When the Next Animal Plague Hits, Can This Lab Stop It?

There were 16 pathogens on the terrorist’s list, written in tall, spiky scribbles that slanted across the page. Next to each one was the incubation period, route of transmission, and expected mortality. Pneumonic plague, contracted when the bacterium responsible for bubonic plague gets into the lungs, was at the top of the list. Left untreated, the disease kills everyone it infects. Farther down were some names from pandemics past—cholera, anthrax. But what struck General Richard B. Myers was something else: Most of the pathogens didn’t affect humans at all. Stem rust, rice blast, foot-and-mouth disease, avian flu, hog cholera. These were biological weapons intended to attack the global food system.

Myers was the chairman of the Joint Chiefs of Staff in 2002, when Navy SEALS found the list in an underground complex in eastern Afghanistan. US intelligence services already suspected that al Qaeda was interested in biological weapons, but this added weight to the idea that, as Myers put it, “they were indeed going about it.” Later that year, he said, another intelligence source reported that a group of al Qaeda members had ended up in the mountains of northeastern Iraq, where they were testing various pathogens on dogs and goats.

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Photograph: Djeneba Aduayom

“To my knowledge, they’ve never gotten to the point where it was of use for them in the battlefield context,” Myers told us. “But since al Qaeda, as we found out with the World Trade Center in New York City, never quite give up on an idea, it’s not something you can just dismiss.” In fact, he said, “I think there’s other, probably classified information that would tell you that’s not the case—but I’m not privy to all that or privy to talk about it.”

Even if al Qaeda moved on, other groups appear to have picked up the bioterror baton: In 2014 a dusty Dell laptop retrieved from an ISIS hideout in northern Syria—the “laptop of doom,” as it was later dubbed by Foreign Policy—was found to contain detailed instructions for producing and dispersing bubonic plague using infected animals.

For a would-be bioterrorist, Myers says, farms and feedlots are a “soft target.” They aren’t well secured, and effective pathogens are not particularly difficult to manufacture and deploy. Foot-and-mouth disease, a virus named after the large, swollen blisters it causes on the tongues, mouths, and feet of cloven-hoofed animals, is so contagious that the discovery of one case in a herd usually triggers mass culls. “All you do is put a handkerchief under the nose of a diseased animal in Afghanistan, put it in a ziplock bag, come to the US, and drop it in a feed yard in Dodge City,” Senator Pat Roberts told a local NPR affiliate in 2006. “Bingo!”

Farming is also highly concentrated: Three states supply three-quarters of the vegetables in the US, and 2 percent of feedlots supply three-quarters of the country’s beef. What’s more, both crops and livestock are genetically uniform. A quarter of the genetic material in America’s entire Holstein herd comes from just five bulls. (One of them, Pawnee Farm Arlinda Chief, contributed nearly 14 percent.) Monocultures like this are exceptionally vulnerable to disease. They are an all-you-can-eat buffet for pests and pathogens. With or without the assistance of a studious terrorist, the world is just as susceptible to an agricultural pandemic as it was to Covid-19—and, if anything, less prepared to fight it.

To diagnose deadly diseases and develop treatments and vaccines for them, researchers need to work with them in a lab, but very few facilities are secure enough. Foot-and-mouth disease, in particular, is so easily transmitted that the live virus cannot be brought to the US mainland without written permission from the secretary of agriculture. The only place researchers can work with it is Plum Island Animal Disease Center, built on a low-lying islet 8 miles off the Connecticut coast. (“Sounds charming,” as Hannibal Lecter, the homicidal antihero in The Silence of the Lambs, murmured when offered the possibility of a vacation there.)

Plum Island has the advantage of a natural cordon sanitaire—the ocean. But it opened in 1954, and its laboratories are outdated. They aren’t certified to handle pathogens that need the highest level of containment, Biosafety Level 4. According to the Centers for Disease Control and Prevention, BSL-4 microbes are “dangerous and exotic, posing a high risk of aerosol-transmitted infections.” Typically, they can infect both animals and humans and have no known treatment or vaccine. Ebola is one. So are the more recently emerged Nipah and Hendra viruses. Only three facilities in the world are currently equipped to accommodate large animals at this level. If there were an outbreak of foot-and-mouth disease in the US tomorrow, researchers here would have to beg their Canadian, Australian, or German counterparts for lab space.

That will change next year, when the Department of Homeland Security opens its new $1.25 billion lab, the National Bio and Agro-Defense Facility. Located in Manhattan, Kansas, a college town in America’s agricultural heartland, the NBAF will follow the 21st-century trend in infectious disease control: Rather than relying on a Plum Island–style geographic barrier for security, it will use extraordinary engineering controls. Here, amid the corn and cattle, researchers will work to protect the food supply from a coming plague.

We visited the NBAF’s 50-acre construction site on a muggy spring day in 2019. One of the late-afternoon thunderstorms for which the Great Plains are famous had just swept through, sending sheets of rain down across the Gothic castles and limestone halls of the Kansas State University campus. The site was selected after a three-year national competition, in part because of Manhattan’s existing expertise: It is also home to the Biosecurity Research Institute, a BSL-3 lab completed in 2007. Senator Tom Daschle has hyped this area as “the Silicon Valley of biodefense.”

Still, you can see why critics questioned the wisdom of situating a lab designed to work with the world’s most devastating large-animal diseases in a state where ruminants outnumber people by more than two to one. Trace a 200-mile radius around Manhattan and it will include one in 10 of America’s cows. If foot-and-mouth were accidentally released here, estimates show it could easily infect herds in surrounding states—nearly half the nation’s cattle—and cause as much as $50 billion in damage.

And then there’s the weather. After Manhattan won the bid for the NBAF, the Texas Biological and Agro-Defense Consortium, whose preferred site in San Antonio finished runner-up, immediately filed suit with a 50-page list of complaints. In claim 103, the consortium noted that anyone familiar with The Wizard of Oz should be aware of Kansas’ reputation for dangerous tornadoes. (The suit was dismissed without prejudice a few months later.) According to one estimate, from a report prepared in 2010 for the National Academy of Sciences, the probability of a pathogen escaping over the NBAF’s 50-year projected life span is an astonishing 70 percent. In response to these concerns, the Department of Homeland Security “hardened” the design to resist a Category 5 tornado, the most intense possible, then commissioned another risk assessment, which rated the likelihood of an accidental pathogen escape at 0.1 percent.

From our view onto the enormous construction site, this hardening mostly seemed to take the form of an awful lot of concrete. “Enough to build a sidewalk from here to Oklahoma City,” said Ron Trewyn, a former cancer researcher who led the effort to get the NBAF built. “Sixty thousand cubic yards, I believe, poured over two and a half years.” (It’s also a high-performance variety, with a built-in controlled chemical reaction that causes the concrete to expand after setting, leaving no room for cracks.) The site itself was off-limits, but the project’s technical director, Eugene Cole, agreed to have coffee with us in a nearby hotel lobby.

Cole, a soft-spoken Southerner, came to the NBAF after leading the design of Building 18, the CDC’s new lab for emerging infectious diseases. His passion for animal welfare initially led him to veterinary school, but then he realized he didn’t want to smell like formaldehyde for the rest of his life, so he got into architecture. Now he is something of a star in the small world of bio-containment design. His work on Building 18 received several awards and a special mention in R&D Magazine’s Lab of the Year feature. The NBAF, much to his delight, will receive LEED certification, something many in the field considered impossible. (Labs tend to use at least four times more energy per square foot than offices.)

Cole cares about technical specifications—ventilation, cooling, sanitation—but he spends almost as much time thinking about natural light and areas for socializing. “How do I make the space appealing to the best researchers, when it’s more or less a tornado bunker?” he said. “You won’t find many BSL-4 environments that have an outside window.”

Nonetheless, containment is the NBAF’s most important function. Cole told us that the windows he has managed to smuggle in are blast- and impact-resistant, with a metal grille on the outside to meet Nuclear Regulatory Commission guidelines for high-wind events. “But in a tornado, it’s the pressures that are difficult,” he said. BSL-4 rooms are built using the box-inside-a-box principle, in which a negative-pressure lab is surrounded by a positive-pressure buffer, ensuring that air is always sucked inward, deeper into the building, rather than escaping out into the atmosphere. If a slow—moving storm caused a sudden drop in external air pressure, that flow could reverse. But Cole assured us that the NBAF will have barometric systems that can quickly recalibrate.

A BSL-4 laboratory, as Cole described it, is something like a layer cake. At the bottom is an “effluent-handling” floor, then the laboratory floor where all the germs are studied; stacked above that are a filtration level, a mechanical level, and an exhaust-venting “penthouse.” All the pipes and wires and ducts are in their own compartmentalized, containable spaces—but they also have to be accessible for regularly scheduled tests and preventive maintenance. This, Cole pointed out, will actually be the largest line item on the facility’s annual budget. “Many times, from a design perspective, the focus is all on the science,” he said. “That’s a huge mistake.” Cole and his colleagues have carefully designed pathways through the spaghetti of piping to make access as quick and easy as possible. The building has a computerized maintenance management system that all but tells the operating staff what it needs.

The NBAF is both bigger and better than its neighbor, the Biosecurity Research Institute. One area of improvement is carcass disposal. The older facility has a tissue digester that dissolves animals in an alkaline soup, reducing bones and teeth to crumbly calcium-phosphate “shadows,” stripped of all organic matter. These solids are dried and incinerated. The remaining liquid, a soapy solution of amino acids and peptides, is sterile enough to be released into the municipal sewer system. The only issue is that it is still so full of organic molecules that it can easily overwhelm the capacity of the wastewater treatment plant. So, before every release, Cole explained, the team at the older facility “has to call the city to see if they’re ready to take that slug.” This usually occurs late at night—the corpses of liquefied animals passing through Manhattan’s sewers while residents sleep, blissfully unaware, in their homes above.

At the new facility, Cole said, “our carcass material will never go down the drain.” Instead, the NBAF has two thermal tissue autoclaves—”basically a big pressure cooker with a paddle in it,” he explained. The autoclaves produce a kind of tissue smoothie that is sterile enough to use as fertilizer. Out of an abundance of caution, it will be put into 55-gallon drums and incinerated instead. “There are just redundancies on top of redundancies,” Cole told us.

Cole is most proud of the flooring. Vinyl and tile work well for human foot traffic, but cows, sheep, and pigs have special requirements. Cole didn’t want anything that would chip, peel, or crack. He settled on a compound that binds to the concrete subfloor at a molecular level, forming a water—resistant layer that can be efficiently decontaminated again and again. He knew he needed to mix in some grit to keep the animals from slipping, but not so much that it would tear up their hooves and cause discomfort. He consulted the literature and discovered that no one had ever taken the time to scientifically determine what the right amount of grit should be. So he did the research himself, in his basement.

First, Cole acquired a machine used to test the slip resistance of shoes on carpet. Then he persuaded the necropsy lab at Kansas State’s veterinary school to give him some hooves. “They’re like your fingernail, just big,” he explained. Cole attached the hooves to the slip tester’s mechanical foot, then set it in motion. As it stepped in place, he measured the friction and durability of the floor material at varying grit levels, as well as any hoof abrasion. “Yeah, my wife was not happy,” he said, recalling the parade of disembodied hooves marching endlessly toward nowhere. But the outcome, he pointed out, is perfect flooring—cleanable, easy on the animals’ feet, and completely nonslip. He has published his findings and hopes to have them enshrined as a new international standard.

“We all suffer from OCD,” Cole said, with a slightly embarrassed laugh. “I mean, to be in containment design, you do have to be worried about the details.”

The first permanent quarantine facility in the world was a brick plague hospital, or lazaretto, built on an island in the Venetian lagoon in 1425 to protect the city from the Black Death. Since then, the architecture of containment has failed repeatedly. Often, the escapes have been intentional, if not necessarily malicious. In the 1780s, a guard at the lazaretto in Split, Croatia, smuggled home a beautiful white scarf as a gift for his wife, inadvertently releasing bubonic-plague-infected fleas that killed one in 10 of the city’s residents. In the 1830s, a bored Boston ship’s pilot took advantage of the temporarily frozen harbor to walk from Quarantine Island to shore, triggering a cholera panic. Other times, pathogens have simply hitchhiked across boundaries with the help of unwitting human carriers; wheat stripe rust, a fungal disease that reduces harvests by up to 40 percent, is thought to have been brought to Australia on an international traveler’s trouser cuffs.

“Everyone will tell you, it always comes down to the people,” Trewyn said. They have been the Achilles’ heel of lazarettos throughout history. Of course, the NBAF is carefully engineered to lower the risk of human error. On the lab floor, people, animals, and stuff can move in only one direction, from clean to contaminated, “cold” to “hot.” Everything—including the animals, in carcass form—exits through a fumigation vestibule, a chemical dunk tank, or an autoclave, with the sole exception of people, who have to take two chemical showers and one regular shower before they can leave. (At Plum Island, researchers often complained that the showers had only a curtain separating them from the adjacent corridor. At the NBAF, decon happens in a personal air lock. “Times have changed,” Cole said.)

The NBAF will implement continuous training, detailed record-keeping requirements, and a buddy system, so that staff can inspect one another for trace contamination after showering out. Everyone who works there will have to pass background screening and security checks. The building has concentric rings of facial-recognition and PIN-code checkpoints. The precautions even extend into researchers’ private lives: They will not be allowed to keep chickens, on the off chance they bring home a pathogen that jumps species. Even so, the National Research Council has complained that Homeland Security’s risk assessment—a 0.1 chance of a pathogen escaping—was “based on overly optimistic and unsupported estimates of human error rates.” (The assessment didn’t even attempt to quantify the likelihood of malicious or deliberate acts.)

Certainly, Plum Island has had a handful of documented close calls, as have other such facilities around the world. But Trewyn believes that the risk of accidental pathogen escape, in all its uncertainty, is worth taking. These diseases will arrive in the United States anyway, he says, and cause equally incalculable damage.

Trewyn pointed to the very different courses taken by two outbreaks of the same disease in the UK—one caused by a lab leak, the other by an inadvertent introduction. In 2007, foot-and-mouth disease virus slipped out of the Pirbright Institute, an animal—disease research facility, into the Surrey countryside, with the help of heavy rains and poorly maintained pipework. It was quickly caught and contained. Within hours of the first case, the government halted all movement of livestock in the entire country; within two months, the virus was mopped up, having infected just eight farms. The system worked, Trewyn concluded, especially when compared with a very different incident six years earlier.

That outbreak began in Northumberland in 2001, when contaminated pork that had likely been illegally imported from Asia was fed to a herd of pigs, triggering a national epidemic of foot-and-mouth disease. Soldiers were brought in to help slaughter the affected herds. Six million sheep, pigs, and cattle died. As footage spread of the British countryside alight with animal pyres and bulldozers shoveling rigid carcasses into huge piles for incineration, tourism dropped 10 percent. By the time the outbreak was finished, at least 60 farmers had taken their own lives.

Calculating the cost of such an outbreak is almost as tricky as assessing its risk. It’s simple enough to put a price on slaughtered animals and their disposal, but the ripple effects are harder to quantify. Farmers with healthy animals can’t sell them at market; governments impose restrictions on export and import. Although animal diseases are unlikely to cause famine, disruptions to the national meat supply can cause prices to skyrocket, leading to deeply discontented consumers. (In 1902, when the price of kosher beef jumped from 12 cents to 18 cents a pound, the women of New York’s Lower East Side rioted, breaking windows and throwing steaks.) As Myers told the Senate Agriculture Committee in 2017, “Hungry people are not happy people.”

One top priority for NBAF researchers will be to develop a treatment or vaccine for African swine fever, the deadliest outbreak most Americans have never heard of. This highly contagious hemorrhagic disease does not infect humans, but in the past couple of years it has killed a quarter of the world’s pigs. The symptoms are indistinguishable from those of hog cholera, item No. 10 on the al Qaeda bioweapon wish list: vomiting, diarrhea, fever, and a distinctive blue—purple discoloration of the snout, tail, and ears, typically followed swiftly by death.

African swine fever hasn’t yet been detected in the United States. As the US Department of Agriculture’s web page on the disease says, “We want to keep it that way.” But in China, the virus has claimed at least 40 percent of the country’s pig population, and the price of pork more than doubled from 2018 to 2019—a serious problem for a commodity whose cost has roughly the same political significance in China as gasoline prices do in the United States.

According to a 2019 exposé by Xinhua, the state news agency, criminal gangs, referred to as “swine stir-fry syndicates,” have taken advantage of the outbreak. In some cases, they have used drones to drop infected feed onto farms that had yet to be touched by the disease, then swooped in with an offer to buy the animals at a steep discount, supposedly to cull them. In reality, though, they resell the herd in another province—despite a national ban on pork and pig movement. The report claimed that one gang had smuggled as many as 4,000 pigs between provinces in a single day, bribing inspectors and faking quarantine certificates to get the animals across checkpoints.

In response, one pig farmer in the country’s northeast installed an anti-drone device that unfortunately also jammed the navigation systems of planes heading to a nearby airport. China’s largest pig producer has recently invested in 12-story bio-secure piggeries. Each floor has its own air—handling and disinfection system to limit the spread of disease, while staff live in dedicated housing onsite, spending two days in quarantine every time they enter the facility, unable to leave until their day off. One farmer in Hunan Province told a New York Times reporter that pigs have become so rare in his region that when he transports his animals, people gather around the truck to stare. “It’s like they were seeing a panda,” he said.

Fifty countries have now confirmed the presence of African swine fever in their herds, as far afield as the Philippines and Poland. Denmark, a porcine powerhouse, has begun construction of a wild-boar-proof fence along the length of its border with Germany to keep the virus out. In Australia, sniffer dogs have been stationed at airports, and mail is screened in order to catch pork being smuggled into the country; the pathogen survives for months on surfaces and in even heavily processed and cooked meat. “Only one country has been able to eradicate this disease,” the Australian agriculture minister told reporters in 2019, referring to the Czech Republic’s successful four-year elimination campaign. “They sent their army into forests night after night to shoot every single feral pig.”

For many experts, the pressing question is not whether the NBAF’s containment will fail but what the US will do when African swine fever finally arrives. Myers, who in 2016 moved to Manhattan to become president of Kansas State, his alma mater, says that when is the right word. “It has not come to North America—that’s great,” he said. “To say that it won’t in this globalized economy of ours—that is probably a foolish statement for somebody to make.” In 2013, more than 10 percent of American pigs died when a porcine epidemic diarrhea virus arrived on the reusable bulk bags used to transport feed; the half-life of African swine fever virus in shipped feed is two weeks. Pig farmers in the US have been advised to implement disinfection protocols at farm gates, ban foreign visitors, and inspect farmworkers’ packed lunches for contraband bacon or hot dogs.

Since Myers’ troops discovered al Qaeda’s list of pathogens in an Afghan cave, there has been a huge federal investment in research, but not much in the way of local planning. Ron Trewyn told us of one sheriff—the exception, rather than the rule—who had mapped the optimal locations for the 40 roadblocks needed to create a cordon sanitaire, quarantining his entire county in the event of an outbreak. Inside the exposure zone, according to the plan, “all cloven—hoofed animals would be destroyed.”

“I wish I could say that every county in this state had that,” Trewyn said. Myers agreed: “I think we’re intellectually better prepared, but I don’t know if we’re operationally better prepared. Are we really ready to destroy millions of pigs?”

The logistics of what animal-health experts euphemistically term “depopulation activities” can rapidly become overwhelming. Faced with the need to cull almost 11 million pigs during a swine fever outbreak in the Netherlands, the government resorted to mobile electrocution devices, described chillingly by journalist and WIRED contributor Maryn McKenna as “a pig-sized box that forced the animals to walk over a wet metal plate while zapping an electric current through their heads.” In 2015, 38 million chickens, ducks, and turkeys had to be slaughtered in Iowa because of avian flu. Local landfills stopped accepting diseased carcasses, for fear of lawsuits from their neighbors, and the birds rotted on farms. “I’ve been in the landfill business probably 26 years, and I’ve never ever seen this kind of volume, and I hope I never do again,” the director of the Northwest Iowa Area Solid Waste Agency told a local public radio affiliate.

In the US, a federal indemnity scheme entitles farmers to compensation for the animals they have sacrificed—although not for income lost because of quarantine measures and wasted production time. What’s less clear is who pays for it; the division between state and federal responsibilities is blurred. “How do you interdict the transportation network to make sure sick animals aren’t moving around the United States, infecting more herds?” Myers asked. “What authority do we have to stop them?” These gaps—in terms of legal authority, inter-agency coordination, and the lack of financial and logistical infrastructure to contain disease—are, by now, disturbingly familiar. They are the same issues that plagued the US response to Covid-19.

Myers pointed out that in emergencies, the Department of Defense is responsible for enforcing USDA policies. “Local authorities generally get overwhelmed pretty quickly and then call the DOD,” he said. But that’s usually where the plan ends. Over the course of his military career, Myers told us, he took part in several role—playing exercises in which government agencies practiced their response to livestock disease outbreaks. Each of these simulations ended in almost exactly the same place: with the pandemic having spread out of control and the USDA requesting assistance.

“When we got to the point where it said, ‘Now we’re going to call the DOD for help,’ the scenario would end,” Myers told us. “It’s ludicrous, right? The scenario would end and we, the DOD, never got to play out what it is that was needed—is it communications, is it security, is it helicopters? What is it?” Hosting the NBAF at Kansas State might be his best shot at making sure no one ever needs to see what happens next.

Adapted from Until Proven Safe: The History and Future of Quarantine, by Geoff Manaugh and Nicola Twilley. Published by MCD/Farrar, Straus and Giroux. Copyright 2021 by Geoff Manaugh and Nicola Twilley.


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