Researchers from UC Davis have collected nearly 3,000 samples from six species in Cueva Culebrones, located within the Mata de Plátano Reserve in Arecibo.
From Cueva Culebrones, situated in the Mata de Plátano Reserve in Arecibo — managed by the organization Ciudadanos del Karso — a group of researchers seeks answers to the mysteries surrounding the ecological and evolutionary processes behind viruses that are capable of jumping from animal species to humans (“spillover”). One small mammal plays a key role in these efforts: the bat.
“By studying these viruses and these places, can we gain valuable information about pandemics? Can we, so to speak, open a window into the pre-emergence phase and understand the ecological and evolutionary processes that shape these viruses, determine where they exist, define their characteristics, and control and limit their change? It’s not about predicting spillover, but about understanding how the system works,” emphasized Dr. Simon Anthony, virologist and professor at the UC Davis School of Veterinary Medicine, during a recent virtual presentation organized by Puerto Rico’s Department of Natural and Environmental Resources (DRNA).
During the event, Anthony explained that his team — assisted by local experts and organizations — has spent about three years studying the six bat species found in Cueva Culebrones: Monophyllus redmani, Pteronotus portoricensis, Brachyphylla cavernarum, Erophylla bombifrons, Pteronotus quadridens, and Mormoops blainvillei. These species are divided into two families — which share physical traits, evolutionary pathways, and other similarities — called Phyllostomidae and Mormoopidae.
“Most of our work focuses on what we call the pre-emergence phase of pandemics, which recognizes that viruses that eventually spread to humans have a long history of circulation and evolution in their natural hosts long before they reach a person. If we want to improve spillover prevention, we need to advance research and start studying these viruses in their natural systems, trying to understand viral dynamics, their ecology, and their evolution in their natural environment,” Anthony added, noting that they are also pursuing similar research in places such as Nigeria.
Multiple outbreaks of high-impact zoonotic diseases have been linked to bat-transmitted viruses. According to a study published in 2019, the Ebola virus, Marburg virus, Nipah virus, Hendra virus, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), Middle East Respiratory Syndrome coronavirus (MERS-CoV), and SARS-CoV-2 are among those associated with various bat species over the past 50 years.
Caleb Huntington, a member of the research team, highlighted that the diversity of species within the cave — where an estimated 75,000 to 150,000 bats may be found, depending on the season — makes it a “perfect natural laboratory.”
“Having this diverse group of species is really fantastic for us because we expect each bat species to carry its own coronavirus. So when we want to ask questions about coronavirus evolution, there are many of them present in this cave, and we can better understand how they evolve, how they change, and what the ecology of these viruses looks like across different species,” said the member of Anthony’s lab.
At present, the scientists have collected samples from nearly 3,000 bats. They are also conducting air sampling to determine whether viruses can be detected from the cave entrance. One distinctive feature of this cavity within the Mata de Plátano Reserve is that it is known as a “hot cave,” a phenomenon where the concentration of thousands of bats creates unusually high temperatures, making sampling and exploration inside more difficult.
According to Huntington, so far they have detected 14 mammalian viral families, divided into three broad viral groups: dsDNA (double-stranded DNA), ssDNA (single-stranded DNA), and ssRNA(+) (positive-sense single-stranded RNA). They were also able to classify them into 25 different genera, including Mastadenovirus, Macavirus, Circovirus, Alphacoronavirus, and Betacoronavirus.
“We have found coronaviruses in air samples, which is really exciting because it’s a viral family that interests us and shows interesting behavior from an evolutionary perspective. They are known to recombine, so the fact that we can detect them in the air allows us to refine our individual sampling through air samples, because we can detect them quite consistently,” Huntington shared.
Meanwhile, Anthony emphasized that “there is absolutely no evidence that these viruses pose a threat to people or other animals.”
On another note, the researchers shared that in 2024 they observed what appeared to be tumors in species such as Pteronotus portoricensis and Erophylla bombifrons, a topic that — they noted — has not been widely studied. Although they have not identified these anomalies since then, Anthony said they currently hold a permit from the DRNA to collect samples if they observe them again.