The Nipah virus doesn’t spread in predictable waves or seasonal patterns. Instead, it emerges at the intersection of ecology, climate, and human behavior – often surfacing only after it has crossed from animals to people. To improve early detection, scientists are rethinking disease surveillance, shifting focus from hospital wards to bat roosts, wastewater systems, and rapidly changing landscapes where the risk of spillover 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 goal 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 become deadly.
As deforestation, agricultural expansion, and climate-driven habitat loss force fruit bats of the Pteropus genus into closer contact with farms, livestock, and human settlements, scientists warn that traditional surveillance models are falling short. The response is a shift in perspective – attempting to detect viral signals in water, soil, and other environmental samples, while researchers in the field track bat roosts, movements, and everyday interactions across increasingly fragmented landscapes.
“Part of the problem is that it just doesn’t behave the way most systems expect viruses to behave,” explained Erik Karlsson, head of the virology unit at Institut Pasteur du Cambodge. Unlike many pathogens that appear regularly and follow discernible patterns, Nipah outbreaks are rare and highly localized, often detected late, after transmission has already occurred.
The World Health Organization (WHO) classified the Nipah virus (NiV) as a priority pathogen in 2018 due to its high fatality rate, zoonotic transmission, and pandemic potential. With no approved vaccine or targeted treatment currently available, and outbreaks remaining infrequent but unpredictable, Nipah continues to pose a serious global health risk.
Concerns resurfaced in late January after Indian authorities confirmed at least two cases of Nipah in West Bengal, prompting heightened alerts across South and Southeast Asia. In response, the Cambodian Ministry of Health reinforced preventative measures against potential cross-border transmission. On , the Minister of Health, Chheang Ra, inspected health control measures and emergency response systems at the Techo International Airport, alongside officials from aviation, border control, and health agencies.
Lethality Rates Reaching 75%
The virus was first identified during an outbreak in Malaysia in 1998. Since then, the majority of human cases have been reported in India and Bangladesh, where outbreaks are sporadic but often fatal, with WHO-estimated fatality rates ranging from 40 to 75 percent.
The situation is further complicated by the virus’s zoonotic cycle, deeply influenced by environmental changes. Nipah doesn’t follow a simple, traceable path from animals to humans. It can spread through contaminated food, shared environments, and daily human practices, influenced by land use and ecological disruption.
“It sits right at the intersection of ecology, environment, and public health,” Karlsson stated. “That’s precisely what makes it so difficult to monitor.”
Environmental surveillance is designed to work where clinical surveillance cannot – before people become sick. Researchers analyze wastewater, surface water, soil, air, and high-touch surfaces for Nipah virus RNA, the genetic material that serves as the virus’s fingerprint. It’s crucial to note, however, that this doesn’t necessarily indicate the presence of live, infectious virus.
“When we talk about RNA, we’re not talking about infectious virus,” Karlsson emphasized. “Detecting genetic material doesn’t mean someone can be infected from it.” Viral RNA can persist even after the virus itself has degraded, leaving evidence of its past presence in the system.
This distinction is essential, he explained, as environmental detections are sometimes misinterpreted as signs of active outbreaks. Finding RNA in water or other samples doesn’t mean people are currently infected. rather, it provides indications of where and when the virus has circulated – information that can help identify increasing risk.
“It’s not just about public health. It’s about animal health and environmental health, all happening at the same time. Environmental signals aren’t diagnostics – they’re clues. They help us understand the risk,” Karlsson said. “Environmental surveillance works upstream. It’s an early warning layer, not a clinical tool. It helps us see a potential hazard before people arrive at the hospital.”
The duration for which Nipah virus – or its genetic material – persists in different environments is a crucial area of ongoing research, as this persistence enables early detection.
Two Nipah Virus Lineages in Cambodia
Surveillance is further complicated by the genetic diversity of Nipah. The virus has two distinct lineages, each associated with different transmission dynamics. One lineage has historically been linked to transmission 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 transmission, particularly in healthcare settings where close contact is frequent.
“What’s particularly important is that both lineages are circulating in Cambodia,” Karlsson noted. In some countries, only one lineage is present. The presence of both lineages in Cambodia increases the challenges of accurate detection.
Environmental and wastewater surveillance relies on laboratory tests – analyses designed to identify viral RNA. These tests must be capable of identifying both lineages, Karlsson cautioned. If adapted to only one, critical signals may be missed. “We end up creating blind spots in the system.”
While laboratory detection is essential, scientists emphasize that it cannot function in isolation. Understanding where risk emerges requires detailed knowledge of bat ecology and evolving landscapes.
“It really starts with a clear vision of the landscape,” explained Farah Ishtiaq, a principal researcher at the Tata Institute for Genetics and Society in Bengaluru, India. “Where are the bats, where have outbreaks occurred in the past, and where are people getting infected – this contextual information matters more than we sometimes admit.”
Ishtiaq explained that the approach relies on close collaboration between molecular biologists and field researchers. Ecologists track bat seasonality, feeding behaviors, and movements between roosts – patterns increasingly shaped by forest fragmentation, agricultural expansion, and climate stress.
“Changes in land use are altering where bats go and how they interact with humans,” she said. “Much of the viral genetic changes we’re observing in bats is happening under these environmental pressures.”
Despite the central role of bats in Nipah ecology, significant gaps remain. Researchers still lack comprehensive data on roost locations, their stability over time, and how bats move between roosts as landscapes evolve. Studies on interactions between bats, other animals, and human-altered environments also remain limited.
“If we could combine ecological knowledge with basic, consistent, and ongoing surveillance,” Ishtiaq said, “we would be in a much better position to anticipate areas where outbreaks are likely to occur.”
Preventing interspecies transmission, Karlsson added, ultimately requires integrating environmental signals with social realities. How populations cultivate, collect food, handle animals, and share space with wildlife strongly influences risk.
Together, this knowledge enables targeted interventions – risk communication, behavioral changes, and prevention strategies tailored to the right places and communities. For a virus as elusive as Nipah, scientists believe this combination represents the best chance of staying ahead, listening for early warning signals not only in hospitals, but also in the environments where interspecies transmission begins.
