A Bad Case Of the Flu

In early 2022, as the United States was beginning to emerge from the worst of the COVID-19 pandemic, another virus started to wreak havoc across much of the country. While not a significant threat to human health, the pathogen — known as highly pathogenic avian influenza, or HPAI — ravaged commercial and backyard poultry flocks. The outbreaks continued into the new year, directly killing or leading to the culling of nearly 59 million birds in 47 states by summer 2023.

Pennsylvania has not been spared. According to the U.S. Department of Agriculture, more than 4.6 million chickens, turkeys, ducks and other birds from 31 commercial and 36 backyard flocks have perished in the Keystone State as of July 2023, mostly in and around Lancaster County, the epicenter of the state's $7.1 billion poultry industry. The full economic impact of the 2022-23 outbreak has yet to be calculated — in fact, the outbreak may not be over — but it's safe to say that costs for flock losses and clean-up will be in the tens of millions of dollars.

But it could have been worse, if not for the lessons learned from previous outbreaks and the collaborative efforts of faculty and Penn State Extension educators in the College of Agricultural Sciences, the Pennsylvania Department of Agriculture, the USDA, and the state's poultry industry.

A pernicious pathogen

According to the USDA's Animal and Plant Health Inspection Service, avian flu is caused by influenza Type A virus. These viruses are broadly categorized based on a combination of two groups of proteins on the surface of the virus: hemagglutinin, or "H" proteins, of which there are 16 (H1-H16), and neuraminidase, or "N" proteins, of which there are nine (N1-N9). Many different combinations of "H" and "N" proteins are possible.

Avian flu viruses vary greatly in their numbers of "H" and "N" proteins, and most are relatively harmless. The viruses are carried and spread by wild migratory birds such as waterfowl and shorebirds, which usually show few or no symptoms. These viruses are classified as either low pathogenic or highly pathogenic based on their genetic features and the severity of the disease they cause in poultry. Most viruses are "low path," meaning that they cause no or only mild symptoms in poultry. The virus responsible for the current outbreak is a "high-path" H5N1 strain.

The last time a high-path avian flu struck Pennsylvania was in 1983, when 17 million chickens died, costing the state's poultry industry an estimated $65 million. Researchers have said that the 1983 outbreak started as a low-path H5 virus that may have originated in urban live-bird markets in the Northeast and was allowed to spread. At the time, scientists didn't know that low-path H5 and H7 viruses, when allowed to circulate among poultry, can mutate into a high-path strain. Since then, authorities have treated low-path outbreaks almost as if they were highly pathogenic.

Then, in 2014, the U.S. experienced the largest HPAI outbreak it had ever recorded. The USDA deemed it "arguably the most significant animal health event in U.S. history." The virus ripped through 21 states, primarily in the Midwest, killing about 50 million chickens and turkeys. Of the four North America migratory flyways — paths taken by wild birds when migrating in the spring and fall — the Atlantic flyway was the only one not affected, and the outbreak missed Pennsylvania.

An action plan

The 2014-15 outbreak, however, got the attention of Pennsylvania agriculture officials, who created an HPAI task force — with Penn State as a key player — to develop plans for how to prevent, respond to and recover from any potential outbreak in the state. Composed of state animal health authorities, university specialists and industry representatives, the task force has addressed topics such as biosecurity, emergency management, depopulation and disposal of infected flocks, issues relevant to small or backyard flocks, and education for youth poultry exhibitors at county fairs and other shows.

"We wanted to make sure that biosecurity was at the top of producers' minds because even before HPAI was known to be affecting commercial flocks in Pennsylvania last year, we knew that there were threats in our environment," said Penn State poultry scientist John Boney, a member of the task force. "There are other diseases and other viruses that can impact poultry. We had a lot of industry-wide planning meetings, including training on the National Poultry Improvement Plan's 14-step process for writing a biosecurity plan that, if implemented, should help protect flocks from disease."

Boney, the Vernon E. Norris Faculty Fellow in Poultry Nutrition and leader of extension's poultry team, said tabletop exercises simulating a large layer complex helped producers understand what might happen if their flocks test positive for HPAI.

"How will we handle the euthanasia? How will we handle the bird composting? How will we handle the cleaning and disinfection?" Boney said. "Extension was at the table helping plan that out with compost calculators to understand the material needs, helping source these materials in mock situations, determining how much it was going to cost and the logistics of making that happen in various settings."

Task force member and Poultry Extension Educator Gregory Martin is based in Lancaster County, which ranks among the top four counties nationally in sales of poultry and eggs. He noted that previous HPAI outbreaks informed planning, thereby mitigating the impacts in 2022-23, but not all producers bought in to recommendations.

"We had an action plan on the shelf ready to go for a long time," he said. "But just like the fire department, unless you practice, you don't know exactly how that plan is going to work. So, we did a lot of planning and training, and we've been talking to producers about biosecurity plans since before 2015. But there were some who, perhaps, tuned us out after awhile, thinking it wouldn't happen to them. Nobody wants flood insurance until their house goes floating down the street, so sometimes the lessons are hard."

A rapid response

As the spring 2022 northward migration of wild waterfowl was underway, the first confirmed case of high-path avian flu was reported in February in a commercial turkey flock in Indiana. More confirmed cases followed in Virginia, New York and Delaware — states, like Pennsylvania, within the Atlantic flyway.

In mid-April 2022, HPAI was confirmed in a nearly 1.4 million table egg layer operation in Lancaster County, followed five days later by two more farms in the county housing a total of about 2 million more "layers." Already on high alert, the state task force and agricultural authorities leapt into action.

"Once we had our first presumptive positive flock in Pennsylvania based on some of the clinical signs — even prior to lab confirmation — our subject matter experts worked with those producers on site calculating the material needed to be able to compost over 1 million hens on the first premise," Boney said. "Extension served as a sounding board to the state veterinarians and USDA for understanding the physiology of the bird and how to properly execute a depopulation and disposal effort of that magnitude."

The Pennsylvania Department of Agriculture immediately established 10-kilometer quarantine areas or "control zones" and 20-kilometer "surveillance zones" around the affected farms. Within days, infected flocks were depopulated. Carcasses were composted in place to kill the virus before they were removed and the house disinfected. Affected producers were required by protocol to get approval before repopulating the facility. During that time, unaffected producers within the quarantine areas needed a permit that required negative HPAI tests and approved biosecurity plans to move poultry products from or to their farms.

Boney, as extension poultry team leader, coordinated Penn State's involvement, acted as a liaison between the farms and state and federal agriculture officials, and assisted with biosecurity education. Martin, due to his proximity to the affected premises, was often in the field helping to direct depopulation and disposal efforts. He also assisted with hands-on training for producers on the protocol for taking samples from birds for virus testing.

Gino Lorenzoni, assistant professor of poultry science and avian health, created a task force of students and faculty members to temporarily assist the state Department of Agriculture with auditing biosecurity plans from the commercial poultry industry. Later, he and Poultry Extension Educator Hope Kassube provided education on biosecurity for the Amish and other Plain sect communities.

"Approved biosecurity plans were needed to move product out of the control zones, and that was a difficult requirement for many Plain sect farmers because they didn't have the proper training," Lorenzoni said. "So, we held educational sessions to help members of the Plain community develop and implement biosecurity plans."

He noted that Kassube also helped deliver online trainings to Spanish-speaking audiences, to ensure that vital information was not lost in translation.

"That was very important, because sometimes there was a gap in communication, and the farm managers weren't able to pass down instructions to Spanish-speaking employees," Lorenzoni said. "We were there to help make these connections. We work as a team, and pretty much everybody involved in poultry in some way at Penn State got deployed."

This kind of grassroots biosecurity education was crucial in changing the path of the HPAI outbreak, according to Christian Herr, executive vice president of PennAg Industries Association, a trade group that represents a large number of the state's poultry producers. He cited Penn State Extension workshops that helped farmers prepare customized biosecurity plans and learn how to implement a biosecurity system pioneered in Denmark that creates barriers for pathogens to enter poultry houses.

"Penn State provided a great demonstration of how the virus spreads and how highly pathogenic it is, as well as several demonstrations of how Danish entry systems can help producers protect their farms and their neighbors' (farms)," he said. "This education was important for producers in maintaining their business continuity during the outbreak."

Martin's time spent on affected farms included working with Craig Williams, a dairy extension educator with expertise in the disposal of livestock mortalities, to compost multitudes of dead birds.

"In a typical day, I would go out early and check on the construction of the compost windrows, and then monitor the windrows as they were 'cooking,'" Martin said. "They would cook for 14 days. Then, I would turn the pile and cook it again for another 14 days to ensure that we were killing the virus. On some farms, it was only one row, maybe two, 300 feet long. But on one farm, there were 3 1/2 miles of windrow, and I walked every mile. During the height of the outbreak, I lost about 15 to 20 pounds sweating in my protective suit."

An accurate diagnosis

Back on campus, the college's Animal Diagnostic Laboratory was doing its part to rapidly test submitted samples for avian flu. One of three labs in the state-funded Pennsylvania Animal Diagnostic Laboratory System, Penn State's lab performed more than 16,600 polymerase chain reaction, or PCR, tests for avian influenza from February 2022 to May 2023, according to Megan Lighty, associate clinical professor and avian diagnostic and outreach veterinarian at the lab.

"In 'peacetime,' so to speak, a lot of our avian flu surveillance is serology based, where we're looking for antibodies," she explained. "But serology is really geared to detect low path avian flu, because with low-path AI, birds may show no or only mild clinical signs, and they have time to develop antibodies. Whereas with high path AI, they get very sick and start dying quickly, and they don't have time to develop antibodies, so we have to shift to molecular testing such as PCR."

That meant that some lab technicians who normally would conduct serology — or blood-based diagnostic testing — had to train and become certified to do PCR tests. With the three state diagnostic labs working seven days a week during the early months of the outbreak, having additional staff trained in PCR allowed for a rotating schedule.

"We've really learned to appreciate the value of cross-training our laboratory staff so that we can pivot if there is a disease outbreak," Lighty said. "Even so, some of us, including in receiving, were putting in very long hours."

Lighty, who served as the liaison between the Animal Diagnostic Lab and the HPAI incident command center, noted that additional funding appropriated to the lab by the state legislature to combat avian flu has helped boost response and testing capacity.

"That funding allowed us to purchase additional reagents and supplies that we needed for AI testing," she said. "It also helped the lab pay staff for overtime hours that they were working since our annual budgets are calculated assuming 40-hour work weeks. We were able to obtain signage and personal protective equipment as we set up a separate workflow for sample drop-off, so clients coming from control zones didn't have to enter the building and risk bringing in pathogens. Some of the funds are being used for continuing education for our faculty and staff to better prepare us for the future."

And that future could include more outbreaks of more diseases, affecting more species, Lighty warned.

"We need to take the things that we've learned from this outbreak and apply them to future situations," she said. "If there was an outbreak of African swine fever or foot-and-mouth disease, how would we ramp up for those things? Or, in a worst-case scenario, what if we had an outbreak of high path AI and African swine fever at the same time?

"The important thing to remember is that this isn't over," she continued. "This will be an ongoing challenge and a continuous threat for the poultry industry. And then, obviously, there are other similar threats for all of the livestock species. So, disease preparedness, diagnostic testing and outreach are important roles for the diagnostic lab, for the college and for extension moving forward."

Mitigating a disaster

Despite the losses caused by the outbreak to date — and the potential for additional cases as the fall wild bird migration gets underway — there is a belief that the emergency planning and preparedness, the heightened awareness of the need for biosecurity and the rapid response by all involved helped to limit what could have been an even greater disaster.

"There were 151 other commercial poultry premises within the control zone around the initial infected flock," Boney pointed out. "To see the response and understand that we really limited the spread of that virus to just a few other flocks is really noteworthy, because that could have spun out of control very quickly, like it did in 1983 and 1984. And that did not happen here. Producers intensified their biosecurity efforts. They took it very seriously. And because of that, we were able to limit the total impact across Pennsylvania."

Herr, of PennAg Industries Association, credited the "all hands on deck" approach: "The poultry industry, PennAg, Penn State, the Pennsylvania Department of Agriculture, the animal diagnostic lab system, USDA, the Pennsylvania House and Senate, Govs. Wolf and Shapiro, and state Agriculture Secretary Russell Redding and Executive Deputy Secretary Greg Hostetter all worked closely to help mitigate the largest animal health outbreak in American history."

By Chuck Gill
Illustrations by Jonathan Ziegler