How Kerala Is Handling Repeated Nipah Spillovers

In late April, Amina had developed symptoms of Nipah Virus (NiV), a highly virulent and fatal zoonotic pathogen that has a case fatality ratio (CFR) between 40% and 100%. May. She became the first NiV case of the four reported independent spillovers in the state this year, and the 10th overall. Two of four confirmed Nipah patients have died, and another survivor, a woman in her 30s from Palakkad, is critical and on ventilator support.

Amina fell into a coma soon after she was admitted to a hospital in north Kerala’s Malappuram district, 30 km away from her home in Valanchery, in late April. And Sajid, a manual labourer, has longed for his wife of 25 years to be back to her old self.

“I thought she would die given the seriousness of the disease,” Sajid told IndiaSpend at Manjeri’s Government Medical College. “She is much better owing to doctors' efforts and people’s prayers. At least our three children can see their umma [mother].”

As her condition improves gradually, Amina has moved her fingers, and responds by moving her forehead and eyes, a relieved Sajid said. But she can only be discharged after the feeding tube is removed when she can eat independently, and when she regains her mobility.

IndiaSpend travelled to Malappuram and Palakkad to understand how and why the deadly virus is being reported repeatedly, and how health systems are working to contain it--in a state that is considered to have a robust health system, and was the first in India to report Covid infections in 2020.

Virus has the potential to infect millions

Fruit bats of the Pteropodidae family are the natural hosts of NiV, a zoonotic illness that is transmitted to people from animals--an event termed as a ‘spillover’. It can also be transmitted through contaminated food or directly from person to person. It was first recognised in Malaysia in 1999, and presently does not have licensed treatment or drugs. The fruit bats which carry and spread the virus are found in many parts of the world, potentially putting 2 billion people at risk of infection.

India reported its first outbreaks in West Bengal in 2001 and 2007. Since 2018, at least one case has been reported in Kerala each year except 2020 and 2022. Kerala's first NiV outbreak in Kozhikode, a district to the north of Malappuram, reported 23 cases of which 21 people died--including the 27-year-old index patient. The outbreak that lasted more than three weeks led to the screening of more than 2,600 close contacts for symptoms and infection. The outbreak, the subsequent public panic and the government's response was eventually depicted in a feature film a year later.

Since 2018, the 37 confirmed cases showed a case fatality ratio of 76%, varying from 33% in 2023 to 100% in three spillovers, depending on the health system’s ability to detect and manage the disease early.

In July, the state government issued a special alert to six districts--Kannur, Kozhikode, Malappuram, Palakkad, Thrissur and Wayanad--to monitor and report symptoms of NiV infection. After earlier outbreaks in Kozhikode, Ernakulam and Malappuram, this year, Palakkad became the latest district to report NiV disease.

The Union government's National One Health Programme for Prevention and Control of Zoonotic Diseases aims to strengthen prevention, detection, and response capacities for zoonotic diseases in India, including NiV. Last year, the government allocated Rs 15.7 crore for the programme of which 65% was spent.

Kerala established a One Health Centre for Nipah Research and Resilience in Kozhikode’s Government Medical College in 2023. “ We do not have specific evidence on how virus is transmitted and under what context; through excreta, or intermediaries like other animals etc.,” the nodal officer of the research centre, Anish T.S., told IndiaSpend in a July 2025 interview.

Year-round surveillance is vital

C. Shubin, the surveillance officer of Malappuram district, looked relieved that it was the final day of quarantine for the last few close contacts of patients in the district. Between answering calls at his desk at the Civil Station (the government’s administrative centre) with a sense of familiarity, he explained the constant need for vigilance throughout the year to detect Nipah spillovers in the community. This was not his first tryst with a NiV spillover.

In July last year, a 14-year-old boy from Pandikkad, 20 km away, showed symptoms of acute encephalitis syndrome (AES). He was admitted to the hospital due to fever and altered sensorium. His condition quickly deteriorated and he had seizures, before he died a day after Nipah was confirmed. Shubin said that year-round surveillance for AES and acute respiratory distress syndrome (ARDS) is crucial to identify a probable NiV infection in the community and prevent an outbreak.

“The symptoms were unusual for AES and we suspected Nipah. The test, including at National Institute of Virology [NIV], Pune became positive," he said.

Constant vigilance and year-round surveillance is vital to detect Nipah spillovers, explains C. Shubin, surveillance officer for Kerala’s Malappuram district.

AES symptoms include an acute onset of fever and a change in mental status, including confusion, disorientation, delirium and coma, as IndiaSpend reported in June 2018. The term was first applied to the surveillance of Japanese encephalitis but now includes a wide range of infectious and non-infectious causes, including viruses, bacteria, fungus, parasites, chemicals and toxins.

In India, 375 million people are at risk of contracting AES, we had reported. In more than 80% of about 10,000 AES cases detected each year, the cause remains unknown.

Last year, following the boy’s death and confirmation of Nipah, authorities announced containment zones and initiated contact tracing. While fruit bats, that can be found aplenty in Malabar’s Western Ghats, are a natural reservoir for NiV, it is difficult to exactly ascertain the source of transmission to the boy, Shubin said.

“We are always looking for AES [in the surveillance], but Nipah gets people’s attention. It is rare for Nipah to show during surveillance,” he said. “The probable source of transmission was a fallen fruit that may be infected [by a bat] that the boy may have eaten, but it is difficult to conclusively ascertain the route or source for a child who liked being outdoors.”

In 2024, it was reported that a 24-year-old man had died in a private hospital in Malappuram of hepatitis. Shubin followed up with the block medical staff who found that the deceased patient had exhibited symptoms of AES, and not hepatitis like the news reported. Luckily, his blood samples had not been disposed of, and screening confirmed Nipah.

This year too, an 18-year-old woman from Makkaraparambu panchayat in Malappuram, who developed symptoms including chest pain and fever in June, died in hospital. Her health started deteriorating quickly at the hospital following seizures which indicated a suspected case of Nipah, according to the state’s Nipah guidelines. When her samples were tested posthumously, Nipah was confirmed.

The virus affects three organs mainly, said Vidhya K.R., district medical officer (DMO) of Palakkad, who was involved in handling the Nipah spillover in Ernakulam in 2019. “The brain may show encephalitis-type features, lungs [may get affected by] respiratory illness, and heart with myocarditis.” she said. “Unlike Kozhikode in 2018, both cases in Palakkad were encephalitis [affecting the brain] due to which close relatives were not infected, and a reason why there was no outbreak.”

There are two confirmed Nipah cases in Palakkad--a woman on ventilator support and a 57-year-old man who died on July 12. While his son, a close contact, was reported to have tested positive in the screening, it was not confirmed by NIV Pune’s Bio Safety Level-4 lab, which indicates a probable false positive in the initial sample tests, officials told IndiaSpend.

NiV outbreaks in India have predominantly shown encephalitis among index cases due to which there is a lesser potential for widespread human-to-human transmission, according to a July 2025 analysis by Rima Sahay, a scientist at NIV, Pune and co-authors including Shubin. Symptoms like altered mental status and seizure may lead to a faster hospitalisation and reduction of transmission as has been seen in many cases in Kerala.

“In contrast, individuals with respiratory presentations, particularly those with cough followed by ARDS, may remain undiagnosed and in the community for a longer period, potentially shedding higher amounts of virus and contributing to more extensive transmission,” the authors wrote, highlighting a need to identify those with respiratory distress in NiV-prone regions through surveillance.

Nipah-related IEC in Palakkad government medical college

Nipah control room in Malappuram

Routine surveillance for Nipah in Kerala certainly is of much better quality than anywhere else, but its unique climate and ecology also render it more suitable for the types of fruit bats that are Nipah carriers, according to Gautam Menon, dean (research) and professor, departments of physics and biology, at Ashoka University. “Lack of extensive bat-human contact, unlike in some communities in the Northeast, might mean that antibodies to infection don't exist in those who might encounter infected fruit,” said Menon, who is also a commissioner on the Lancet Commission on Strengthening the use of Epidemiological Modelling of Pandemic Diseases.

3 km containment radius and fever survey

Once a Nipah case is confirmed, the protocol mandates contact tracing, which restricts an outbreak in the community. Contacts are classified based on the time spent, distance maintained, and the protective equipment worn while interacting with an infected patient.

According to data accessed by IndiaSpend, there were 720 primary contacts--that is, people who had direct contact with a patient confirmed to have Nipah. Of these, 37 were classified as ‘highest risk’ and 138 as ‘high risk’.

As it was the first time the Malappuram health team was encountering NiV in 2024, two whole panchayats were declared containment zones as a matter of caution. The containment zones are declared to restrict movement of people and contact-trace quickly, follow up possible contacts and create a route map using CCTV and cell phone tower locations.

But considering it was inconvenient for the people as it was not as contagious as Covid, for the second case, they decided to be more scientific by restricting the containment to a 5-km radius, said Shubin. This year, in Palakkad and Malappuram, 3-km radius containment zones were announced. The radius is a rough estimation of the flight path of fruit bats that forage for food. This was followed by an active fever survey to check if any household reported symptoms of fever, AES or ARDS.

In order to manage and control a probable spread, 26 committees including officials from departments like health, education, local self government, animal-husbandry and forest department coordinated for various tasks. A control room, similar to the action taken during the initial phase of the pandemic, was created to follow up on contacts and quarantined people.

Contacts are tested only if they have any symptoms like fever. Asymptomatic highest and high risk contacts are required to be in home quarantine for 21 days from last contact with a patient, and are monitored twice daily by the call centre and/or health workers. Low-risk contacts are not required to be quarantined but are monitored for any symptoms for 21 days.

“Physical infrastructure was set up in the medical college including 21 rooms as isolation ward and another floor for call centre management,” G. Priyanka, Palakkad district collector told IndiaSpend. While the public’s familiarity with Covid protocols has made it easier to establish containment zones, it is a challenge because it affects lives and livelihoods of people, particularly those in the informal sector and daily wagers.

A National Joint Outbreak Response Team, comprising of experts in animal husbandry and dairying, forest & wildlife and human health, and bat survey team were deployed for reviewing these outbreaks, the Union health ministry told the Lok Sabha this month.

In Makaraparrambu gram panchayat where the 18-year-old woman died, Salini P., a junior health inspector at the primary health centre, was part of the team that administered the fever survey. The activities began on July 4 after the confirmation of NiV from the samples, and a day after Salini met the family of the deceased woman to get more details.

The survey in the 3-km radius to identify fever or AES symptoms was conducted by around 200 field staff comprising 94 teams that included junior health inspectors, public health nurses, accredited social health activists (or ASHA workers), and other staff associated with various health schemes. To ensure that that survey was completed in three days, anganwadi teachers were also roped in. They covered 20 wards and more than 40,000 people.

“We visited each house and asked for details based on the form, and also created a route map including travel details. We had 22 people in our panchayat,” said Salini, who was handling Nipah-related work for the first time in her five-year career as field staff. “It is scary, but it is an achievement to get so many health staff to do the survey [in a short span].”

A copy of the Nipah related active fever surveillance form administered in containment zones

The form for the fever survey accessed by IndiaSpend notes details of members of the household, fever and AES or ARDS details, and additionally, records information on the presence of bat roosts and pigs, animal deaths, and possible interactions with a patient.

Exact source of transmission to humans is difficult to identify

One of the challenges for researchers is to exactly ascertain the source of transmission to humans from animals. Sajid, who did not develop symptoms, did not know how Amina may have got the infection. “There are no bat roosts that I know of near our house although there are bats like any other place,” he said. Meanwhile, for the comatose NiV patient from Palakkad who lived near a huge bat roost, there is a higher probability of transmission, said experts

Due to its highly contagious nature, testing and research on NiV requires the highest bio safety requirements. IndiaSpend has reported that the diagnostic RT-PCR and serology on inactivated samples can be done under biosafety level 2 (BSL-2) conditions; the virus inactivation has to be done at BSL-3; and virus propagation, isolation, quantification and neutralisation require BSL-4 facilities--which have the highest biosafety level requirements. Presently Indian Council of Medical Research National Institute of Virology (ICMR-NIV), Pune alone has BSL-4 facilities for high risk viral pathogens.

“With careful epidemiological work, the precise modes of transmission can be established,” said Menon. “From what we know earlier, transmission through close contact and the potential exchange of bodily fluids remains the most likely scenario.”

According to a hypothesis proposed by T. Jacob John, virologist and public health expert, and ICMR researchers Nivedita Gupta and Manoj Murhekar, air-borne virus transmission is a potential spill-over route in Kerala and possibly elsewhere. John told IndiaSpend that air-borne transmission is a hypothesis, which needs verification--to prove or disprove. But limiting spillovers will be a real challenge.

“The pattern [in Kerala] is stray cases with multiple secondary cases as an exception. If such episodes are occurring elsewhere, aetiological diagnosis [causes for a disease] is not guaranteed,” he said. “Unless clinically suspected and virologically tested, cases can be missed.”

A March 2022 analysis said that there was a “heightened need of constant surveillance of NiV in bats, animals and humans”, considering there was no identified route of transmission either through an intermediate host or confirmed mode of entry. It showed that 20% of throat and rectal swabs as part of NiV serosurvey in specific fruit bat species showed that sera samples had anti-Nipah Immunoglobulin G antibodies, indicating possible earlier infection, but specimens did not detect a virus.

Presently, as we said, there is no licensed drug or treatment for NiV. The post-exposure treatment includes remdesivir and favipiravir, antivirals employed by some doctors even during the Covid pandemic, albeit without evidence. The state insists that due to inadequate scientific evidence to support the use of either remdesivir or favipiravir, “an informed consent should be obtained prior to initiation of these drugs for chemoprophylaxis [use of drugs to prevent disease or infections].” Two vaccines against Nipah virus are set to enter human clinical trials in Bangladesh next year.

Public participation is crucial in such circumstances as are proper insurance and safety net measures to cover any income loss due to quarantine, said Menon. “If people trust the public health system to take care of them, they will report, rather than cover up.”

IndiaSpend has written to the National Centre for Disease Control and NIV Pune for comment on the concerns about repeated spillovers, research and challenges, treatment, and community and government response. We will update this story when we receive a response.

*Names of individuals have been changed to protect identity

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