THE WILD SIDE OF AVIAN INFLUENZA

By Erica Cirino

Most people think of bird flu as a poultry disease. But where it starts is inside the bodies of wild migratory birds.

Left: Backyard chickens, Long Island, NY. Credit Erica Cirino. Right: Northern pintail duck (male), Japan. Credit U.S. Geological Survey.

Left: Backyard chickens, Long Island, NY. Credit Erica Cirino. Right: Northern pintail duck (male), Japan. Credit U.S. Geological Survey.

On a typical December day at Wiser Lake in Whatcom County, Washington, thousands of ducks and geese can be found energetically quacking, honking, splashing and swimming. But the lake is also occasionally shaded with the quiet pallor of death, as was the case in early December 2014 when Washington Department of Fish and Wildlife biologists noticed a small bird die-off there.

A small bird die-off on a big lake isn’t something to be too worried about. Die-offs happen sporadically on large water bodies with large populations of birds, like Wiser Lake, during migration season. If lake or pond water is contaminated with illegal lead hunting shot or a naturally occurring fungal disease called aspergillosis, it’s not unusual for some birds to die.

Yet the biologists were very concerned. That same week, a deadly bird disease had been detected on two poultry farms just miles across the U.S.-Canada border in Fraser Valley, British Columbia: thousands of chickens and turkeys on two commercial farms had been sickened and killed by avian influenza.

That North American waterfowl migrate from north to south in winter meant the wild birds then in Canada would soon be flying into the U.S. And highly pathogenic avian influenza in America, the biologists knew, could spell disaster for the $50 billion U.S. poultry industry.

"Waterfowl are carriers of the disease, but often don't show symptoms,” said Don Kraege, the department’s Waterfowl Section manager. “The primary risk is to domestic chickens and turkeys.”

Normally, avian influenza in North America isn’t concerning—so long as it’s of the North American low pathogenic variety. This milder form of the virus circulates among ducks and geese throughout the continent each year without posing a high risk of infecting poultry. But, as its name suggests, highly pathogenic avian influenza—the type detected on those farms in British Columbia—is notorious for killing poultry. So potent are these viruses that they can infect and kill birds of prey, such as hawks and owls.

“Free-range” poultry kept for hobby or commercial purposes on outdoor farms can pick up avian influenza through direct contact with wild birds—or more often, their droppings. Yet the vast majority of poultry in the U.S.—chickens and turkeys kept on the country’s 233,770 commercial farms—are kept indoors.

Crammed into enormous barns the size of airplane hangars in groups of hundreds or thousands, most of these birds never go outside and thus do not have direct contact with wildlife. But they can still contract disease from poor farm hygiene—anything from cross-contaminated equipment to workers who don’t disinfect their boots before entering a barn from the outdoors. After it enters the closed confines of an industrial barn, avian influenza spreads rapidly among the thousands—sometimes hundreds of thousands—of birds inside. Poor farm hygiene can work just as efficiently in reverse, spreading disease from inside a poultry barn to wild birds outside.

Very concerned after a week of persistent waterfowl deaths, “Paul DeBruyn, a biologist with the Washington Department of Fish and Wildlife, contacted the National Wildlife Health Center and notified us of a small-scale wild bird mortality event at Wiser Lake,” said microbiologist and avian influenza expert Dr. Hon Ip. The United States Geological Survey-National Wildlife Health Center in Madison, Wisconsin, is one of the nation’s top wildlife disease research facilities, and Ip is section head of its diagnostic virology laboratory, where he studies viruses like avian influenza.

Debruyn told Ip he’d be sending over nine carcasses—eight ducks and one swan. The carcasses were bagged and boxed up with ice packs, then swiftly overnighted to Ip. As soon as they arrived, the boxes were dropped from the center’s loading dock to its basement-level necropsy room with a dumbwaiter—garnering the same level of care and caution a confirmed shipment of deadly rabies virus samples would receive. Ip’s colleagues in the necropsy room examined six of the carcasses closely to help determine a primary cause of death.

Several carcasses showed hemorrhaging and inflammation of organs, especially the lungs and air sacs, classic signs of aspergillosis. But determining if the birds had avian influenza would take a little more work. Because waterfowl can carry avian influenza without showing signs of sickness, the only true way to diagnose it is through viral analyses of body tissue and blood from their primary body cavities.

So scientists in the necropsy lab collected samples from all carcasses and sent them back up to Ip’s diagnostic virology lab on the center’s first floor. A first round of testing quickly determined that avian influenza was present in five of the birds. A second round revealed that four of them were carrying only the low pathogenic version. But the the fifth, a Northern pintail duck, tested positive for highly pathogenic avian influenza—the same strain as the one that hit the poultry farms in British Columbia. It was the first U.S. case of what was to become a global avian influenza outbreak.

Highly pathogenic Eurasian/North American H5N2 is a hybrid of mild North American avian influenza and Eurasian lethal H5N8. H5N8 itself was a new lethal strain that had spread rapidly across Asia and Europe throughout 2014.

Along with H5N8 and another new hybrid strain, Eurasian/North American H5N1, H5N2 would be one of three lethal avian influenza viruses to be detected in the U.S. after December 2014. And for the following six months, it was primarily H5N2 that would go on to cause catastrophe on U.S. poultry farms.

As Ip and his team were analyzing the samples from Wiser Lake, North American waterfowl continued their migration south, carrying with them lethal strains of avian influenza.

“First, several backyard farms in the Pacific Northwest were hit” with H5N2 and H5N8, Ip said. “On these backyard farms poultry were sickened after coming into direct contact with diseased waterfowl.”

From there, migratory birds continued to spread lethal avian influenza, primarily H5N2, across the West and Midwest to Indiana. In major commercial turkey- and egg-producing regions like Minnesota, Iowa and South Dakota, H5N2 spread rapidly from farm to farm, brought into indoor poultry barns and spread by contaminated farm workers, vehicles and equipment.

Between December 2014 and June 2015, more than 48 million individual chickens—mostly egg-laying hens—and turkeys on 211 commercial and 21 backyard poultry farms across the American West and Midwest died or were euthanized after being infected with H5N2 or H5N8.

According to USDA data, the $10 billion U.S. egg industry lost about 10 percent of its flock and the $5 million U.S. turkey industry lost three percent of its flock in those six months. The precipitous drop in supply sent the national average retail price of a dozen eggs to $2.72 in August, a five-year high and twice the price of a year earlier, according to commodities firm Urner Barry.

Similarly, the average national retail price of a pound of a whole frozen turkey went up from a dollar a pound in the spring to $1.26 a pound over the summer, according to an October USDA agricultural supply and demand report. However, this price increase was relatively short-lived: to keep the country’s turkey supply steady, farmers on the East Coast unaffected by avian influenza ramped up production when their western counterparts were hit. It prevented any major dip in total U.S. turkey production and averted a shortage at Thanksgiving as Americans gobbled down their usual 46 million turkeys, according to the National Turkey Federation, America’s major turkey industry trade group. In fact, the supplemental turkeys helped drive down the cost of a whole frozen turkey in the U.S. to about 90 cents a pound, according to the USDA.

Still, the outbreak dealt a major blow to the U.S. poultry industry. In July, agricultural economist Dr. Tom Elam, president of agribusiness consulting firm FarmEcon LLC, testified before the Senate Committee on Agriculture, Nutrition and Forestry that the disruption in poultry production as a result of the outbreak cost the U.S. economy a “conservatively estimated $3.3 billion.” Excluding the costs of euthanasia and facility cleanup, which is mandated by the USDA when the virus is detected in a poultry facility, Elam estimated the direct hit to producers at $530 million for turkeys and $1.04 billion for eggs.

The ability of avian influenza to spread from wild waterfowl to poultry is well known among wildlife and animal disease experts, including one from USDA’s Animal and Plant Health Inspection Service, the primary agency charged with monitoring and managing the outbreak.

“When we have [lethal] avian influenza [in wild birds] in the United States, consider that to be a major problem because that is a foreign animal disease to the U.S.,” said Dr. Brian McCluskey, chief epidemiologist of the USDA Animal and Plant Health Inspection Service’s Veterinary Services branch, by phone from his office in Fort Collins, Colorado. “But once it got into a big commercial flock we got even more concerned because the potential spread of that is considered to be of greater likelihood.”

Once a wild bird carries avian influenza to a geographic region, poor farm hygiene can bring it into a closed commercial poultry barn. This appears to be what happened on the first U.S. commercial farm infected, a turkey farm in Stanislaus County, California. However, in major poultry-producing regions such as Minnesota and Iowa, farms often share workers and equipment. In these cases poor farm hygiene spread the virus from one farm directly into another, according to new USDA research initiated in March, shortly after the first commercial farms in the U.S. tested positive for lethal avian influenza.

The USDA initiative, one of two major federal avian influenza research efforts triggered by the 2014-2015 outbreak, focuses on understanding how farm hygiene and avian influenza are linked so farm management practices can be improved and future outbreaks avoided. The other major effort, in which Ip is involved, entails surveying wild birds—acting as the proverbial canary in a coal mine—to stay ahead of any potential future outbreaks, a strategy his agency has used to monitor previous U.S. lethal avian influenza outbreaks.

 “This virus is not a superbug, it’s not too difficult to prevent,” Ip said, “Knowing what the science is, I can tell it’s clear many farms—especially those that produce animals in very high numbers—don’t have adequate biosecurity practices.”

On farms, biosecurity refers to management procedures meant to keep animal diseases at bay. While the USDA and poultry producer associations encourage farms of all types and sizes to adhere to biosecurity best practices such as requiring all workers to clean their boots in bleach baths before entering and exiting barns and disinfecting farm vehicles after use, no law mandating or regulating any specific biosecurity standards currently exists.

To make matters worse, once avian influenza—especially in its lethal form—begins to spread, it has a high tendency to mutate, especially in poultry.

“‘Will it evolve?’ is always a major question when dealing with avian influenza,” Ip said. “Past and present research indicates that avian influenza’s virulence tends to increase in poultry once it gets onto a farm.”

Increased virulence, combined with changes in a virus’s genetic code, Ip said, could together create an avian influenza virus capable of infecting other animals, like swine, or even humans.  

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I traveled to Wisconsin in late September to meet Ip and others involved in avian influenza research, and got my first taste of the state after exiting my plane into the Dane County Regional Airport in Madison. The airport in Madison is like most places in Wisconsin—filled with cheese. You can buy it in the form of official Green Bay Packers Cheesehead hats, key chains and t-shirts. Of course, you can also get the real thing: blocks of cheddar and bags of curds are tantalizingly displayed in refrigerator cases in several airport shops.

Indeed, Wisconsin is “America’s Dairyland,” its license plates proclaim. But the state is also home to a decently sized poultry industry. During the outbreak, one backyard flock and nine commercial poultry operations—mostly turkey farms—were hit across the state. In terms of state with the highest number of poultry farms impacted, it’s tied for third place with South Dakota, tailing only Minnesota (101 farms) and Iowa (75 farms).

The National Wildlife Health Center is about 15 miles from the heart of Madison and with nothing but a small green-and-white sign marking its entrance, the place is easy to miss. Follow its long rural driveway to the end, and you’re greeted first by a small array of freestanding solar panels. The center itself is just beyond the solar panels, composed of two single-story brown brick buildings straight out of the 1960s, tucked into a luminously lush green-and-gold prairie landscape teeming with songbirds. 

Before meeting with Ip, I saw the necropsy room where the Wiser Lake birds were first brought for examination in December 2014 and the basement support room where beakers of chemicals used in disease testing are whipped up for use in the center’s labs. I also saw the labs, which each focus on the study of one class of diseases, such as parasitology. Ip’s lab, diagnostic virology, studies viruses.

Hon Ip is an energetic, bespectacled man: a runner and a scientist. He is the microbiologist in charge of the diagnostic virology lab at the National Wildlife Health Center. Nationally, he is considered a leading avian influenza expert.

Ip met me in the center’s brightly lit lobby, which was decorated with informational displays, framed nature photography and a healthy dose of taxidermy. Then he led me to the access room to his lab, where he and I donned matching teal green lab scrubs. Now we were ready to go into his lab, or so I thought. Ip’s hand paused on the door handle, and he suddenly spinned around to face me.

“Wait,” he said. “Before we go in, I must ask: Do you have any birds at home?” Ip had asked me this earlier, in the lobby where we first met.

“No,” I said again. “Just a dog.”

“Okay,” he said, still facing me with his hand on the door handle. “Please remember, you cannot go near any live birds for five days, starting tomorrow. You will not come into contact with any live birds, correct?”

“No,” I said. “I won’t go near any birds.” Ip smiled. A five-day quarantine from live birds, I learned, is mandatory for anyone who enters Ip’s diagnostic virology lab, whether a worker or visitor. Though no new cases of lethal avian influenza had been detected in the U.S. since late July, it was still possible that the new samples coming into his lab for analysis could test positive. And if even one person were to pick up the virus and carry it outside, the U.S. poultry industry could face disaster all over again.

Presumably satisfied with my verbal promises, Ip swung open the door to his lab and hurried me to an empty chair, placing a sheaf of paperwork and a pen on the table in front of it. Now I had to put my promises in writing.

No contact with live birds for five days. Signature. Acknowledgement I was entering a “biosafety level three” facility, where there was just a very small chance that I may come into contact with viruses that may cause me to develop dangerous or potentially lethal disease(s) after inhalation, such as West Nile virus, Eastern equine encephalitis virus, and, of course, avian influenza. Signature....

Like biosecurity on farms, biosafety measures in laboratories are meant to protect the people who work in the labs—and the outside world—from disease. But lab biosafety is more stringent, established on a scale of one to four depending on what’s inside. At just one step down from the level of biosafety required for ebola lab (level four), biosafety in Ip’s lab is taken very seriously.

“In this lab we may study wildlife viruses, but many of these viruses have a strong impact on people,” Ip said, pulling up a chair and taking a seat. “West Nile, monkey pox, and of course, [lethal avian influenza].”

Avian influenza is an influenza A virus. These viruses are named according to the two types of proteins they’re made of. These two proteins, hemagglutinin and neuraminidase, represented by the letters “H” and “N,” respectively, come in various subtypes, each indicated by a number. Also usually denoted is the virus’s geographic origin and pathogenicity (either low—mild—or highly pathogenic—lethal). Influenza A viruses—both animal and human—tend to “mutate readily, and that’s why you need to get a new flu shot every year,” Ip explained.

This isn’t the first time Ip’s lab has been involved in lethal avian influenza research: The virus has been on his radar since 1996. That year, lethal Asian H5N1 was first discovered on a goose farm in China, and went on to cause both poultry and human deaths there and in Egypt, Indonesia and Vietnam.

But it was a string of very large lethal Asian H5N1 outbreaks from 2003 to 2007—which hit four continents and sickened both birds and people—that set into motion Ip’s first serious lethal avian influenza research effort. Under directives from the USDA, from 2006 to 2011, Ip and his colleagues tested swab samples from thousands of wild migratory ducks. The hope was that ongoing testing would serve as an early monitoring system, detecting any cases of the deadly virus in wildlife before it infected the nation’s poultry, and possibly humans.

The advent of the 2014-2015 U.S. outbreak sparked a similar monitoring initiative. The USDA’s current effort calls for the collection and subsequent testing of, at minimum, 31,150 samples from wild migratory ducks living in “targeted watersheds.” These include 98 areas across the nation with lakes and ponds popular among waterfowl during migration season, and where avian influenza has been detected in the past.

All this is a yearlong effort to be completed by the end of next March. Each state is responsible for coordinating its natural resources and wildlife management agencies to collect swab samples from both live and deceased wild ducks at targeted watersheds, then send those samples to an approved animal health lab for avian influenza testing. Positive samples are then sent to the USDA’s National Veterinary Services Lab in Ames, Iowa, for a final diagnosis. The data from each sample, positive or negative, is collected and added to a USDA database.

Wisconsin’s designated animal health test center is Ip’s diagnostic virology lab at the National Wildlife Health Center. There, Ip receives samples primarily from Wisconsin Wildlife Services, part of USDA’s Animal and Plant Health Inspection Service, the agency tasked with safeguarding the health of the nation’s livestock and crops. Each U.S. state has its own Wildlife Services team. USDA Wildlife Services was originally named Wildlife Damage, and that still describes the major focus of the branch’s work. Whereas the Wildlife National Health Center concentrates on wildlife and ecosystem conservation, Wildlife Services seeks to manage wildlife in a way that balances natural conservation with the activities and economic interests of humans.

A day after meeting Ip I took a short cab ride from my hotel in downtown Madison to USDA Wisconsin Wildlife Services’ headquarters. There I was scheduled to meet with two experts involved in the collection efforts: Dan Hirchert, director and biologist at Wisconsin Wildlife Services, and J.D. McComas, a Wisconsin Wildlife Services technician. Located in a plain, pale-blue building nestled in a commercial office complex in Sun Prairie, a quiet Madison suburb, it’s where Wisconsin’s wild waterfowl sample collection efforts are planned.

The inside of the building was almost as plain as its outside: aside from the oversized U.S. government crest that hung on the façade of the front desk, the office’s lobby was decorated sparingly.  A smiling receptionist wearing a polished skirt suit greeted me. Things felt so ordinary that I was actually fairly surprised to later learn that a trigger to the building’s security system summoned not the local police department, but Homeland Security.

 “The best time of year to collect samples in Wisconsin are fall and winter,” said Hirchert. This is when migratory ducks fly south for the winter down a major North American bird migration route called the Mississippi flyway, he explained, periodically landing in the U.S. to rest and refuel. The Mississippi flyway is one of four vertical paths North American migratory birds use to travel. Each of the four flyways overlaps with another so birds on different routes interact with each another.

During the outbreak, lethal avian influenza hit three flyways: the Pacific, Central and Mississippi. By sheer geographic luck, the virus was not carried into the Atlantic flyway runs down the East Coast—home to the country’s $32.7 billion broiler chicken industry.

In August, before wild waterfowl were to begin their fall migration, Wisconsin Wildlife Services capitalized on the Wisconsin Department of Natural Resources’ annual bird banding effort to help meet its surveillance quota.

Bird banding is the practice of securing numbered bands made of hard plastic to the necks or legs of waterfowl so individual birds can be identified as they migrate. Biologists and techs use net guns to capture and temporarily hold many birds at once, then release them after they are banded. Since the birds only have to be captured once to perform two wildlife research tasks, “to use a pun, it’s like killing two birds with one stone. It’s a perfect opportunity for us to collect samples from wild birds without causing them too much extra stress,” said Hirchert.

In all, Wisconsin Wildlife Services biologists and techs swabbed the front and back ends of more than 300 live ducks temporarily detained for banding. While interagency cooperation is not unusual, for the fall Wisconsin Wildlife Services is relying on what might be considered an ironic ally: hunters.

Wisconsin Wildlife Services coordinated two major hunter-harvested duck sampling events this fall. On these collection weekends, biologists and technicians flock to popular hunting spots, waiting at boat landings armed with avian influenza sample kits—boxes filled with screw-topped test tubes, sterile cotton swabs, barcoded stickers and log sheets. After nabbing a day’s worth of ducks from their boats—a popular method of hunting waterfowl—hunters return to the landings, where the biologists and techs ask for permission to swab each returning hunter’s catch.

Because I hadn’t visited on a major sample collection day, Hirchert and McComas took me behind their office to show me what does happen on such days. Together, they carried out their not-so-glamorous task in a quiet grassy area below a pure cerulean sky.

First up was a small duck with a mostly gray-and-brown body with a flashy gleaming green head and curling tail feathers: an adult male mallard, called a drake. Hirchert jotted onto a log sheet the duck’s age, species and sex, fixing a barcode pulled from a long roll of stickers next to that information, while McComas pulled out a tube and stuck a matching barcode sticker onto its side.

Hirchert put down the log and picked up the duck, offering McComas its front end first. McComas swabbed the duck’s windpipe. After a quick flip of his swab and the duck, he swiped its anal/reproductive cavity, or cloaca. Once finished sampling he snapped the swab in two and stuck both ends into the tube, which contained about a tablespoon of a cloudy liquid called culture media that helps preserve the swab samples for transport to the lab.   

The two repeated this process with the drake’s counterpart, a less-flashy female mallard of about the same size with a mottled-brown body.

The process doesn’t take too long. But I wondered how willing hunters are to give up some of their hunting time. “Hunters are very patient, I think, because they know healthy wildlife is a benefit to them,” Hirchert said. “If it wasn’t for their cooperation, we’d have no data.”

One hunter I later spoke to, Dan Riese, of Columbus, Wisconsin, said he was happy to allow the wildlife workers to test his three freshly caught wood ducks while ata popular duck hunting spot in Wisconsin’s southern zone called Horicon Marsh on opening day. “I think it’s important for them to track the present and [future] spread of diseases,” he said, “plus nothing they were gong to do would have any effect on how I was going to use the birds.”

Back at the office, McComas is tasked with entering information from the collection log sheets into the USDA’s avian influenza database. Once logged samples are tested, the database is updated with their virology results.

This data provides the USDA and other federal agencies involved in the surveillance plan with a detailed picture of what birds tested positive for avian influenza, where they tested positive, and which strain—if any—they carried. This picture can then be used to predict where the next poultry farm may fall prey to avian influenza, and if any circulating strains pose human health risks.    

 

*          *          *

Wisconsin Wildlife Services’ samples are shipped to Ip’s lab overnight and on ice. Once they get there, lab techs crosscheck each tube’s barcode with its corresponding log sheet, and assign it a specimen ID number. This information is copied into a thick black binder for safekeeping. Once checked into Ip’s lab, samples are ready for what is a decidedly long and somewhat tedious testing process.

Before any testing can happen, Ip explained, each tube must be properly prepped. Techs extract a small amount of each sample from its tube with a very delicate high-tech device called a micropipette that measures out extremely precise tiny quantities of liquid. Most micropipettes measure out liquid one sample at a time. Designed for speed, this one does 12.

The techs then use the micropipette to deliver the samples into smaller tubes containing tiny weak magnetic beads. These small tubes are thoroughly shaken on a vibrating tray the size of a shoebox, and then placed en masse into the hundred-plus rings of a magnetic tray made of rare earth metals. This very expensive and very heavy tray pulls the metal beads toward the tubes’ sides, along with any possible contaminants. The pure liquid left in the middle of each tube contains a trace amount of the genetic material Ip needs to test.

But before this genetic material can be tested, it must be amplified so there is enough to analyze. To do this Ip uses a technique called PCR, or polymerase chain reaction, which copies and duplicates the material with a machine that acts like a molecular photocopier. PCR is carried out in a thermal cycler, a nondescript white machine roughly the same the size and shape of a cash register, into which Ip places his samples.

Once the PCR process is complete, Ip uses another boxy white machine to compare the replicated genetic material from the samples he receives from Wisconsin Wildlife Services with that of confirmed samples of avian influenza. Wildlife samples that test positive for lethal avian influenza are injected into embryonic chicken eggs to identify the specific virus strain.

On the day of my visit, the National Wildlife Health Center had just received a fourth thermal cycler to add to its collection. The new machine, Ip said excitedly, would increase his lab’s avian influenza research output by about 25 percent.

“Understanding the genetics behind the virus is important for understanding possible future mutations that may occur. With mutations, it’s possible [lethal] avian influenza could become infectious in people or swine,” Ip said.

But genetic testing has also helped him map out how the current virus spread. This is critical to preventing another outbreak “that would again devastate the U.S. poultry industry.”

Genetic analyses allow Ip to determine the relationship between each case of avian influenza he receives. Specifically, he compares information from the USDA’s avian influenza database to published results from genetic analyses of avian influenza strains found in other countries. The more closely related the viruses, the more likely they are to have come from the same region—or even the same source.

Based on these data, Ip and other infectious disease experts across the world believe the outbreak happened something like this: In 2013 wild waterfowl summering in northeast Siberia, called “Beringia” for its proximity to the Bering Strait, carried various mild avian influenza strains related to lethal Asian H5N1. The waterfowl began to migrate south in the fall and by late November 2014 they reached their winter feeding grounds in South Korea. There, the wild birds came into direct contact with poultry on outdoor farms (in Asia, most poultry, both backyard and commercial, are kept outside), which picked up mild avian influenza.

This is where things really went south.

Once inside the bodies of poultry, the viruses mutated, increasing in virulence and creating a new strain: lethal Eurasian H5N8. Poultry infected with the new virus then passed it into the wild birds, which—with the help of poor farm hygiene and the proliferation of live poultry markets in Asia—spread the virus on both backyard and commercial poultry farms throughout South Korea, spreading to nearby Japan in January 2014..

Wild waterfowl infected with H5N8 left South Korea and Japan in the spring of 2014 to return to their summer breeding grounds in northeast Siberia and northwest Alaska. As in North America, flyways in Asia overlap with those of other regions, so groups of wild waterfowl that spend the summer in northeast Siberia mingle with birds from several continents other than Asia, including Europe, Australia, Africa and North America.

During the summer of 2014 lethal H5N8 circulated among wild waterfowl in Siberia and Alaska. In September 2014, some of these wild birds again began migrating south toward Southeast Asia, where outbreaks sprung up in poultry starting in November 2014 and lasting well into 2015.

“Some birds that spent the summer in Siberia migrated further west” Ip said, with lethal H5N8 outbreaks in poultry striking Western Europe by November 2014 and lingering until early spring 2015.

While in late August 2014 some wild waterfowl migrated west from Siberia and Alaska, others traveled east, most destined for winter feeding grounds in the Southern U.S., Mexico and South America. But first these birds flew into Canada, stopping to rest and refuel in Fraser Valley, British Columbia—a Canadian agricultural region flanking the U.S.-Canada border—in late November. There, poor farm hygiene facilitated the spread of H5N8 and several mild strains of North American avian influenza from the outdoor environment into a large commercial farm with 28,000 turkeys.  

Inside the turkeys, the various viruses merged to create a new lethal strain: H5N2, which became the first lethal avian influenza virus to be detected on commercial farms in North America. Around the same time, another new lethal strain, H5N1, was similarly formed on a nearby commercial chicken farm when H5N8 and mild avian influenza strains merged. Both H5N1 and H5N2 exited the farms back into the surrounding environment—through lapses in farm hygiene—where the same migratory waterfowl that had carried H5N8 and mild avian influenzas into Canada picked them up.

These wild waterfowl then carried all three lethal strains—H5N1, H5N2 and H5N8—across the U.S.-Canada border to Wiser Lake, a major migratory waterfowl stopover. H5N1 and H5N2 were both diagnosed in wild birds harvested from the lake, while H5N8 was diagnosed in a captive falcon that had died after eating a wild duck it caught there.

From Wiser Lake, some wild birds carried H5N2 and H5N8 to nearby backyard poultry farms in the Pacific Northwest. At least one wild bird carried H5N8 all the way down the Pacific flyway to Stanislaus County in Southern California by late January, where the virus managed to make its way into the nation’s first commercial poultry farm. By early March, migratory birds brought H5N2 to a backyard poultry farm in the Central flyway. Later that same month migratory birds introduced H5N2 to the Mississippi flyway—the heart of the U.S. commercial turkey industry—after which point farm-to-farm spread of the virus predominated.

 “Research suggests that wild birds naturally have only [mild] avian influenza,” Ip said. “The evolution and spread of these hybrid viruses in poultry support the hypothesis of spillback. It seems as though poultry is responsible for infecting wild birds with [lethal] avian influenza.”

But that should not happen on industrial farms where chickens and turkeys are typically kept indoors and do not encounter wild birds, Ip said. The fact that lethal avian influenza “appears to evolve exclusively in the poultry system is a result of inadequate farm biosecurity.”

Major poultry companies contract several farms in order to meet demand for their products. These contracted farms tend to share workers, vehicles and equipment, which can facilitate the spread of disease from one farm to another, or from the outside environment into a farm, McCluskey said.

However, biosecurity practices are supposed to prevent such so-called linear spread of disease from occurring. Though Veterinary Services stops short of identifying any specific cause or causes of this, a research report it published in September emphasized that “comprehensive and stringent biosecurity practices remain crucial to reducing the risk of [lethal avian influenza] infection.”

“I wish there was an education tool to help farmers really see how their farm biosecurity practices are working,” Ip mused. “Imagine if we could make pathogens fluoresce—if farmer’s boots or truck tires were glowing with avian influenza then maybe they would understand that what they’re doing isn’t working.”

Use this map to better understand how wild migratory bird flyways overlap and intersect across the globe.

*          *          *

McCluskey, chief epidemiologist of the USDA Animal and Plant Health Inspection Service’s Veterinary Services branch, acknowledges farm biosecurity as a whole isn’t perfect. But unlike Ip, he said that he did not explicitly implicate U.S. poultry industry as the main offender in the recent outbreak. McCluskey said both wild birds and farmers appear to be at fault.

For several months McCluskey’s USDA Veterinary Services branch has been working to discern what makes poultry farms so vulnerable to avian influenza. As part of this effort, branch techs and scientists visit farms to conduct surveys—with questions focusing on biosecurity practices—and collect samples (mostly air and bird manure) to be analyzed in the lab. Positive cases of lethal avian influenza are mapped.

Based on his branch’s research, especially genetic analyses of the viruses found on farms, McCluskey said, the outbreak’s earliest cases occurred independently from one another, while its later cases “include potential for human involvement,” McCluskey’s euphemistic acknowledgment of the consequences of  poor farm biosecurity.

During the outbreak, many of the earliest avian influenza cases on U.S. poultry farms, including the first five, were detected on backyard farms, which can be anything from a small backyard hobby coop holding a handful of laying hens to a commercial flock of 100 free-range turkeys. On backyard farms, poultry typically live at least partly outdoors and thus have a greater chance of interacting with wild waterfowl and contracting disease from those birds independent from other farms. This runs in line with Veterinary Services’ findings that the genetic makeups of virus samples taken from these farms were slightly dissimilar, suggesting a different wild bird infected each farm.  

By contrast, later lethal avian influenza cases on U.S. poultry farms were detected almost exclusively on commercial farms.  There most birds are kept in indoor facilities their whole lives and thus do not interact with wild birds. Veterinary Services reports reveal that the virus samples taken from these farms were very similar, implying a common source of infection.

 “We found some poultry operations with good biosecurity practices, but also a few places that could use improvement,” said McCluskey. “USDA is now discussing with industry how to monitor biosecurity practices, and is performing audits to ensure those practices are being followed.”

I was curious to learn about what, if anything, commercial poultry corporations changed about their farms’ biosecurity in the wake of the outbreak. Aware that Turkey giant Jennie-O, a major employer in Wisconsin and Minnesota, was impacted by the outbreak, I called the company’s headquarters in Wilmar, Minnesota, and asked to discuss the biosecurity practices employed on its contracted farms and the outbreak’s impact on its business. But Pat Solheid, Jennie-O’s vice president of human resources and administration said, “We are not sure on what level we’d like to contribute,” suggesting there was “plenty of public information” detailing how avian influenza impacted the company, available on the company's website.

So, I wasn’t able to inquire whether or not the company holds its independently contracted farmers to any specific biosecurity standards and whether or not those standards changed after the outbreak. However, their website does reveal the extent to which the company was impacted with the virus: in all, 58 of Jennie-O’s turkey facilities—both independently contracted farms and farms owned directly by the company in Minnesota and Wisconsin—were hit by lethal avian influenza.

Jennie-O’s contracted farms were also unavailable for comment—not because they declined, but because they couldn’t be identified. Most states have statutes, usually called “livestock premises registration” laws, which require livestock facilities managers to register their premises, or farm, along with personal and business information with their state of residence. This information includes the number and type of animals on their farm, along with the farm’s address, and is meant to help account for farms during disease outbreaks. But the laws keep this information confidential. This is done to protect the privacy of farm owners, [MOU1] for whom “these farms are their homes,” said Keith Williams, vice president of communications and marketing of the National Turkey Federation.

What is known is this: the 58 Jennie-O’s turkey farms that tested positive for lethal avian influenza—all of which were hit between March 27 and June 4—were forced to undergo a federally mandated process of quarantine, depopulation and disinfection, like all poultry farms that test positive for lethal avian influenza. McComas was deployed to Minnesota to oversee this process on several infected turkey farms during the outbreak. He explained the federal response process he witnessed firsthand but wouldn’t disclose the farms’ corporate affiliations.

Once avian influenza is suspected on a farm, farmers are required to contact their local animal health department or the USDA. Once alerted to a possible positive case, these agencies restrict the movement of the farm’s workers, vehicles, equipment and birds off-site, said McComas. If avian influenza is confirmed, all birds are euthanized, composted and buried on site. A farm’s barns are rid of the “three Fs: feathers, feces and feed,” then are sprayed with a disinfectant solution. After three weeks, the farm can begin to repopulate with new birds.

McComas said the farm managers he worked with appeared to embrace a new culture of improved farm hygiene, even though some appeared leery at first of government intervention.

“Most farmers don’t exactly want people in white Tyvek suits with respirators on their property,” said McComas. “It doesn’t look good; it’s upsetting. We had to let them know we were there to help.”

But besides the emotional difficulty of coping with the process of handling a case of lethal avian influenza, farmers, and often their entire communities, are forced to face a harsh economic reality in the virus’s wake. Contracted farms are provided a federal stipend to cover the costs of euthanasia and hazardous material cleanup teams, as well as compensation for the live birds they must destroy. But the government does not reimburse farmers for birds that succumb to avian influenza before the euthanasia process, and farmers’ losses tend to trickle down to their workers.

“When poultry farms are shut down, even for a relatively short period, it can profoundly effect whole communities,” said Hirchert. “In an area with several huge farms, hundreds of people are out of work both on farms and in processing facilities—no one is getting paid. Some may be laid off.”

With birds destroyed and contracted farms shuttered across two states, in May Jennie-O laid off more than 200 employees at a major processing plant in Minnesota, and cut the hours of many employees it kept. Rembrandt Enterprises, one of the nation’s largest egg producers, implemented similar layoffs and cuts after a positive case found on a major contract farm in Iowa led to the euthanasia of over 250,000 hens.

*          *          *

The experts agree that better farm biosecurity can help prevent a future outbreak. Yet federally mandating better biosecurity on the nation’s commercial poultry farms, which would require routine inspections by USDA officials, is no small task. Recognizing this challenge, USDA is now ready to deploy a quicker and less expensive fix in the case that another avian influenza outbreak does occur: an avian influenza vaccine.

Almost immediately after the outbreak struck, several federal, university and private labs turned their attention to avian influenza vaccines. Such vaccines have been previously developed and tested for use in chickens, but only in labs. Protecting only six out of 10 inoculated hens from lethal avian influenza, these vaccines haven’t yet hit the efficacy level USDA seeks. Nor have they been tested in turkeys. For these two reasons, the USDA hasn’t approved them for use on poultry farms.

However, in October, the USDA found what it believes may be a vaccine effective enough for farm use. After running efficacy studies on the newly developed drug, the USDA awarded its creator, animal vaccine developer Harrisvaccines, a $6 million contract to create a 48-million dose stockpile of avian influenza vaccines, with 25 million doses ready in 45 days.  

Creating a stockpile may seem risky, said Joel Harris, Vice President of Harrisvaccines, lest the nation stock up on a treatment for the “wrong” lethal avian influenza strain. But he said this would not be a problem with his company’s vaccine, which, unlike typical vaccines, can be “easily updated” to treat any problematic strain that may arise.

“Our vaccines are made with a synthetic replica of a virus’s genetic code rather than a live virus, which is what most drug makers use to create vaccines,” said Harris. “This technology is more adaptable and can be produced more rapidly than the traditional technology.”

The USDA says it plans to rapidly distribute vaccines from Harrisvaccines’ stockpile if another lethal avian influenza outbreak occurs in the U.S. in the future.

At this point, the big looming question is whether the current outbreak is over for good. Wildlife health experts such as Ip are hesitant to declare it over just yet.  The key, he and others have said, will be the continuation of the wild bird surveillance and poultry farm research efforts currently underway.

“We are concerned with the possible reappearance,” Ip said, pointing out that new strains of avian influenza appeared in Asia while the U.S. outbreak played out. “These viruses or additional variants could be introduced into North America by the fall migration. So in the words of Mad-Eye Moody in J. K. Rowling's Harry Potter books: ‘Constant Vigilance’ is what it’s all about.” 

2014-2015 U.S. AVIAN INFLUENZA OUTBREAK PHOTO GALLERY:

PUBLISHED JANUARY 14, 2016

ABOUT THE STORY

Besides being a journalist, artist and runner, I am a wildlife rehabber and lifelong birder. It's the journalist, rehabber and birder in me that drew me to the 2014-2015 U.S. avian influenza epidemic, which lead to the combined death and euthanasia of almost 50 million chickens, turkeys and other domestic fowl nationwide. With keen interest, I pursued this story across the country.

With my knowledge of wildlife, I had known that avian influenza in poultry and avian influenza in wild migratory birds are tightly related. In fact, transmission of the virus between both groups of birds occurs rapidly. While most news media had focused on the poultry side of the story, I sought to learn more specifically about avian influenza in wildlife. To do so, I shadowed wildlife health scientists in the lab and in the field, interviewed poultry industry representatives and analyzed piles of studies and data.  

UPDATE: On January 15, 2016, USDA confirmed highly pathogenic H7N8 avian influenza in a commercial turkey flock in Dubois County, Indiana. Learn more here on my blog.