For These Bird Flu Researchers, Work Is a Day at the Very ‘Icky’ Beach

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The H5N1 virus poses "a great unknown threat" to birds and humans alike. Understanding and thwarting it begins with excrement collection.

By Emily Anthes

Reporting from southern New Jersey.

It was a glorious day for field work on the shores of the Delaware Bay. The late afternoon sun cast a warm glow over the gently sloping beach. The receding tide revealed a smattering of shells. The dune grasses rustled in the breeze. The beach vines were in bloom. And the bird droppings were fresh and plentiful.

"Here's one," said Pamela McKenzie, a researcher at St. Jude Children's Research Hospital in Memphis, pointing a gloved finger at one tiny white splotch and then another. "There's one, there's one, there's one."

For the next two hours, Dr. McKenzie and her colleagues crept along the shore, scooping up avian excrement. Their goal: to stay a step ahead of bird flu, a group of avian-adapted viruses that experts have long worried could evolve to spread easily among humans and potentially set off the next pandemic.

Every spring, this part of southern New Jersey becomes a bird-flu hot spot. Shorebirds winging their way north alight on local beaches to rest and refuel, excreting virus along the way. And every year for the last four decades, scientists from St. Jude have flown into town to pick up after them.

The work requires patience — waiting for the movements of the birds and the movements of the tides to align — keen eyes and resilient knees, sturdy enough to withstand hours of shuffling and squatting along the sometimes rugged shorelines. "They’re not nice, sandy beaches," said Lisa Kercher, a member of the St. Jude team. "They’re thick, muddy, icky beaches that are full of bird poop."

But these dropping-covered shores are helping scientists learn more about how avian influenza evolves, how it behaves in the wild and what it might take for these bird viruses to become a global public health threat. These scientific questions, which have driven the St. Jude team for decades, have become even more urgent as the United States grapples with its largest bird flu outbreak in history, caused by a new, highly pathogenic version of a virus known as H5N1.

"Delaware Bay has turned into an influenza gold mine," said Robert Webster, the St. Jude influenza expert who first discovered the hot spot in 1985. He has been back, or his colleagues have, every year since. "And we will continue to mine that gold mine until we’ve found the answers."

In June, the southern New Jersey shore fills up with vacationing families, their colorful beach umbrellas sprouting up across the sand.

But in May, the beaches belong to the birds. Hundreds of thousands of migrating shorebirds and gulls make pit stops here en route to their summer breeding grounds, some arriving, bedraggled and depleted, after days-long journeys from South America. "They’re in a desperate need to replenish their weight," said Lawrence Niles, a wildlife biologist who leads local shorebird conservation projects through his company, Wildlife Restoration Projects.

Fortunately, the birds arrive just as hordes of horseshoe crabs are hauling themselves up onto shore, laying eggs by the thousands. The birds might spend two weeks gorging on the gelatinous green eggs, "almost doubling their body weight," Dr. Niles said. During that time, they blanket the beaches, mingle with local birds and, like children in an overcrowded classroom, give each other the flu.

Wild water birds — including ducks, gulls and shorebirds — are the natural reservoirs for influenza A viruses, which come in a variety of subtypes. Generally, wild birds carry relatively benign versions of these viruses, which pose little immediate threat to birds or people. But flu viruses can change quickly, accumulating new mutations and swapping genetic material. These changes can, and sometimes do, turn a ho-hum virus into a lethal one, like the version of H5N1 that is currently circulating.

Much of the time, flu circulates in shorebirds and gulls at low levels, often turning up in fewer than one percent of samples. But at the Delaware Bay in May and early June, it explodes, passing easily from bird to bird. Over the years, the St. Jude team has found it in 12 percent of their samples, on average, though that figure has climbed as high as 33 percent. They have found almost every subtype of influenza A, in addition to novel remixes, which can emerge when an animal is infected by more than one version of the virus at once.

To keep an eye on what's circulating, the St. Jude scientists work closely with Dr. Niles and his colleagues, who use the spring stopover as an opportunity to assess the health of the shorebirds, which face a variety of threats, from climate change to the over-harvesting of horseshoe crabs. Dr. Niles and his team typically head out to the beaches first to count, catch, examine and tag the birds. They then relay the birds’ whereabouts to the flu-hunting avian-clean-up crew. "We will then go out and pick up the poop," Dr. Kercher said.

But on the team's first full day of field work this spring, by the time the conservationists had finished their work, the tide was roaring back in. So for hours, the St. Jude scientists bided their time, waiting for the water to recede and hoping that they would still be able to find some flocks. "We are at the mercy of the birds, and the birds don't tell us what they’re doing," Dr. Kercher said.

It was nearly 4 p.m. when they finally rumbled down a gravel road, past the pine forests and the marshes, and arrived at one local beach, where shorebirds had been spotted earlier.

Dr. McKenzie, clad in black joggers and a hooded, gray waffle-knit top, climbed out of the car and surveyed the beach. Horseshoe crabs stretched out along the high-tide line. In the distance, a flock of small birds scuttled around in the water. Dr. McKenzie lifted her binoculars. Bingo: They were ruddy turnstones, sandpipers whose tricolor markings are sometimes compared to those of a calico cat. These birds, the St. Jude team has learned, are especially likely to carry flu viruses.

The scientists donned gloves and masks, a recently added safety precaution. "It's not something that we’ve done in the past," Dr. McKenzie said, "but this is a unique year."

The new H5N1 strain first showed up in North America in late 2021 and spread rapidly across the continent. It led to the death of nearly 60 million farmed birds, killed scores of wild ones and even felled some unlucky mammals, from red foxes to gray seals.

The St. Jude team found no trace of H5N1 at the Delaware Bay last spring. But at the time, the virus had not yet made its way to the shorebirds’ South American wintering grounds. By this spring, it had, which means that the birds could bring it back with them. "We absolutely are worried it's going to show up," Dr. Kercher said.

So the scientists were doubling down on their surveillance, aiming to collect 1,000 fecal samples instead of their standard 600. They began picking their way down the beach, eyes cast down as they searched for the right white splotches. Not any droppings would do; it had to be fresh excrement, ideally from ruddy turnstones and red knots, another sandpiper species. The scientists have become good at telling the two types of droppings apart. "The turnstones are mostly logs," Dr. McKenzie said. "The red knots kind of have more of a splat."

When the scientists spotted a suitable splotch, they dropped to their knees and unsheathed round-tipped swabs. Sometimes it took a few tries to successfully collect a sample. "It's not the easiest technique with these tools," said Patrick Seiler, a member of the research team. "In the blowing wind, trying to scoop up poop and put it in a little vial."

They stowed the samples in a small plastic cooler, of a kind that a vacationer might bring to these same beaches. Later, the samples would be shipped back to the lab in Memphis for testing and analysis.

Typically, the researchers sequence the viruses they find, looking for notable mutations and charting their evolution over time, and then select a subset to study in different kinds of cells and animal models. Over the past few decades, this work has helped the scientists learn more about what "run-of-the-mill" bird flu viruses look like and how they behave, said Richard Webby, an influenza expert on the St. Jude team.

It has also helped them spot outliers. "And that leads us on a chase," Dr. Webby said, which can end up revealing "something about the fundamental biology of these viruses." In 2009, some of the viruses they found turned out to be surprisingly good at spreading among ferrets. Further study of those viruses helped the researchers identify genetic mutations that might facilitate the airborne transmission of flu among mammals.

If the team finds H5N1 this year, Dr. Webby and his colleagues will look for changes that the virus might have acquired as it moved through the shorebirds, as well as any that might make it more dangerous to humans or resistant to vaccines and treatments.

The virus has already evolved markedly since its arrival in North America, Dr. Webby and his colleagues reported in a recent paper, which was based on analysis of viral samples isolated from birds outside of the Delaware Bay region. The new variants they found have not gained the ability to spread easily among mammals, but some are capable of causing serious neurological symptoms in mammals that become infected.

If the virus shows up in this year's Delaware Bay samples, it will be yet another sign that H5N1 is becoming increasingly entrenched in North America. It could also spell trouble for some of the shorebirds, especially the red knots, whose numbers have dropped precipitously in recent decades. For these birds, H5N1 is "a great unknown threat," Dr. Niles said.

And so, although the excrement collection process remains as unglamorous as ever, the stakes feel high as the scientists work their way down the beach.

All they can say is that they haven't found the new H5N1 virus yet. "But that doesn't mean that we won't," Dr. McKenzie said, carefully scooping up the scatological clues the birds had left behind. "I guess we will find out."

Emily Anthes is a reporter for The Times, where she focuses on science and health and covers topics like the coronavirus pandemic, vaccinations, virus testing and Covid in children.

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