Trying to crack the Nipah virus code: How does it spill from bats to humans? : Goats and Soda Nipah virus, which can rapidly infect and kill members of a community, is carried by bats. Exactly how does it cross over into humans? Researchers in Bangladesh are trying to find out.

The Nipah virus has a kill rate of 70%. Bats carry it. But how does it jump to humans?

The Nipah virus has a kill rate of 70%. Bats carry it. But how does it jump to humans?

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A field researcher holds a male bat that was trapped in an overhead net as part of an effort to find out how the animals pass Nipah virus to humans. The animal will be tested for the virus, examined and ultimately released. Fatima Tuj Johora for NPR hide caption

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Fatima Tuj Johora for NPR

A field researcher holds a male bat that was trapped in an overhead net as part of an effort to find out how the animals pass Nipah virus to humans. The animal will be tested for the virus, examined and ultimately released.

Fatima Tuj Johora for NPR

It's dusk in central Bangladesh, in a community within the district of Faridpur. A 50-year-old man sits outside his home beside a rice paddy. His name is Khokon. A fiery beard, dyed a bright orange, rings his chin.

He says the procession of disease and death all started in the spring of 2004. "So the first one was the mother-in-law of my elder brother. She was really sick," Khokon says. "She had been sick for some time. Then she died. We took her to the grave. Then my father got sick."

Khokon stares off into the distance as he explains that his father was a spiritual leader in the community. When he became ill, many came to pay their respects and offer their prayers. "Just 12 days after, my father died," he says. "Suddenly, he was no more."

Hidden viruses: how pandemics really begin

NPR is running a series on spillover viruses — that's when animal pathogens jump into people. Researchers used to think spillovers were rare events. Now it is clear they happen all the time. That has changed how scientists look for new deadly viruses. To learn more, we traveled to Guatemala and Bangladesh, to Borneo and South Africa.

We have a quiz to test your spillover knowledge. But we'd also like you to quiz us. Send your questions about spillovers to with "spillovers" in the subject line. We'll answer questions in a follow-up post when the series concludes in mid-February.

Many of his visitors also got sick. One person traveled to an adjacent village, where four more people fell ill. "It was not understood what was happening," says Mahmudur Rahman, who worked for the Bangladeshi government around that time as director of the Institute of Epidemiology, Disease Control and Research. "Some people who were transporting the patients to the hospital were also getting sick."

Sick often meant encephalitis — a swelling of the brain. Epidemiologist Emily Gurley led an on-site outbreak investigation back then and is now based at Johns Hopkins University. She says, "The signs and symptoms of encephalitis are fever, headache, but often altered mental status or coma." Disorientation and seizures were common. "But many of these patients also had respiratory disease," Gurley adds, which often led to coughing, vomiting and difficulty breathing.

The virus appeared to be spreading through respiratory droplets and saliva. And the sicker people got, the more infectious they became.

For Khokon and his wife, Anwara, the nightmare continued for weeks as they watched relative after relative get sick, suffer and die. Khokon's older brother, his sister, two uncles, his aunt, his nephew and his mom and dad ... all dead. It was numbing. "In Bangla, they say 'it is a bad wind' or 'an act of God,'" explains Rahman.

An aerial view of Faridpur, the district that's witnessed the most Nipah outbreaks in all of Bangladesh.
Zabed Hasnain Chowdhury for NPR

Anwara says, "When people started dying out of the virus, people were very afraid. No one came here! Nobody, not even a dog came to this house."

And then, the two of them came down with the virus. (Because the disease carries such a stigma, we are using only their first names.) "I actually have no recollection of that time," says Khokon. "I don't even remember who carried me to the hospital or who carried me to the bed. I was in no shape to remember anything. Me and my wife were unconscious. People couldn't say if we were dead or alive."

In addition, Khokon says those caring for them "said that we had high fever, very high fever." Anwara says a neighbor told her, "Like whenever they were touching us, it was like touching fire."

Somehow, they survived. "It was a miracle," says Khokon.

Anwara prays beside the grave of her father-in-law, a religious leader who died from Nipah virus in the 2004 outbreak in Faridpur, Bangladesh. Fatima Tuj Johora for NPR hide caption

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Fatima Tuj Johora for NPR

This outbreak, says Rahman, made something brutally evident. The as yet unidentified virus was "obviously showing that we are unable to control it, and it is spreading," he says, from person to person. "That is the clear message."

And with a kill rate of roughly 70%, what virus could be that deadly? At the time, Gurley says, "We didn't know! I was just looking at the data to see what do we think is going on here?"

Gurley wondered, could it be SARS — a coronavirus that infected some 8,000, mainly in China and Hong Kong, from 2002 to 2004?

Or perhaps another, and even more disturbing possibility — could it be a rare, poorly understood virus called Nipah?

"Nipah is terrifying, unusually terrifying," says Dr. Stephen Luby, currently a professor of medicine at Stanford University, who was in charge of the outbreak investigation for eight years at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b). He says it's terrifying, in part, because the virus is so deadly in people. Also, the outbreaks are tightly clustered. "And so the people who are sick know each other," he says. "And because of this, it is a clear community crisis."

In addition, part of what makes Nipah so worrisome is that its history offers evidence that it might, under the right conditions, launch a pandemic. It had first shown up in Malaysia and Singapore in the late '90s. Around that time, Malaysia had started farming pork at an industrial scale — huge numbers of pigs wedged into cramped conditions. When the pigs got Nipah from local fruit bats, the virus spread easily. And then, pig farmers caught it as well.

But in Bangladesh, things were different. "There were a few pigs being raised in this village," says Gurley. "None of them had been sick. And none of the cases had had any contact with these pigs. Pretty clearly," she says, pigs didn't seem to be behind these Nipah outbreaks.

A puzzle to solve: How does the virus spill from bats into humans?

A few weeks later, the Centers for Disease Control and Prevention in Atlanta sent an email to Gurley and her colleagues confirming the deadly virus to be Nipah. So they wondered: Just how was the virus spilling over from bats into humans? This was the puzzle that needed solving for two reasons. First, to prevent more people from getting sick. And second, to rein the virus in.

"So what we did is walk through the village and thought about all the possible ways people could come into contact with bats or bat secretions, bat urine, bat saliva," says Gurley.

They thought that maybe it came from climbing trees where the bats had fed or roosted. Or eating fruit off the ground that bats had already taken a bite out of. They considered a much beloved local delicacy: the sap traditionally harvested from date palm trees. "And we thought, 'Well, this would be a great way to have contact with bat secretions because I'm sure the bats love the sap and so do people,'" says Gurley.

The urgency to figure out the connection between bats and humans continued to mount, as Nipah flared again the following year. The investigators came to realize there had also been earlier outbreaks — in 2001 and 2003. Bangladesh decided to set up its own Nipah surveillance system.

Finally, a link emerged, but the researchers needed more evidence. In 2007, they got their chance with yet another outbreak, this time in Thakurgaon in northwest Bangladesh. Of the seven people who contracted Nipah, three were dead. People were again in a panic.

Rebeca Sultana, an anthropologist with the icddr,b, remembers a call to join the investigation team. "Our colleague called me and asked, 'Rebeca, would you like to go? Are you ready?' I said, 'Yes, I am ready to go there.'"

The next morning, Sultana drove with the team from Dhaka to Thakurgaon. Once she arrived in the village, she went straight to the home of patient zero. "I tried to talk to the elder sister-in-law of the guy who died," she says, "and she was so upset and she just ran and came to me, and hugged me and started crying."

Getting that close to her scared Sultana. As Syed Moinuddin Satter, who leads the Emerging Pathogen research group at icddr,b, says, doing this work is like putting "your soul in your hand. You don't know what is waiting for you in the field."

But Sultana's heart went out to the woman. And she hugged her back. She said to her, "Please don't worry. We're here." She explained that although they didn't know for sure what had caused her relatives to fall ill, "we are here to understand why this happened" by listening openly to the people who had witnessed Nipah firsthand.

(At the research center icddr,b, anthropologists are routinely asked to join these kinds of outbreak investigations when trying to piece together routes of transmission. Their job, in Sultana's words, is "to learn from the community." As Sultana's colleague, Shahana Parveen, says, "Our role as anthropologists, when we get into the community, first we give them space to listen to them — their anger, their stress. But we didn't respond, 'OK, this is not right, or this is wrong.'")

After Sultana finished her preliminary interviews, she then asked the community to meet her in the town market to help draw a map of the village. About two dozen people showed up. "I don't do anything," she explains. "I just ask questions. And then they draw it."

Using sticks in the dirt, the residents roughed out houses, roads, bat roosts. The shape of the outbreak gradually emerged. Soon, the villagers began sketching in date palm trees.

"This is the first time the people informed me," Sultana says, of multiple date palm trees and "a sap harvester in this community."

She hadn't seen the date palm trees on the drive in. But staring back at her from the dirt was the possible link between how the fruit bats had passed Nipah into this community. In particular, when the bats drank the sap, the researchers suspected that Nipah could have moved from their saliva or urine into the sap stream, contaminating the sweet liquid. So someone who drank that sap would be in danger of becoming infected.

Photos captured by an infrared camera show proof of bats licking the date palm sap. The photo on the left shows the container used to collect the sap. Researchers believe bat saliva or urine can infect the sap with Nipah virus, which is later drunk by locals. Ausraful Islam, icddr,b hide caption

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Ausraful Islam, icddr,b

Sultana and her colleagues tracked down the sap harvester. And he led them to some friends of the guy who was patient zero for this outbreak.

"They said 'we all used to drink raw sap in the morning,'" she says. This was Sultana's aha moment — that patient zero had drunk raw sap before falling ill. She says this helped the researchers trace a line between the bats, the sap and the outbreaks. "It's a long journey," she admits. This journey included work over the next few years where researchers took infrared cameras and caught the bats (among other creatures, including rats, bugs and owls) at night drinking from the same stream of sap that people were harvesting.

Eventually, the government had enough evidence to launch a campaign against the drinking of raw sap. However, it was a lot to ask people to set aside something that had been a cultural practice for hundreds of years. So despite the warnings, people continued to drink the sap.

Ausraful Islam, a veterinarian and infectious disease specialist at the icddr,b, explains that the consumption of raw date palm sap "is not something you can control. You cannot send police to every house, every village to stop them drinking it. It is not possible."

Sultana and her team developed an alternative messaging campaign to promote "safe sap." They helped produce a couple of TV docudramas in which the actors explain how to collect the sap safely — by putting a protective skirt (called a "bana") around the part of the tree with the tap, which keeps the bats out. But people don't always do it. So not every tree is protected. And the spillovers of Nipah virus from bats to people have continued.

Two tricks are the key to Nipah's persistence

It has been 20 years since the harrowing, practically yearly outbreaks started rocking Bangladesh, claiming more than 200 lives to date. And still there's no treatment for Nipah. There's no vaccine. It remains on the World Health Organization's list of viruses with pandemic potential. That's because it has two main tricks.


First, it can jump between species. "We've shown cattle, goats, pigs, cats, dogs can all get infected with Nipah and have been infected with Nipah in Bangladesh," says Gurley. "We don't know how." Perhaps, she says, it's through sap or dropped fruit. Or for pigs and carnivores, it may be through scavenging bat carcasses or placentas. "We're starting a new study to try to figure this out," Gurley says.

The second trick is that Nipah spreads from person to person. So far, Nipah doesn't do a particularly good job of that because the virus tends to kill its host. That means that despite these nearly yearly outbreaks in Bangladesh (with a larger one every four or five years), each has fizzled relatively fast. But each time Nipah makes that leap from bat to person, it gets another chance to find the right combination of mutations to become more transmissible, which could propel it into the realm of a deadly pandemic.

"If we want to contain the virus," says Islam, "we have to understand the virus."

That's why, at 3 a.m. on a cold December morning, Islam stops at the edge of a forest and looks up into the sky, some four stories above the ground, where a 70-foot net stretches between two mahogany trees. He's out here early "because the bats will start coming back from foraging after 3, so this is the best time to catch them," he says.

Early December marks the beginning of what's notoriously known as Nipah season: the four months when the virus is most likely to show up in people. This is when the date palm sap is flowing.

Every month, Islam brings a team out near Faridpur to capture bats. This place is nestled inside the "Nipah Belt," the chunk of central and northwest Bangladesh where — in the words of local physician Dr. Abu Faisal Md Pervez — the virus is synonymous with "death."

The answer isn't getting rid of the bats. Islam has enormous respect for the animals and their importance to the local ecosystem.

Rather, years of studying and sampling thousands of greater Indian fruit bats out here have shown that most of them carry Nipah virus. However, fewer than 1% of them actually release it into the environment. Islam is trying to work out why that is — what's prompting those few animals to shed it.

Most likely, it's connected to some kind of stress the bats are facing. "Is it lack of food?" he wonders. "Is it pregnancy stress? Is it lack of habitat?"

And knowing the answers to those questions could help Islam and his colleagues figure out what action to take to keep Nipah from finding its way into people in the first place.

On and off over the past 15 or so years, Islam and his team have analyzed which strains of the virus are circulating and — in so far small and unconcerning ways — how it's evolving. One of Islam's colleagues, Mohammed Ziaur Rahman, who heads up the One Health Laboratory at icddr,b, says this is the information they need to ultimately conquer the virus. And yet, "we are at the very earliest stages of preparing ourselves to combat Nipah," he confesses.

Nabbing bats and pondering a glass of date sap

The coming dawn is full of sound. Multiple calls to morning prayer from nearby mosques envelop the small research team. Jackals cackle. And birds flute.

Finally, about an hour before daybreak, a female bat is caught in the net. The team brings her down to earth and untangles her with care. She's big — an adult's wingspan easily reaches 3 feet. Her body is brown and furry. The wings are deep black, like a silky, papery fabric. Islam points out her big eyes, like two orbs of amber staring back.

"If it gets the chance," Islam cautions, "it will bite you, like, 10, 15 times. They're very bite-y." To avoid such an outcome, the team has the bat well restrained. The researcher whose hand is in the most vulnerable position has protected himself with a thick glove.

The team finishes untangling the bat and places her in a cotton bag. For now, the bag hangs from a line strung between two trees. It's possible to just make out the contorting and wriggling bat inside.

The researchers nab one more bat, then call it quits. It's getting too light, and any remaining bats will easily spot and avoid the net. They'll transport the animals to a local one-room lab, but not in a van. "Sometimes bats urinate on themselves to mark them," Islam explains. "So if you carry it in the van, the whole van will be stinking."

So they put the bats into a little three-wheeled car and ferry them to the lab some 20 minutes away, where they'll take blood and urine samples. When they're done, they'll release the two bats.

A researcher releases a bat in a wooded area in the district of Faridpur, Bangladesh, after it has been sampled for Nipah virus. Fatima Tuj Johora for NPR hide caption

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Fatima Tuj Johora for NPR

On the drive to the lab, Islam makes a pit stop at a village with a household that's harvesting date palm sap. "It is possible that they will offer you a glass of sap," he remarks to the group. "Please gently deny it, OK?"

When Islam arrives, he walks up to a huge metal tray over a fire. The air is sugary. Gallons of caramel-colored sap are at a rolling boil. It's thickening into molasses.

"It's really sweet," says Muhammad Seraj Khan, the 74-year-old property owner. "It gets sold all around the village. People will buy it to make household sweets and cakes."

The molasses, says Islam, is harmless — any virus gets cooked away. But that's not the case with raw sap. Still, the villagers like to down glasses of the traditional delicacy when they have the chance. And before Islam leaves, Khan offers some of the raw sap.

A glass of raw date palm sap is a traditional delicacy in Bangladesh — even though there is a chance it contains the deadly Nipah virus. Fatima Tuj Johora for NPR hide caption

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Fatima Tuj Johora for NPR

And there it is — a slightly cloudy liquid. A delicacy and possible poison all at once, because you never know if that invisible menace is lurking within the sweetness.

Ahona Tasnuva served as the interpreter for the reporting team.