In mid-February, the owners of a backyard flock in Suffolk County, New York, noticed two guinea hens and three of their chickens were sick. Three days later, the birds were dead.

Within five hours of getting a swab of the birds’ airways, Cornell’s Animal Health Diagnostic Center and the New York State Veterinary Diagnostic Laboratory determined it was New York state’s first case of a deadly strain of avian influenza – the same strain that has killed millions of domestic poultry and devastated wild birds in dozens of countries.

Cornell researchers knew highly pathogenic avian influenza, or bird flu, was coming. They had been tracking the disease’s spread in northeast Canada and then in the Carolinas for months.

“We knew it was almost inevitable that we were going to get hit. So we put everything in place to prepare for it,” says anatomic pathologist Gavin Hitchener, director of Cornell’s Duck Research Laboratory on Long Island, just 15 miles from the backyard flock. “There was no shock moment for me. Fear? Yes. Because it was like, ‘It’s really in my backyard now.’ But we were prepared.”

Within hours of confirmation by the National Veterinary Services Laboratories in Ames, Iowa, and an announcement by the U.S. Department of Agriculture’s (USDA) Veterinary Services, Hitchener started calling commercial poultry operators to advise them on enhancing their biosafety protocols. The idea is to keep the birds inside, where they won’t mix with the wild waterfowl that carry the disease; limit interaction with other farms; and prevent cross-contamination within the farm, Hitchener says.

“We knew how to implement strategies to prepare, and prevent potential losses,” he says.

Hitchener and others at the Animal Health Diagnostic Center, part of the College of Veterinary Medicine (CVM), have been helping to keep New York’s avian flu incidents remarkably low, with education, outreach and testing that help safeguard commercial producers and backyard flock owners from the devastating disease.

Those measures have helped to minimize New York’s avian flu cases. As of April 6, the state has had just one outbreak in a small commercial flock and seven in backyard flocks, for a total of 9,500 birds affected.

So far, all of the state’s large commercial operations have remained unscathed, including the flock of more than 100,000 ducks that Marcus Henley oversees in the Hudson Valley.

“The ability for poultry farmers to reach out and get answers to these questions is so important to us all. It’s a really vital resource to the state,” Henley says. “Cornell having that depth of understanding of how the virus is spread – it’s just critical.”

What is bird flu and why can it be so devastating?

New York is currently in what Hitchener calls an avian influenza “lull.” But he and other Cornell researchers and staff are taking measures now during the fall migration, when migrating birds will flood the Atlantic flyway, from Greenland to South America, crossing New York state along the way.

When migrating birds land near bodies of water, their feces and other secretions spread the virus to commercial and backyard flocks and wild birds – say, when a bird drinks water contaminated with the virus.

“Because backyard flocks are usually outside, free-range, they’re mixing and mingling with migratory birds. They may pick the virus up from the feces of wild birds in their environment,” says veterinarian Jarra Jagne, DVM ’90, head of the Animal Health Diagnostic Center’s Avian Health Program.

There are 144 types of avian influenza. Some cause just mild respiratory infection. But the current strain, H5N1, is highly pathogenic and causes extreme mortality, says Jagne, who is also an associate professor of practice in the Department of Public and Ecosystem Health at CVM.

When the virus takes hold, it replicates rapidly in the respiratory, neurologic, digestive and reproductive organs. “It is systemic – throughout the whole body. This virus just enters and destroys the tissues,” Jagne says. “And so within 24 to 48 hours after seeing the first sick or dead birds, you will see very high mortality.”

Waterfowl, like geese and gulls, are the natural reservoirs of all avian influenza. Other wild birds can be infected, such as bald eagles, owls, and other birds of prey, says Krysten Schuler, director of the Cornell Wildlife Health Laboratory, which is part of the Animal Health Diagnostic Center. “A lot of birds of prey – eagles and vultures – were quite affected, because they scavenge dead birds,” she says. “And we have seen the virus too in some mammals. We have several cases of infected and dying young foxes.”

Because it is so devastating, “high path avian influenza is at the top of the list” of diseases the center tracks, says François Elvinger, executive director of the center, and professor of population medicine and diagnostic sciences and associate dean for diagnostic operations and government relations at CVM.

The H5N1 strain has been circulating in various parts of the world since 1997, Jagne says. “But it had not affected New York state,” Jagne says. “It was just a matter of time.”

The first case in New York

In the first case in New York, the owner of the backyard flock in Suffolk County contacted the New York State Department of Agriculture and Markets, which sent a technician to take a swab from the birds. That swab was mailed overnight to the Animal Health Diagnostic Center.

The center also tests wild bird samples sent by the New York State Department of Environmental Conservation and by the USDA’s Wildlife Services. And the center is one of 60 labs throughout the country in the National Animal Health Laboratory Network that tests sick and dead birds. “They send us samples from other states as well, from Maine, from the Carolinas, from Tennessee,” Elvinger says.

The Suffolk County sample was one of about 1,500 submissions of all kinds of samples that the center tests every day, from a single blood sample to an entire cow or horse for necropsy. The center tested 280,000 submissions in the last fiscal year and has completed about 3,500 tests for the current bird flu outbreak, Elvinger says.

While New York is not a big poultry producer, commercial farms do contribute significantly to the state’s economy, Jagne says. New York has nine large commercial poultry operations, and several medium-sized farms owned by Amish and Mennonite communities in the Finger Lakes region, for a total of 5.6 million egg-laying chickens. If avian influenza circulates through those flocks, “it’s going to be devastating, definitely, in terms of jobs and livelihoods,” Jagne says. “So anything that comes into our lab that has either neurological signs, or respiratory signs, coupled with high mortality, will be tested for highly pathogenic avian influenza.”

The Cornell team was tracking reports that the strain was circulating in eastern Canada in January and February. “As soon as we saw highly pathogenic avian influenza in Canada, we started upping our game,” Hitchener says.

That meant encouraging commercial producers and backyard flock owners to call if they saw any sickness or reduced egg production. And it meant advising them on how to enhance their biosecurity measures.

For Henley, that meant making sure the birds he processes from local farmers were virus-free, restricting the public from visiting the farm, preventing employees from working in multiple buildings, and making sure every vehicle that enters or exits rolls through a concrete basin of disinfectant. “Suddenly we went from a routine maintenance of security, where we knew of no serious cases in the state, all the way to condition red,” Henley said.

Within 16 days of the first case, Hitchener and the Cornell Duck Research Laboratory partnered with Cornell Cooperative Extension, the Long Island Farm Bureau and New York State Department of Agriculture and Markets to create a presentation on the science of the virus, the risks it poses, how it spreads, how to protect birds with biosecurity plans, and what happens when the virus is detected.

Duck producers like Doug Corwin ’80 are especially at risk, because some have been breeding their birds for generations. Corwin, a fourth-generation duck farmer, operates Crescent Duck Farm in Aquebogue, New York, Long Island’s last remaining duck farm. It produces 1 million ducks per year, selling to fine-dining restaurants in New York City, Philadelphia and Boston.

“If I had a strain of avian influenza here, I would lose my genetics. If I lose my genetics, I’m out of the poultry industry,” Corwin says. “Because my selling point is, I’ve made my genetics so much more different than my competition.”

The guidance of the Cornell team has been invaluable, says Corwin, who is president of the International Duck Research Cooperative, which creates and produces USDA-licensed vaccines through the Duck Research Lab.

“I owe a huge thanks for gratitude to Gavin and his outreach. He could speak as a Cornell University diagnostician, which carries an awful lot of weight,” Corwin says. “He’s helping to keep an awful lot of people in business right now.”

The Cornell team will continue their efforts to keep the number of cases low as the fall migration ramps up, Jagne says. “We’ve been spreading the word: If you see any mortality, or unusual mortality, in your flock, give us a call.”