Up First Sunday & Hidden Viruses: 3 years since WHO declared COVID-19 a pandemic Three years ago, on March 11, 2020, the World Health Organization declared COVID-19 a pandemic. The virus had spread across the globe, and the WHO announcement triggered unprecedented measures – governments ordered people to quarantine, borders were closed and mandatory masking became commonplace. Today, science reporter Ari Daniel tells us about a new series from NPR: "Hidden Viruses: How Pandemics Really Begin." From bats in Bangladesh to dogs in Malaysia, NPR's Global Health and Development team traveled far and wide to learn how scientists are studying spillovers – when a disease crosses from animals to humans – and what makes some viruses more deadly than others.

The Sunday Story: Hidden Viruses

  • Download
  • <iframe src="https://www.npr.org/player/embed/1162612925/1162821182" width="100%" height="290" frameborder="0" scrolling="no" title="NPR embedded audio player">
  • Transcript


This weekend, we are marking one of the most significant anniversaries in recent history.


MARTIN: Three years ago, March 11, 2020, the World Health Organization made this chilling announcement.


TEDROS ADHANOM GHEBREYESUS: WHO has been assessing this outbreak around the clock, and we're deeply concerned both by the alarming levels of spread and severity and by the alarming levels of inaction. We have therefore made the assessment that COVID-19 can be characterized as a pandemic.

MARTIN: That was the director-general of the WHO, Tedros Adhanom Ghebreyesus. He went on to say that this pandemic was the first ever sparked by a coronavirus. Now, there are many different kinds of viruses - right? - but coronaviruses belong to a small but important club, one for viruses with, quote, "pandemic potential," meaning they've got certain characteristics that a pathogen needs in order to go global.

I'm Rachel Martin. This is UP FIRST Sunday. My colleagues on our global health and development team here at NPR are just wrapping up a series called Hidden Viruses: How Pandemics Really Begin. Their stories look at efforts to track these viruses with pandemic potential, study them and hopefully stop them. Joining me now to talk about their work is science reporter Ari Daniel. Hey, Ari.

ARI DANIEL, BYLINE: Hi, Rachel. It's great to be here.

MARTIN: I'm so glad that you're here. I have so many questions. I want to hear about this series, but we're just going to put a spoiler alert at the top because I think this is the question on everyone's minds - are we any closer to being able to predict and possibly stop a future pandemic?

DANIEL: Well, Rachel, you know, if you ask a simple question, you're going to get a complicated answer. I mean, I guess I could say that in some ways yes but in many ways no. Is that at all helpful?

MARTIN: (Laughter) No, it's not. Flesh that out for me.

DANIEL: OK, so let me put it like this - we are getting better at understanding what sets some of these viruses up to become pandemic-level viruses. So the approach that scientists have used for years in how to find worrisome viruses - where to look for them - it's changing a lot, and that's actually what our series set out to explore. What is this new science? Where did it come from? And where might it be taking us?

MARTIN: So it took you to Bangladesh, right?


MARTIN: You had this really incredible experience there in a country that's had some serious run-ins with an especially bad virus. Tell us.

DANIEL: Yes, exactly. So I went to Bangladesh because they've been dealing with this virus called Nipah for more than 20 years now. And to understand just how terrible this thing is, I want to take you to a village in the district of Faridpur, in a part of central Bangladesh that is plagued by this virus, so much so that they call this area of the country the Nipah Belt.

MARTIN: Wow. The Nipah Belt.

DANIEL: That's right. Now, Nipah is actually named after a village not in Bangladesh but in Malaysia, where the virus first turned up in the late '90s. And at that time, it was infecting pigs. Farmers were getting sick from their animals, but it was not spreading between people. Malaysia slaughtered nearly a million pigs to stop the spread, and it worked. But then, several years later, the virus - it started showing up in Bangladesh, and this village that I went to in the Nipah Belt - this is where an outbreak erupted in 2004 that was especially concerning.

MARTIN: How so? What happened?

DANIEL: Well, that particular outbreak revealed not only how bad this virus is, but it showed that the virus had changed, and that caught the attention of scientists. It was behaving differently in a couple of important and startling ways.

KHOKON: (Non-English language spoken).

DANIEL: So this man that you're hearing now - his name is Khokon. He's 50 years old, and he's one of the few survivors from that 2004 outbreak. You could say he was at the epicenter. So I sat with him, and he told me about that spring 19 years ago when all of a sudden, for no apparent reason, people that were around him - they just started getting seriously ill and dying.

KHOKON: (Through interpreter) The first one was the mother-in-law of my elder brother. She was really sick. She had been sick for some time. Then she died. We took her to the grave. Then my father got sick.

DANIEL: Khokon stares off into the distance as he tells me his father was a spiritual leader in the community. When he became ill, many came to pay their respects.

KHOKON: (Through interpreter) Just 12 days after, my father died. Suddenly, he was no more.

DANIEL: Those visitors, Rachel - they also got sick. Several of them died. One traveled to a neighboring village, and even more people fell ill.

MARTIN: OK, so, Ari, what about pigs? Because Nipah was infecting pigs in Malaysia - was that happening in Bangladesh, too?

DANIEL: Well, that's what was so puzzling. You see, Rachel, Nipah is a bat-borne virus. Bats are the natural reservoir for Nipah. So in Malaysia, the pigs had somehow gotten sick from these fruit bats that were in the area, but in Bangladesh, pigs weren't getting sick. In fact, pigs weren't involved at all. It was just people, and 70% of the people who were infected - they were dying, and it was a real mystery as to what was going on. I talked with Mahmudur Rahman. He's the former director of the Institute of Epidemiology, Disease Control and Research for the Bangladeshi government. And he told me that they just couldn't piece together how people were contracting Nipah. Here's a clip from my story.

MAHMUDUR RAHMAN: Some people who were transporting the patients to the hospital were also getting sick.

DANIEL: Sick often meant encephalitis, a swelling of the brain. Epidemiologist Emily Gurley, now at Johns Hopkins University, was leading an on-site investigation at the time.

EMILY GURLEY: The signs and symptoms of encephalitis are, well, fever, headache, but often altered mental status or coma, seizures.

DANIEL: Then Khokon and his wife, Anwara, fell ill. It's why I'm only using their first names, because the disease carries stigma.

ANWARA: (Through interpreter) People couldn't say if we were dead or alive. They said that we had high fever. Like, whenever they were touching us, it was like touching fire.

DANIEL: Miraculously, they both survived. But Khokon's older brother, his sister, two uncles, his aunt, his nephew and his mom and dad - all dead. This outbreak, says Dr. Rahman, made something brutally evident.

RAHMAN: This is obviously showing that we are unable to control it, and it is spreading.

DANIEL: And that, Rachel - that was the game changer. This virus had not been seen spreading between people before. And a virus that can jump from an animal, like a bat, into a person and then spread from person to person, as Nipah was now doing, well, that's one of the traits of a virus with pandemic potential. Emily Gurley - she told me that it was a really scary time.

MARTIN: Yeah, I'd imagine. So here's my question, Ari. How are people getting the virus in the first place? You said it's a bat-borne virus. Do these communities have a lot of contact with bats?

DANIEL: That was the million-dollar question, Rachel, and one that all these investigators, the epidemiologists, the doctors, the infectious disease experts - they all wanted to know how this bat-borne virus was spilling over - that is, jumping into people. Here's epidemiologist Emily Gurley again.

GURLEY: 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.

DANIEL: Now, Rachel, it might seem like this shouldn't be so hard to figure out, but, you know, finding a link between the bats and the people who were falling ill, it was agonizingly slow work. It took years to prove. I mean, yeah, they had their theories, but, look, these outbreaks, they blaze quickly. Most of the victims are dead, and eyewitnesses often run away or just won't talk about it. You know, it's painful. There's stigma, and they're afraid of being blamed.

MARTIN: So did they finally figure it all out?

DANIEL: Yes. There was a lot of pressure to get to the bottom of it because the outbreaks kept happening, pretty much year after year, and people kept dying. But eventually, yes, the pieces of the puzzle started to take shape. In fact, let me play you another excerpt from my story. We're picking up a few years later, in 2007, with another outbreak and a phone call.

REBECA SULTANA: Our colleague called me and ask, Rebeca, would you like to go? Are you ready? I said, yes, I'm ready to go there.

DANIEL: The next morning, anthropologist Rebeca Sultana joined the Nipah outbreak investigation team. She's with the International Centre for Diarrhoeal Disease Research, Bangladesh, or ICDDR,B for short. When she arrived in the village, she went straight to the home of patient zero.

SULTANA: I tried to talk to the elder sister-in-law of the guy who died, and she was so upset. And she just ran and came to me and hugged me and started crying.

DANIEL: Getting that close to her scared Sultana. As one Nipah researcher told me, doing this work is like putting your soul in your hand. But Sultana, she hugged her back and said...

SULTANA: Please don't worry. We are here to understand why this happened.

DANIEL: She asked the community to meet her in the town market to help her draw a map of the village. About two dozen people showed up.

SULTANA: I don't do anything. I just ask question, and then they draw it.

DANIEL: Using sticks in the dirt, the residents roughed out houses, roads, bat roosts, and then they began sketching in date palm trees.

SULTANA: This is the first time the people informed me in Puno there is a date palm tree and there is a sap harvester in this community.

DANIEL: Sultana hadn't seen the date palm trees on the drive in, but staring back at her from the dirt, there it was, the possible link between how the fruit bats had passed Nipah into this community - through the drinking of the sweet sap. Emily Gurley.

GURLEY: I 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.

DANIEL: So Rebeca Sultana and her colleagues tracked down that sap harvester, and he led them to a few pals of the guy who is patient zero.

SULTANA: They said, we all used to drink raw sap in the morning.

MARTIN: Raw sap. So raw sap was like the smoking gun in all this.

DANIEL: Totally. Sultana, she told me that this was her aha moment, that patient zero had consumed raw sap before getting sick.

MARTIN: So that was the missing puzzle piece?

DANIEL: Well, yes, it helped, but they needed to get more evidence. So over the next few years, researchers actually spied on the bats at night by hanging these infrared cameras from the trees and then catching them in the act of drinking from and sometimes peeing into the same stream of sap that people were collecting and drinking.


DANIEL: Yeah, I know. Eventually, there was enough evidence for the government to launch a campaign against the drinking of raw sap.

MARTIN: And did that work?

DANIEL: Well, some people listened, but many have continued to drink the stuff.

MARTIN: So does that mean people are still getting sick from Nipah?

DANIEL: Yep. The spillovers have continued. And I want to remind folks that, of course, the concern here is for the villagers and people in this part of the world, in the Nipah belt. But there's also real worry that this virus - it could move far beyond Bangladesh because Nipah has this pandemic potential.

MARTIN: So if that campaign by the government didn't work, what happens? Like, is there anything that can be done to help the people who are already dealing with this in the Nipah belt and to prevent it from spreading beyond Bangladesh?

DANIEL: Hopefully. And that brings us to the bats themselves. So when I was in Bangladesh, I woke up in the middle of the night one night. It was December 1. And it's the beginning, Rachel, of what's known around there as Nipah season, notoriously.


DANIEL: It's the four months when the virus is most likely to show up because that's when the sap is harvested. And it's also when a scientist named Ausraful Islam keeps an especially close eye on Nipah.

AUSRAFUL ISLAM: If we want to contain the virus, we have to understand the virus.

DANIEL: And understanding the virus means learning more about how these spillovers happen.

MARTIN: You mean beyond the fact that bats were infecting the date palm sap and people were drinking the date palm sap and getting sick?

DANIEL: Right. What scientists wanted to know is, why are these bats shedding virus in the first place? It clearly doesn't happen all that often or there'd be a lot more outbreaks of Nipah than there are. And so to answer that question, Ausraful Islam has spent years studying the bats - waking up in the middle of the night, tracking them down. Let me play you another part from my story.


DANIEL: It's three in the morning. Islam stops at the edge of a patch of forest and looks up into the sky. Some four stories above the ground, a net stretches between two mahogany trees.

Why are we out here so early?

ISLAM: Because the bats will start coming back from foraging after 3. So this is the best time to catch them.

DANIEL: Islam is a veterinarian and infectious disease specialist at the ICDDR,B. He's searching for another way to stop Nipah. Every month, he brings a team out here near Faridpur to capture bats. The answer isn't getting rid of these animals. Islam has great respect for their importance to the local ecosystem. Rather, years of studying thousands of greater Indian fruit bats have shown that most of them do carry Nipah virus. But here's the thing - fewer than 1% of them actually release it into the environment through their urine or saliva. Why do so few of these animals shed the virus? Islam thinks for that small group, it's likely connected to stress.

ISLAM: Is it lack of food? Is it pregnancy stress? Is it lack of habitat?

DANIEL: Knowing what's behind the shedding could help Islam and his colleagues figure out how to keep Nipah from infecting people in the first place.


DANIEL: The coming dawn is full of sound. There are jackals and fruit bats.

What just happened?

ISLAM: We are able to capture a bat.

DANIEL: OK, so a bat just flew into the net. The bat's body is, like a - brown and furry, and the wings are just deep black, like a silky, papery fabric.

ISLAM: If you go around, you'll see the big eyes.

DANIEL: I gaze into them, like two orbs of amber. She's big. An adult's wingspan easily reaches three feet.

ISLAM: If it gets the chance, it will bite you, like, 10, 15 times. They're very bitey (ph).

DANIEL: Just untangled it.

The team nabs one more bat and then calls it quits. It's getting too light. They put the bats into a three-wheeler and ferry them to a local lab, an unassuming one-room building, and yet a crucial outpost in the battle against Nipah. It's where the researchers will sample blood and urine from the bats. And once they're done, they'll release the animals back into the woods.

MARTIN: Wow, Ari. It's so amazing to hear you out there with this man whose, like, life's work is studying these bats to prevent this disease from spreading. It's pretty incredible. Have they found answers? I mean, have these bat researchers learned anything to help them contain Nipah?

DANIEL: Well, they've learned some things. So, you know, they've been collecting all of these samples over the years, and they're able to kind of figure out what strains of virus are circulating among the bats and how they're evolving and just how infectious they are. And they're hoping that this information can be used, Rachel, to help design an effective vaccine to combat Nipah.

MARTIN: OK, so it sounds like scientists are learning more about how viruses like these, with pandemic potential, jump from animals to humans. That's good. That's important. But you've also said that they are changing how they do this, right? There are new approaches to studying these viruses that is affecting our understanding of these spillovers.

DANIEL: Right. And so for a long time, scientists were looking in animals for viruses that could be problematic, potentially. But animals have all sorts of viruses, and many of them aren't ever going to spill over into people. So scientists have gotten more targeted with where they look, and they're looking in us.

MARTIN: OK. We're going to have more, coming right up after the break. This is UP FIRST Sunday. Stay with us.

I'm Rachel Martin, and this is UP FIRST Sunday. And I'm talking with science reporter Ari Daniel about viruses that have the potential to become global pandemics and how scientists are analyzing that potential.

So when we left off, Ari, we were talking about the fact that there are a whole lot of viruses that incubate inside animals. Not all of them become, like, global pandemics that wreak havoc around the world. So what have you and your colleagues been learning about how scientists are trying to differentiate those?

DANIEL: Absolutely, Rachel. So I want to highlight some of the work that my colleague Michaeleen Doucleff - she's a health correspondent at NPR - has been doing. She's been reporting for years now on emerging viruses, and here's a portion of a recent conversation she had with Steve Inskeep where they discuss this new strategy.


MICHAELEEN DOUCLEFF, BYLINE: So for decades now, the U.S. government has spent hundreds of millions of dollars to hunt for new viruses inside animals. Scientists trap wild animals and then look for viruses inside them. That's where the SARS virus came from, right? But what scientists are figuring out is that this task is nearly impossible. Animals contain millions of different viruses, and only a tiny fraction of those will ever infect people, you know? So how do you know which one's a threat? You know, they missed the early warning signs in China with COVID.

STEVE INSKEEP, BYLINE: Yeah. Well, if that doesn't work very well, what is the better approach, and how did scientists begin to find it?

DOUCLEFF: So in the past few years, scientists have begun to understand something surprising - that new animal viruses are jumping into people all the time.


DANIEL: They're not rare at all, Rachel. Many have just been hidden.


DANIEL: In fact, Michaeleen went to Malaysia to meet a little boy who had a strange illness caused by one of these hidden spillover events. And his story actually has a lot to say about the shift in how scientists are searching for new diseases. Here's Michaeleen again in an excerpt from one of her stories for the Hidden Viruses series.


DOUCLEFF: So the little boy lives in a tiny fishing village on the island of Borneo. The village is right near the South China Sea, and to get there takes quite an effort. We have to cross over nearly a dozen rivers and take several ferries.

It's here? The ferry...

UNIDENTIFIED PERSON #1: The water is not rough, OK?

DOUCLEFF: Drive over gulches where crocodiles hide in the mud, pass giant mango trees rising 40 feet in the air.

The yellow - are those coconuts?


DOUCLEFF: Finally, we reach the village and turn into a neighborhood with colorful houses, pink and yellow, all built high up on stilts. We stop at a green house with a motorcycle parked out front.

Oh, we're here. Oh, great. After four days of traveling, we have finally arrived. Should we put on a mask?


DOUCLEFF: A woman in her 30s greets me at the door and leads me into her living room.


She's the little boy's mom. We're calling her by her initial, N. We aren't using her full name to protect the family's privacy and any stigma there might be around the cause of her son's illness.

Oh, thank you.

N has six kids. Her fifth is a boy, Muhammed. She and her family gather around and tell a remarkable story about him.

N: (Non-English language spoken).

DOUCLEFF: Back in 2017, Muhammed was only a baby.

N: (Non-English language spoken).


One summer evening, he started to have a fever.

N: (Non-English language spoken)


DOUCLEFF: And so the baby was (panting) - like, could not breathe?

N: (Non-English language spoken).

DOUCLEFF: Were you afraid?

N: (Non-English language spoken).


N: (Non-English language spoken).

DOUCLEFF: N rushed Muhammed to the hospital near their home, but the baby's condition worsened. So they traveled three hours to the nearest city, called Sibu. Doctors quickly admitted Muhammed to the ICU.


DOUCLEFF: Because he was - was he getting worse?

N: (Non-English language spoken).

DOUCLEFF: Much worse, she says. Muhammed's lungs were failing, and his blood wasn't getting enough oxygen.

MARTIN: Whoa. So what was going on, Ari?

DANIEL: Well, Muhammed had pneumonia. But the doctors, they couldn't figure out the virus that was responsible, that was causing it, which is pretty much the standard, actually, for respiratory viruses. Michaeleen spoke to one of the top virus hunters in the world who pegged it at, like, 60% of the time, doctors have no clue what virus is causing a particular respiratory infection.


DOUCLEFF: But at the hospital in Malaysia, where Muhammed was, one doctor wasn't satisfied with that. His name is Dr. Teck-Hock Toh. He's a pediatrician, and he's treated thousands of children like Muhammed with severe respiratory illnesses that they can't find a cause for. And around the time he was taking care of Muhammed, he was also trying to figure out why. What's making each of these kids sick? He really wanted to know.

TECK-HOCK TOH: We are interested in all these infections that has been making trouble for a lot of our children.

DOUCLEFF: So he took a little white swab, like the one in a COVID test, scraped the inside of Muhammed's nose and froze the sample. He and his team have taken samples like this for years.

TOH: We are looking for an infection that we don't know, essentially.

DOUCLEFF: If you think about it, doctors not knowing what causes an infection 60% of the time - that means there are these groups of viruses out there, perhaps other new coronaviruses or flu viruses, making people sick all over the world that scientists have no clue about. They've been hidden.

GREGORY GRAY: There are a whole bunch of viruses that we are missing. We probably have novel viruses here in North America. We're just missing them because we don't have the tools to pick them up.

DOUCLEFF: That's Dr. Gregory Gray. He's an infectious disease epidemiologist at the University of Texas Medical Branch in Galveston. A few years ago, he teamed up with Toh and developed a tool to find new coronaviruses inside patients.

GRAY: A diagnostic that would pick up all coronaviruses. It's a very sensitive diagnostic.

DOUCLEFF: Then he started to test Toh's patients with this new tool. They started with only about 300 patient samples, including Muhammed's. Right away, they found something. Inside Muhammed's upper respiratory tract, Gray and his team found a new coronavirus, one that comes from dogs.

GRAY: You know, it's very canine-like, primarily.

DOUCLEFF: At the time, scientists didn't think dog coronaviruses had the ability to infect people. Gray wondered if his team might have made a mistake.

GRAY: I was surprised. And, you know, you always wonder if you have some sort of problem with the lab.

DOUCLEFF: But then Gray and his colleagues looked to see if this dog virus had cropped up in other patients around the world. They looked in a genetic database, and Gray says what they discovered is that this family of dog viruses has jumped into people or spilled over at least four times in the past 20 years. And here's where the story really gets crazy, because if they were barely looking and they found this, that means these viruses...

GRAY: They're probably spilling over or threatening to spill over all the time.

MARTIN: Oh, man.

DANIEL: And so, Rachel, once Gray and Toh published their work, other groups started reporting finding more animal coronaviruses in people in lots of places, like camels in Kenya, pigs in Haiti. Michaeleen has a great way of putting it.


DOUCLEFF: All together, these studies paint a clear and striking picture of spillovers. They aren't like needles in a haystack. Spillovers are more like a rake sticking out of the side of the haystack. Once researchers start looking, they find them easily. In fact, another study estimated that every year, more than 60,000 SARS-like viruses jump into people in Southeast Asia alone, which means, as one scientist put it, spillovers are like snow falling across humanity.

MARTIN: Which sounds like the most nightmarish snowstorm in the world. Like, that sounds hideous.

DANIEL: It does. It does, I grant you that. Except, Rachel, that most spillovers, they don't create much trouble. People usually don't get too sick from emerging viruses, and they tend to not spread very well from person to person. But - and this is, like, the key caveat of this whole thing - each time a virus jumps from animals into people - from the camels into people, from bats into people - it gets another chance at evolving and mutating. So it could start to make people super sick and/or become more infectious.

MARTIN: So Michaeleen's reporting, it shows, maybe, a more efficient way to find worrisome viruses by looking in people instead of looking in animals like we used to. Is that right?

DANIEL: I'll let Michaeleen take that one. Here's another excerpt from her story.


DOUCLEFF: It's a way of narrowing the search, right? So looking in people with pneumonias who doctors don't know the cause, or also looking inside people who are often working with animals. Think of this - if you combine the studies I mention in that story, these scientists searched for new viruses in only about a thousand people. And look what they've already found - three new coronaviruses.

MARTIN: Which really puts things into perspective, right? I mean, we think of these things as being so exceptional and awful, but they're really ubiquitous. Is that what I'm learning?

DANIEL: Yeah, that's right. I mean, we share the world with viruses, and the work that these scientists are doing to try to figure out what's going on and which viruses are dangerous, it's really important.

MARTIN: Yeah. I wanted to ask, what happened to that little boy, Muhammed? He was really sick, and he had pneumonia.

DANIEL: Right, the one that Michaeleen met. Well, it took him almost two years to recover, and he's still small for his age, but he's 5 years old now, and he's this healthy little kindergartner.

MARTIN: That is good. That is good to hear. Ari, we so appreciate you bringing us all this amazing reporting, and Michaeleen as well, as we mark the three-year anniversary of COVID being declared a pandemic by the World Health Organization. Thank you so much.

DANIEL: You're welcome, Rachel. Here's to brighter days ahead, informed by our ever-evolving understanding of all these viruses.

MARTIN: Yes, information is knowledge and it's helpful. Thank you so much. Ari Daniel, talking about NPR's Global Health and Development team's reporting from their series, Hidden Viruses: How Pandemics Really Begin. We will link to the series on our episode page.

This episode was produced by Audrey Nguyen and edited by Jenny Schmidt and Rebecca Davis. The Hidden Viruses series was edited by Vikki Valentine, Rebecca Davis and Marc Silver. Pierre Kattar was the visuals editor. UP FIRST Sunday got engineering support from Josh Newell and Carleigh Strange. It's also produced by Justine Yan. Our supervising producer is Liana Simstrom, and Irene Noguchi is our executive producer. I'm Rachel Martin. UP FIRST is back tomorrow with all the news you need to start your week. Until then, have a great rest of your weekend.

Copyright © 2023 NPR. All rights reserved. Visit our website terms of use and permissions pages at www.npr.org for further information.

NPR transcripts are created on a rush deadline by an NPR contractor. This text may not be in its final form and may be updated or revised in the future. Accuracy and availability may vary. The authoritative record of NPR’s programming is the audio record.