Jan 24, 2022 8:00 AM

Bird Flu Is Back in the US. No One Knows What Comes Next

The fast-moving pathogen, which has already invaded Europe, was found in East Coast ducks. The last outbreak that tore through the US killed 50 million birds.

Worker getting rid of eggs — Photograph: JALAA MAREY/Getty Images

In the first days of the new year, on the marshy coastal edge of South Carolina’s Lowcountry, a hunter shot an American widgeon, a rusty-fronted duck with a pale beak and a brilliant green stripe. This was not a big deal; the state’s duck hunting season runs from Thanksgiving through the end of January. Neither was what happened next: Before taking it home, the hunter let a wildlife biologist affiliated with a government program swab the carcass for lab analysis.

But what happened after that was a big deal indeed. After the sample went through its routine check at Clemson University, it made an unusual second stop at a federal lab halfway across the country, in Iowa. The news of what was in the sample percolated through a pyramid of agencies, and on January 14 the US Department of Agriculture revealed why it had attracted so much scrutiny: The South Carolina duck was carrying the Asian strain of H5N1 avian influenza, the first sighting of that pathogen in the continental US in years.

But not the last. Just a few days later, the USDA disclosed that two more birds shot by hunters also carried the same pathogen: a teal, shot in the same South Carolina county, and a northern shoveler shot in the far northeast corner of North Carolina, about 400 miles away. The virus in all three was what is known as highly pathogenic—meaning it could cause fast-moving, fatal disease in other bird species, such as poultry, though it was not making the ducks ill.

Three birds out of the millions that American hunters shoot each year might seem like nothing—but the findings have sent a ripple of disquiet through the community of scientists who monitor animal diseases. In 2015, that same strain of flu landed in the Midwest’s turkey industry and caused the largest animal-disease outbreak ever seen in the US, killing or causing the destruction of more than 50 million birds and costing the US economy more than $3 billion. Human-health experts are uneasy as well. Since 2003, that flu has sickened at least 863 people across the world and killed more than half of them. Other avian flu strains have made hundreds more people ill. Before Covid arrived, avian flu was considered the disease most likely to cause a transnational outbreak.

It is far too soon to say whether the arrival of this virus in the US is a blip, an imminent danger to agriculture, or a zoonotic pathogen probing for a path to attack humanity. But it is a reminder that Covid is not the only disease with pandemic potential, and of how easy it is to lose focus when it comes to other possible threats. The possibility of a human- or animal-origin strain of flu swamping the world once seemed so imminent that back in 2005 the White House wrote a national strategy for it. But researchers say the surveillance schemes that would pick up its movement have since been allowed to drift.

“In wildlife disease surveillance, we’re always chasing a crisis,” says David Stallknecht, director of the Southeastern Cooperative Wildlife Disease Study, a research institute housed at the University of Georgia. “And as soon as the crisis is over, the interest goes down. It’s difficult to keep going long-term. People are here to do the work, but the money isn't there to support it.”

To understand the importance of those three ducks and the virus they were carrying, we need to take a quick tour through Flu School. Lesson One: The flu virus family tree is vast and sprawling; it contains types—A, B, C, D—and subtypes, designated with Hs and Ns. (Those are short for proteins that let the virus infect cells.) Just within the As, there are almost 200 subtypes; a few affect humans, but almost all of them can infect birds.

Lesson Two: For a long time, scientists thought humans were in little danger from all those other flu strains. That assumption was shattered in 1997, when an avian influenza, H5N1, jumped species in Hong Kong and infected 18 people, killing six of them. To shut it down, the local government slaughtered every chicken in the territory, denying the virus a host. That worked for a few years, but in 2003 H5N1 started to move across the world again, and it has been moving ever since.

Lesson Three: Avian flu can be dangerous to people, but it threatens some birds too. Waterbirds, chiefly ducks, carry it without illness, but it makes chickens sick. Here again, there are subcategories: Avian flu can be low-pathogenic, meaning that it makes birds mildly ill and slows down egg production. Or it can be highly pathogenic, or high-path: a fast-moving infection so vicious that it can kill an entire flock in two days. (A prominent poultry researcher once called it “chicken Ebola.”)

To sum all that up (there will not be a quiz): The flu found in the Carolinas is an H5N1, meaning it is of the subtype that normally infects birds but in the past has sickened people. It is a high-path variety, the kind that can wipe out domesticated flocks. It belongs to a strain related to that first species-crossing jump in 1997. And, to make matters worse, it represents just one instance of a remarkable amount of highly pathogenic H5N1 showing up in the world right now.

Last year, the World Organization for Animal Health (known by its French acronym, OIE) estimated that between May 1 and November 1, 41 countries experienced outbreaks of highly pathogenic bird flu, with 16,000 isolations of the virus reported just in October. Fifteen countries also reported outbreaks between October and December.

Occasional isolations of avian flu in wild birds are not unusual, but last fall high-path H5N1 began erupting in the United Kingdom with extraordinary intensity. Since October and into this year, the virus has been found in wild species, including swans, geese, shorebirds, and birds of prey. But it has also invaded poultry farms, primarily in Lincolnshire and Yorkshire. By January, more than 1 million chickens and other birds had been destroyed to stop it from spreading. In December, the UK’s chief veterinary officer called the occurrence of bird flu there “phenomenal,” saying the strain had spread to the largest number of farm properties ever seen.

At almost the same moment, Dutch authorities were ordering the slaughter of hundreds of thousands of poultry on farms in the country. In the Czech Republic, more than 100,000 hens died of avian flu on an egg farm, and another 100,000 birds and about 1 million eggs were destroyed to stop the virus from spreading further. In France, farmers feared the virus would invade the duck-raising southwest, the home of foie gras. Last week, the agriculture ministry ordered 2.5 million birds killed. In Italy, more than 4 million poultry died or were slaughtered between October and December. And the Friedrich Loeffler Institute, the animal-disease research unit of the German government, said at the end of December that Europe was experiencing “the strongest avian influenza epidemic ever,” with cases reaching as far north as the Faroe Islands and as far south as Portugal.

Those slaughter numbers should make the case that the flu is not only a threat to animal welfare, but an engine of economic damage as well. Rabobank, a financial services and analysis firm based in the Netherlands, has already predicted that these massive culls, layered on top of pandemic-fueled freight problems and rising feed costs, could inflate food prices this year.

For the most part, birds stick to specific north-south migratory pathways and don’t fly laterally around the globe. So to scientists in North America, outbreaks of bird flu in Europe were a cause for worry, but not immediate alarm. But in December and again in January, high-path H5N1 was found in farms in Newfoundland, at the top of the migratory flyway that sweeps down the US coast. That is the same flyway that crosses over the Carolinas, where the virus-carrying ducks were caught—and also over the more than 1 billion chickens grown each year in Georgia, the most poultry-dense state in the US.

Because this flu is highly pathogenic, the challenge is that there is no time for mitigation once it arrives in a flock. As Midwest turkey producers experienced in 2015, it blows up into a destructive epidemic overnight. That requires poultry farmers to harden their defenses now—and while that seems like an obvious task, it requires precision and cost in an industry that runs on thin margins and speed. Carol Cardona, a wildlife veterinarian and chair of avian health at the University of Minnesota College of Veterinary Medicine, likens it to learning to live under Covid: Every daily action requires a calculation of risk and takes a little more patience than you can easily summon.

“It’s the same for growing poultry,” she says. “How do we feed them without introducing a little bit of risk? How do we care for them? In normal times, when we don't have a threat, you can be more efficient in how you do things. But now things have to change. You have to be perfect all the time. That’s a lot of stress.”

Scientists who monitor wildlife fret that there is something else going on in this wave of flu. Wild waterbirds are accidental transport vehicles for the virus, but rarely victims. They pick it up and transfer it to other birds in ponds and wetlands at the ends of their migration journeys and then carry it with them, unharmed, once they return to the skies. But in Israel, where more than a half-million poultry have died or been slaughtered, the first sign of trouble was a mass die-off of thousands of wild cranes in a wetland that lies directly under a migration route. The European Food Safety Authority has identified deaths from flu in at least 80 other species of wild birds, leaving scientists to wonder whether bird flu has evolved into a further threat.

“The catastrophic issue economically is poultry,” Stallknecht says. “But we also have to be concerned with wildlife health. And there are some populations of shorebirds that are already not in good shape, so we need to be monitoring them also.”

There’s also evidence these new waves of bird flu have been leaking into humans. In the first week of January, UK health authorities revealed that a man in Devon who kept ducks as pets had the country’s first-ever human case of H5N1 bird flu. The ducks were all slaughtered; the man was reported to be quarantined and surviving the infection but lonely and missing his birds. In November, the WHO said it has been monitoring a slow surge in human infections in China caused by a known but less common bird flu subtype, H5N6. By the end of 2021, there had been 26 people infected, one of whom died. And in February a year ago, the Russian government revealed that seven poultry farm workers fell ill (and recovered) from yet another subtype, H5N8.

Other bird-specific strains have been surging into humans as well. The Chinese government disclosed last June that a man who had no known contact with poultry developed an infection with a flu strain never before seen in humans, H10N3, and that he was hospitalized but recovered. Since 2013, China has recorded more than 1,600 human cases of yet another strain, H7N9.

Though there have been notifications of those outbreaks—the regulations governing the WHO require countries to send immediate notification of high-path avian flu—they have not all included details about genetic sequences or spread. Researchers are hungry for answers. “The question is: What’s new?” says Daniel Lucey, an infectious-disease physician and senior scholar at Georgetown University’s O'Neill Institute for National and Global Health Law. “The quantity of outbreaks is massive, but has there been a change in qualitative risk? Have the sequences changed so the virus is more likely to infect humans? Can we document person-to-person spread?”

A further concern lurks behind this bloom of bird flu. Until now, biologists have assumed the danger is seasonal, triggered by the movement of waterbirds as they migrate: If there are no visiting birds overhead, or on shores or in ponds, they can’t spread a virus to local birds or people. But researchers are beginning to wonder whether climate change is interfering with migration patterns. The typical pattern for bird flu infections has been for them to begin during the fall migrations and then continue through the winter and into spring. But in Germany last year, scientists were able to identify H5 viruses in wild birds throughout the summer, a first.

It’s difficult for scientists to make the case for year-round surveillance and better financial support when they can’t say whether this wave of flu is a brief aberration or the first moments of a sustained emergency. But the world wouldn’t be facing that uncertainty if the capacity for surveillance and analysis had been built after the massive 2015 outbreak, or any of the ones before that. We didn’t do it earlier, so the time to start is now.