Tracking Nipah at the Fault Lines of Ecology, Climate, and Human Behavior

PHNOM PENH — Nipah virus does not spread in predictable waves or seasonal patterns.

It emerges at the fault lines between ecology, climate, and human behavior — often surfacing only after it has crossed from animals into people. To catch it earlier, scientists are rethinking disease surveillance itself, shifting attention from hospital wards to bat roosts, wastewater systems, and the rapidly changing landscapes where spillover risk quietly builds.

Across South and Southeast Asia, researchers are now combining environmental surveillance—particularly wastewater and surface sampling—with bat ecology, land-use data, and climate analysis. The aim is to detect early warning signs of Nipah virus circulation before human infections appear, offering a chance to intervene upstream rather than respond after outbreaks turn deadly.

As deforestation, agricultural expansion, and climate-driven habitat loss squeeze fruit bats of the Pteropus genus into ever-closer contact with farms, livestock, and human settlements, scientists warn that old surveillance models are falling short. The response is a shift in perspective — trying to detect viral signals in water, soil, and other environmental samples, while researchers in the field track bat roosts, movements, and everyday interactions across landscapes increasingly fragmented by human activity.

“So why does Nipah actually challenge the way we usually do surveillance?” asked Erik Karlsson, head of the virology unit at Institut Pasteur du Cambodge. “Part of the problem is that it just doesn’t behave the way most systems expect viruses to behave.”

Unlike pathogens that appear regularly and follow discernible patterns, Nipah outbreaks are rare and highly localized. They are often detected late, Karlsson said, after transmission has already occurred.

“By the time we notice something is wrong, spillover has already happened,” he told a webinar organized by Singapore’s Duke-NUS Medical School’s Centre for Outbreak Preparedness on February 6.

The World Health Organization classified Nipah virus (NiV) as a priority pathogen in 2018, citing its high fatality rate, zoonotic transmission, and pandemic potential. With no approved vaccine or targeted treatment, and outbreaks that remain rare but unpredictable, Nipah continues to pose a serious global health risk.

Concerns resurfaced in late January after Indian authorities confirmed at least two Nipah cases in West Bengal, prompting heightened alerts across South and Southeast Asia.

In Cambodia, the Ministry of Health responded by strengthening preventive measures against possible cross-border transmission. On January 28, Health Minister Chheang Ra inspected health screening and emergency response systems at Techo International Airport alongside aviation, border, and health officials.

Fatality Rates as High as 75 Percent

The virus was first identified during an outbreak in Malaysia in 1998. Since then, most human cases have been reported in India and Bangladesh, where outbreaks are sporadic but often deadly, with fatality rates estimated by the WHO at 40 to 75 percent.

Complicating matters further is the virus’s zoonotic cycle, which is deeply shaped by environmental change. Nipah does not move through a neat, traceable pathway from animals to humans. Instead, it can spread through contaminated food, shared environments, and everyday human practices, influenced by land use and ecological disruption.

“It sits right at the intersection of ecology, environment, and public health,” Karlsson said. “That’s exactly what makes it so difficult to monitor.”

Environmental surveillance is designed to work where clinical surveillance cannot—before people become sick. Researchers test wastewater, surface water, soil, air samples, and high-contact surfaces for Nipah virus RNA, the genetic material that acts as the virus’s fingerprint. Crucially, this does not mean live, infectious virus is present.

“When we talk about RNA, we’re not talking about infectious virus,” Karlsson stressed. “Detecting genetic material doesn’t mean someone can get infected from it.” Viral RNA can persist even after the virus itself has broken down, leaving behind evidence that it was present in the system at some point.

That distinction is essential, he said, because environmental detections are sometimes misinterpreted as signs of active outbreaks. Finding RNA in water or other samples does not mean people are currently infected. Instead, it offers insight into where and when the virus has circulated—information that can help identify rising risk.

“And that’s where a One Health lens becomes essential. This isn’t just about public health. It’s about animal health and environmental health, all happening at the same time. Environmental signals aren’t diagnoses — they’re clues. They help us understand risk,” said Karlsson. “So environmental surveillance, in that sense, works upstream. It’s an early-warning layer, not a clinical one. It helps us see potential danger before people start showing up in hospitals.”

How long Nipah virus—or its genetic material—persists in different environments is therefore a critical research question, said Karlsson, because that persistence makes early detection possible.

Two Nipah Virus Lineages in Cambodia

Surveillance is further complicated by Nipah’s genetic diversity. The virus has two distinct lineages, each associated with different transmission dynamics. One lineage has historically been linked to spillover involving livestock, particularly pigs. The other is more often associated with direct bat-to-human transmission and has been responsible for documented human-to-human spread, especially in healthcare settings with close contact.

“What’s especially important is that both lineages are circulating in Cambodia,” Karlsson said. In some countries, only one lineage is present. In Cambodia, researchers encounter both, increasing the stakes for accurate detection.

Environmental and wastewater monitoring relies on laboratory assays—tests designed to detect viral RNA. Those assays must be capable of identifying both lineages, Karlsson warned. If tests are tuned to only one, critical signals may be missed. “You end up building blind spots into the system,” he said.

While lab-based detection is essential, scientists emphasize that it cannot stand alone. Understanding where risk emerges requires detailed knowledge of bat ecology and changing landscapes.

“It really starts with having a clear picture of the landscape,” said Farah Ishtiaq, principal scientist at the Tata Institute for Genetics and Society in Bengaluru, India. “Where bats are, where outbreaks have occurred in the past, and where people are getting infected—those background details matter more than we sometimes admit.”

Ishtiaq said the One Health approach depends on close collaboration between molecular biologists and field researchers. Ecologists track bat seasonality, feeding behavior, and movement between roosts—patterns increasingly shaped by forest fragmentation, agricultural expansion, and climate stress.

“Land-use change reshapes where bats go and how they interact with people,” she said. “A lot of the viral genetic change we see in bats is happening under those environmental pressures.”

Despite bats being central to Nipah’s ecology, major gaps remain. Researchers still lack comprehensive data on bat roost locations, how stable those roosts are over time, and how bats move between them as landscapes change. Studies examining how bats interact with other animals and shared, human-altered environments are also limited.

“If we could combine ecological insight with basic, consistent surveillance,” Ishtiaq said, “we’d be in a much better position to anticipate where outbreaks are likely to occur.”

Preventing spillover, Karlsson added, ultimately requires integrating environmental signals with social realities. How people farm, collect food, handle animals, and share space with wildlife all shape risk. “Environmental surveillance helps us identify when and where risk is building,” he said. “But understanding how people live and work is just as important.”

Together, those insights allow for targeted interventions—focused risk communication, behavioral changes, and prevention strategies aimed at the right places and communities. For a virus as elusive as Nipah, scientists say that combination may be the best chance to stay ahead, listening for early warnings not just in hospitals, but in the environments where spillover begins.