Inside the Race to Stop a Deadly Viral Outbreak in India

Quick thinking and medical sleuthing allowed Kerala to contain a potentially disastrous Nipah virus outbreak this month—but with viral spillovers happening more frequently, containment is a fragile shield.

On the morning of September 11, critical care specialist Anoop Kumar was presented with an unusual situation. Four members of the same family had been admitted to his hospital—Aster MIMS in Kozhikode, Kerala—the previous day, all similarly sick. Would he take a look?

He gathered his team of doctors to investigate. Soon they were at the bedsides of a 9-year-old boy, his 4-year-old sister, their 24-year-old uncle, and a 10-month-old cousin. All had arrived at the hospital with fever, cough, and flulike symptoms. The 9-year-old was in respiratory distress, struggling to breathe properly, and had needed to be put on a noninvasive ventilator, with air pumped through a mask to keep his lungs expanded.

Their symptoms were concerning and mysterious—none of the team could pinpoint what was wrong. But delving into their family history, Anoop and his colleagues soon uncovered a clue. The father of the two young siblings, 49-year-old Mohammed Ali, an agriculturalist, had died less than two weeks previously. And when the team at Aster MIMS got in touch with the hospital that had treated Ali, they found that he had been admitted with similar symptoms, pneumonia and fever.

Digging deeper, they learned from the other hospital that Ali had also had some neurological symptoms, which had seemingly been overlooked by his doctors—he’d had double vision, suffered seizures, and spoken with slurred speech. Despite this, Ali’s death had been attributed to “multi-organ failure,” a vague diagnosis with no indication of the cause. Alarm bells started ringing in Anoop’s head.

Ali’s case reminded Anoop of May 2018, when he’d diagnosed five patients with a combination of flulike symptoms, respiratory distress, and neurological problems. Those patients had been suffering with a rare but deadly zoonotic virus called Nipah.

Believed to be spread to people from bats, Nipah has a fatality rate in humans of somewhere between 40 and 75 percent. In the 2018 outbreak in Kerala, India’s first ever, 18 people caught the virus. Seventeen died.

“You can contract it with direct contact with infected animals, such as bats or pigs, or from food or water contaminated with their body fluids,” says Thekkumkara Surendran Anish, associate professor for community medicine at the Government Medical College in Manjeri, Kerala, who leads the state’s Nipah surveillance team. “Close contact with an infected person and their bodily fluids can expose you to Nipah as well.” The virus has since emerged multiple times in Kerala.

Anoop and his team knew they had to act swiftly—there are no authorized treatments for Nipah, nor are there vaccines for protection. If the virus were to take hold or spread outside of the local area, the effects could be catastrophic. But first they needed confirmation.

The cluster of mysterious cases in these patients, their connection to Ali, his concerning neurological symptoms, his lack of a proper diagnosis—“We had strong reason to suspect Nipah again,” Anoop says. “Another red flag was the rapid decline of the patient,” Anoop says of Ali. Within a matter of days, he had fallen sick and died. And then there was one final alarm: “Ali lived close to the epicenter of Kerala’s 2018 Nipah outbreak.”

Fearing the worst, the team immediately isolated the patients and sent the family nose-and-throat swabs for testing. No sooner had they done this than another patient was admitted with similar symptoms. Forty-year-old Mangalatt Haris, who lived in Ayanchery, Kozhikode, arrived at Aster MIMS in a critical condition. He died later that day. His nasal swab samples were sent to test for Nipah as well.

The results came back the following day—three of the patients had tested positive for the virus: Ali’s 9-year-old son, his 24-year-old uncle, and the seemingly unrelated Haris. The hospital where Ali had been treated had taken nasal swabs from him to rule out Covid and various other infections. These, too, were sent for testing, and turned out to be Nipah-positive, seemingly establishing Mohammed Ali as the first case in this outbreak.

But was he? Haris had no link with Ali’s family, nor did he live in the same neighborhood. He might have picked up the virus from someone unknown. Ali might not be the first case, just the earliest to have been spotted so far. Also on Anoop’s mind was the incubation period. The virus takes hold over 14 to 21 days, meaning weeks can pass between getting infected and showing signs of being ill. If others out there were involved in this outbreak, the virus could already have spread widely, unnoticed.

Code Red

The gravity of the situation wasn’t lost on the state authorities. With these positive Nipah diagnoses confirmed, Kerala’s public health mechanism swung into overdrive. On September 13, health authorities divided the district into containment zones and instituted strict lockdown measures across them, just like they did for Covid. Schools, offices, and public transport were shut down, travel into and out of the zones was restricted, and only essential shops were allowed to stay open, and for limited hours. As a precaution, people had to use masks, practice social distancing, and use hand sanitizers. State health workers then set about the arduous task of contact tracing. They isolated anyone with a fever and traced 1,233 contacts of the cases—anyone who had come into contact with Mohammed Ali, his family, and the second patient Haris when they were likely to be infectious. One health worker tested positive.

Meanwhile, doctors were studying the family history of the second patient, Haris, to try to draw a link between the cases. Poring over his every move before he was admitted to Aster MIMS, they eventually made a breakthrough, thanks to some CCTV footage.

“We learned that Haris had accompanied his sick father-in-law, who was admitted in the same hospital [as Ali], and was in an emergency ward next to Ali’s,” says Anish. The two wards shared a health worker, whom authorities suspect may have spread the virus between the two.

On the morning of September 15, yet another case was diagnosed—a 39-year-old man who had also been in the same hospital as Ali while tending to a sick relative, underlining the likelihood that this is where the virus had spread from. The positive cases now numbered six, of which two had died. The fear of an unseen chain of transmission out in the community, though, had diminished.

“It isn’t immediately apparent how the disease is spreading,” says Anish of the hospital transmissions, noting that the virus isn’t airborne. “There’s a lot we don’t know about it yet, but we do know that patients are more infectious as the disease advances.” Hospitals in particular are high-risk settings, Anish says, because Nipah can thrive on surfaces and be passed on to health care workers through contact with body fluids of infected patients. Hand hygiene is important, he points out. In the recent outbreak, 118 health workers were quarantined.

No new Nipah cases have been reported in Kerala since September 16, and there have been no further fatalities. The state’s health minister, Veenu George, has said that the current outbreak is under control. The neighboring states of Tamil Nadu and Karnataka have been on high alert, and no new cases have been reported there, though these states have less vigilant health surveillance systems compared to Kerala.

Efficient, Lucky—or Both?

Diagnosing Nipah quickly has been Kerala’s biggest strength, giving it an edge in the battle with the virus and preventing its spread outside of the state. This has relied on knowledgable doctors, like Anoop and his colleagues, and having testing facilities that can handle samples at breakneck speed. Decisive action—to contact trace, lock down, quarantine—has also made Kerala’s response exemplary. This is how an infectious disease containment strategy should work.

Nevertheless, this is still an uneasy situation. This is Kerala’s fourth outbreak in five years, and with the virus being able to infect someone and then hide for weeks, if Nipah keeps spilling into humans this regularly in Kerala, it will eventually spread beyond the state. And stopping those spillovers hasn’t seen much progress.

Health authorities are still grappling with the puzzle of how the index patient in this outbreak, Ali, contracted the disease in the first place. In 2018, an analysis of fruit bats in Kozhikode proved that they harbored the virus. But while this time, 36 samples have been taken from bats around the area where Ali lived, none of them have tested positive for Nipah so far.

Sreehari Raman, an assistant professor of wildlife science at Kerala Agricultural University, has studied the natural history of bats in Kerala for the past decade. The subject of his ongoing PhD thesis is about identifying bat hotspots and understanding the impact of climate change on bat communities, including endangered species of bats in this region. He recently inspected bats in the areas of Kozhikode involved in this outbreak.

“We found that bat populations were increasingly under stress,” he says. “The evergreen forests in this region were drying up. That means the quality of habitat for bats was quickly changing and degrading.”

Raman located six roosting sites for these fruit bats within a 1-km radius in Kozhikode. Once upon a time, these bats would have made their homes in forests, but none of these roosts were in such an area. In addition to drying out, many forest sites have been disturbed or destroyed by extensive laterite mining, Raman says.

Instead, Raman found three roosts along a national highway, with the rest in sacred groves, protected areas that usually belong to temples and places of worship. It is evidence that when bat habitats are constantly destroyed, Raman says, the animals are forced to live closer to human habitation. On inquiries with the forest department and locals, Raman found that some people even set off fireworks to drive bats out when they find them too close to their homes or offices—signs of both the bats’ close proximity and how they are being increasingly disturbed.

Such stress could explain why spillover events are becoming more common, with bats driven into physical contact with people. But further study is needed to establish a scientific link. The role of parasites in the transmission of Nipah has also been overlooked, Raman says. Parasites that suck blood from bats could be potential vectors, he hypothesizes.

But the influence of our changing world on increasing spillovers is almost undeniable. A confluence of climate change, urbanization, deforestation, and altered human migration, in some cases driven by political instability, have come together to create a perfect storm that makes spillover events more common, says Peter Jay Hotez, a specialist in neglected tropical diseases and the author of Preventing the Next Pandemic. Scientists from different disciplines—biomedicine, social sciences, and climate science—need to work together to raise awareness among communities facing these threats. “Awful epidemics will continue unless we can organize global efforts to understand the ecology of viral infections better,” he says.

If we don’t, and we keep pushing humans and the likely reservoirs of these viruses into closer contact, it will only be a matter of time before Anoop and others like him will be responding to yet another suspected outbreak. And next time, the virus may have spread much farther before doctors and scientists pick it up.

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