns, parks, and pastureland.

“The bats themselves are not affected by Hendra virus,” said Baranowski. “However, they can pass the virus to horses, which pick up the virus by grazing in areas under trees where the bats now visit. Horses are the bridge, or amplifier, species between bats and humans. The virus replicates in horses to levels high enough to infect humans. So far, there have been somewhere around 100 documented cases of horses with Hendra virus but just a handful of human cases. Unfortunately, Hendra virus has proved fatal in more than half of those cases, and even when it’s not fatal, it still causes permanent neurological damage. It’s vital to get a handle on how and why this is happening in these early stages and learn what we can do to prevent it from getting worse.”

There are many layers to understanding how a virus jumps for one species to another, from animal ecology to disease ecology, microbiology, and immunology. The researchers refer to this as the “Swiss cheese model,” where a variety of factors must align for a spillover event to happen. The virus must navigate a path through the holes in each layer to make the jump from animal to human, and the larger team that Bharti and Baranowski work with is looking at each of these factors. Baranowski’s project focuses on the distribution of the reservoir species—the bats.

“I’m looking at where these bats and their native resources are through time,” she said. “My first year and a half was spent taking classes and teaching but also mapping and quantifying their habitat loss. I have really amazingly detailed maps that allow me to track individual diet species to see how their abundance distribution has changed. I can see where important food sources still remain and use this data to model where the bats are likely to roost.”

Satellite images of Eucalyptus vegetation
Satellite images of Eucalyptus vegetation. (top) Satellite image from a Planet

4Band Dove satellite. © 2019 Planet Labs Inc. (middle) The same area on the

Queensland Herbariums’ Vegetation Management Regional Ecosystem map.

(bottom) The same area with the Eucalypt chlorophyll-a reflectance ratio

(ECARR) applied to the satellite image (from Baranowski et al. 2020) Black

areas represent eucalypt vegetation remotely detected by satellite and white

areas designate areas eucalypt vegetation was not detected. Credit: Kelsee


Baranowski has shown that satellite imaging alone is not currently sensitive enough to identify individual species of food sources, so she mainly relies on maps put out by the Queensland Herbarium. These maps, which rely on a combination of remote sensing and field surveys, have been updated every two years since 1997 and provide detailed regional ecosystems including the prevalence of important diet species. She also uses surveys of the bat population that have been done quarterly by the National Flying Fox Monitoring Program in Australia since 2012.

Most of the documented spillover events have occurred during the winter months, when the fruits and nectar that the bats rely on are particularly scarce. Baranowski wants to understand where these limited resources are to better predict how they influence where the bats are going, with the eventual goal of determining how and where to restore these resources to pull the bats away from humans.

Recent wildfires in Australia have also had a major impact on bat habitat, and Baranowski used thermal anomaly satellite data to map where the fires were and quantify the habitat loss with her maps. But, unfortunately, even this type of research is not immune to the impact of COVID-19. The bat monitoring program had to be interrupted, so the team couldn’t measure the direct impact of the habitat loss from the recent fires on the bat population.

“The huge advantage of working with remote data and satellite imagery is that I don’t have to go to a lab and generate the data,” said Baranowski. “I download the images and can analyze them from just about anywhere, so during lockdown I could remain productive. We have decades’ worth of satellite data that has been passively collected, and we can leverage all that data for good. We can look into the past, see how the environment has changed, predict how the environment might change in the future, and use that to develop strategies to restore habitat so they will continue to be productive resources in the future under climate change. By doing this, hopefully we can add resilience to these native forests, help flying foxes survive so they can continue their important pollination services, and reduce the risk of Hendra virus and other diseases from spilling over into other animals and humans.”

Bharti’s and Baranowski’s work on Hendra virus will hopefully also provide important insights into spillover events generally. After the last year and a half, we all know too well the impact that the spillover of a novel virus can have. By remotely looking into the past, documenting the present, and preparing for the future, their research might help prevent future outbreaks that would force us back to the world of remote.