How to prevent the next pandemic virus: Scientists have a new strategy : Goats and Soda Animals carry millions of pathogens. So it's a daunting task to find the one with the greatest potential to spark a pandemic. Now scientists are rethinking the way they hunt for that next new virus.

How do pandemics begin? There's a new theory — and a new strategy to thwart them

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STEVE INSKEEP, HOST:

Scientists think they have learned a lesson during the pandemic, a lesson about how to see the next pandemic coming. For generations, virologists have tried to find early signs of new diseases so they have the maximum time to respond. They've typically looked in animals because new viruses often come from there first. Now researchers think they've been looking in the wrong place. NPR global health correspondent Michaeleen Doucleff has been discovering this story. Hey there, Michaeleen.

MICHAELEEN DOUCLEFF, BYLINE: Good morning.

INSKEEP: What's been going wrong?

DOUCLEFF: 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 is a threat, you know? They missed the early warning signs in China with COVID.

INSKEEP: 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. They're called spillovers. And they aren't rare at all. They've just been hidden. And the story I'm going to tell you is about a little boy in Malaysia who had a mysterious illness and how that illness started to reveal these hidden spillovers, which is leading to a big change in how scientists search for new diseases.

INSKEEP: I want people to know you had to go a long way to get this story. So where did you find this little boy?

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.

(SOUNDBITE OF MUSIC)

UNIDENTIFIED SINGER: (Singing in non-English language).

DOUCLEFF: 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?

UNIDENTIFIED PERSON #1: Oh, yes.

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 greenhouse 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?

UNIDENTIFIED PERSON #1: Yeah.

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

Hello. Hello.

She's the little boy's mom. We're calling her by her initial, N.

N: (Non-English language spoken).

DOUCLEFF: 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.

UNIDENTIFIED PERSON #2: Have a drink.

DOUCLEFF: 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: (Through interpreter) Back in 2017, Muhammed was only a baby.

(Non-English language spoken).

UNIDENTIFIED INTERPRETER: Four to 5 months.

DOUCLEFF: Oh, OK.

N: (Through interpreter) One summer evening, he started to have a fever.

(Non-English language spoken). Shortness of breath, OK.

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).

UNIDENTIFIED INTERPRETER: (Non-English language spoken) is very concerned.

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.

UNIDENTIFIED INTERPRETER: Straight to 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.

The breathing machine?

UNIDENTIFIED INTERPRETER: Correct.

DOUCLEFF: Muhammed had pneumonia. But doctors couldn't identify the virus causing it. Surprisingly, this is actually the norm with respiratory infections. John Lednicky is a virologist at the University of Florida and one of the top virus hunters in the world. He says at any given hospital here in the U.S. or Brazil, anywhere, if you have a respiratory infection, doctors often run a test to see the cause. But...

JOHN LEDNICKY: Something a lot of people don't realize is that a most probable cause is typically generated by these tests in about 40% of the cases. I like to think 60% of the time, they have absolutely no idea.

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 of 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 infections 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.

GRAY: The same virus has been found far away in Haiti. And there's been evidence of other canine viruses in this group infecting people in Thailand and in the USA.

DOUCLEFF: That was in Arkansas, where scientists found the dog virus in people with COVID-like symptoms. 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.

DOUCLEFF: After Gray and Toh publish their findings on Muhammed, other teams started reporting more animal coronaviruses inside people all over. A team in Kenya found a version of MERS coronavirus that jumps from camels into people way more easily than previously thought. And a team at the University of Florida, led by Marco Salemi, found a new coronavirus in several sick children in Haiti. He says this virus jumped from pigs into kids.

MARCO SALEMI: The children had got fever. They got some intestinal problem. But ultimately, the immune system fought successfully the infection.

DOUCLEFF: Altogether, 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.

SALEMI: Every time that we take a breath in, in any environment, even in our own home, we breathe in probably thousands of different virus strains.

DOUCLEFF: 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.

INSKEEP: We've been listening to NPR's Michaeleen Doucleff. And Michaeleen, a couple of reactions first. Someone is choking at this moment thinking about inhaling thousands of different virus strains. So thank you very much for ruining somebody's morning, but I understand. Amazing reporting, though, going to the other side of the world to find out what scientists are learning about how many viruses are out there, which does raise a question. Why aren't there more pandemics?

DOUCLEFF: Yeah. So you know, all those viruses we're breathing in, you know, even if they do infect us, the vast majority of these spillovers don't cause much problem at all, you know? These emerging viruses usually don't make people very sick. And they often don't spread very well from person to person. So that's a big reason why they've remained so hidden. But, Steve - and this is really key - when a virus strain keeps jumping over and over again into people, say, for decades, there's always a possibility it could mutate or change so that it could start making people really sick or even begin transmitting between people.

INSKEEP: So does this story point to a way to be more efficient in finding the viruses we need to worry about, looking at people instead of animals?

DOUCLEFF: Exactly. 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 mentioned 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.

INSKEEP: Can you finish the story for us, though, the story of this little boy, Muhammed?

DOUCLEFF: Yes, of course. You know, when I visited N's home, it was the first thing, you know, I wanted to know, how was Muhammed? And at one point, a little boy came out of a bedroom wearing a Cookie Monster T-shirt. And N says, that's Muhammed. You know, he took nearly two years to recover from the illness he had. He coughed for several years. And he's always been small for his age. But now he's 5 years old. And he's healthy. And he's in kindergarten.

INSKEEP: NPR's global health correspondent Michaeleen Doucleff has the latest installment of an NPR series called Hidden Viruses. Thanks so much.

DOUCLEFF: Thank you, Steve.

(SOUNDBITE OF FUGAZI'S "SWEET AND LOW")

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