Hidden viruses in Madagascar wildlife reveal new clues to evolution

Deep in the forests of Madagascar, a collaborative and interdisciplinary group of scientists are uncovering an invisible world — one that may hold powerful insights into evolution, biodiversity and how life is connected.

A new study led by postdoctoral researcher Elise Paietta — mentored by Arvind Varsani, Arizona State University professor in the School of Life Sciences, Center for Evolution and Medicine and Biodesign Center for Fundamental and Applied Microbiomics — analyzed viruses found in lemurs, rodents and shrews and discovered hundreds of previously unknown viruses, offering a rare glimpse into how viruses evolve alongside their hosts.

“Studying virus ecology in Madagascar with a multidisciplinary international team — including Malagasy scientists and local partners — is exactly the kind of collaborative science we need more of,” said Varsani, a passionate advocate for interdisciplinary and internationally collaborative research.

“We’re really digging deep into the ecology and evolution of viruses in animals that people have rarely studied,” said Paietta, who works in the Varsani Lab at ASU and collaborates on this work with Duke University and Zoo New England in the U.S. and Mahaliana Labs, Centre ValBio and Health In Harmony in Madagascar. 

The research focuses on anelloviruses, a group of viruses found in most mammals including humans that typically do not cause disease. Instead of making hosts sick, these viruses quietly persist as part of what scientists consider a normal microbial community.

“They’re infecting the host, but they’re not causing symptoms,” Paietta said. “They’re just part of one’s microbial community.”

“We study anelloviruses across a wide range of animals — including birds, rodents, bears, dolphins, seals, big cats, rabbits and hares. These viruses are remarkably diverse, and in many cases we find distinct viral lineages associated with specific host species, pointing to a long history of co-evolution between virus and host. This host specificity also gives us a powerful tool: by identifying the anelloviruses present in the fecal samples of apex predators, we can detect traces of their prey — effectively reconstructing who ate whom,” Varsani said.

Despite their harmless nature, anelloviruses are anything but simple. Individuals can carry many different anellovirus types at once, sometimes dozens, forming what researchers describe as a highly diverse and personalized viral community. Using oral swabs collected during field expeditions in southeastern Madagascar, the team identified more than 650 viral genomes, including those that represent eight entirely new species.

Madagascar’s unique ecology made it an ideal place for this discovery. The island is one of the world’s top biodiversity hot spots, where many species evolved in isolation over millions of years. Lemurs, for example, have lived and diversified there for roughly 65 million years, creating a natural laboratory for studying how viruses and hosts evolve together.

What the researchers found reflects that long isolation. The viruses detected in lemurs were strikingly different from those found in other primates, suggesting they have evolved along their own path over millions of years.

“These lemurs have been isolated for so long that their viruses have evolved along with them,” Paietta said. “They’re their own lineage.”

A different pattern emerged in black rats — a species introduced to Madagascar by humans about 1,000 years ago. Unlike the lemurs, these rats carried viruses that closely resembled those found in rodent populations around the world, reinforcing the idea that both animals and their viruses travel together.

Because black rats were so abundant in the study, they also provided a unique opportunity to explore how viruses spread within a wild population. The researchers found that older rats tended to carry a greater number of viruses, likely because they had been exposed to more individuals and environments over time. At the same time, rats that lived closer together were more likely to share viruses, highlighting how proximity and interaction shape viral transmission. Even across very different environments, from inland rainforests to coastal forests and nearby villages, the overall pool of viruses remained surprisingly consistent, suggesting these viral communities are deeply embedded in the landscape and constantly circulating among animals.

For Paietta, these patterns reveal how even invisible, nonharmful viruses can reflect the structure of ecosystems.

“It shows that these viruses are really embedded in the environment,” she said. “Animals are interacting with each other and their surroundings, and that’s shaping these viral communities.”

Collaborator Rachel Johnston, director of conservation genomics at Zoo New England, agrees.

“This work highlights the concept of 'One Health' and how closely wildlife and ecosystems are connected,” said Johnston. “Even viruses that don’t cause disease can reveal how species interact with their environment and with each other, helping us better understand biodiversity.”

Studying viruses that don’t cause disease might seem counterintuitive, but scientists say they can offer important clues about biology and health. Because anelloviruses are so widespread and evolve alongside their hosts, they provide a way to understand how viruses change over time without the added complexity of disease. In humans, they may even act as indicators of immune system health, with viral levels shifting in people who are immunocompromised.

“We cannot identify abnormal or pathogenic patterns without first defining the normal virome; nonpathogenic viruses like anelloviruses provide that essential baseline,” says Santatra Randrianarisoa from Mahaliana Labs. “By studying this baseline, we can later identify when something changes — for example, the introduction of new viruses or shifts associated with disease or environmental disturbance.”

The research team also included members of the 31 villages that border the rainforest where this study took place.

"Frontline communities are the forest's best protectors," said Nina Finley, research manager at Health In Harmony, a nongovernmental organization that has collaborated on community-led initiatives in the region for years. "While anelloviruses are harmless, these patterns could apply to other diverse viruses, highlighting implications for conservation and human health."

More broadly, the research highlights how little scientists know about the viral world, especially in understudied host species. Before this work, there were only a handful of known viral genomes from lemurs, despite their importance in evolutionary biology.

“This level of discovery is actually really rare,” Paietta said. “We identified eight new species, and that’s because these animals and their viruses just haven’t been studied much.”

The team used advanced genomic techniques to identify viruses directly from samples, allowing them to detect not just anelloviruses but many different types of viruses at once. That approach is already leading to the next phase of research, which will examine other virus families, some of which may have clearer implications for animal health. 

Looking ahead, Paietta hopes to expand the work across Madagascar’s diverse environments, from rainforests to deserts, to better understand how viral communities vary across species and habitats. With more than 100 species of lemurs occupying dramatically different ecosystems, the island offers a unique opportunity to explore how viruses track with biodiversity.

Ultimately, the study shows that even the most unassuming viruses can tell meaningful stories. Though anelloviruses may not make animals sick, they reveal how species evolve, how they interact and how human activity, such as introducing new species, can ripple through ecosystems in unexpected ways.

“Even viruses that don’t make animals sick can teach us a lot,” Paietta said. “They’re part of the story of life on Earth.”