Studying pig sh*t to prevent the next pandemic

A pilot program in North Carolina offers one solution to scanning for a potential pig virus in our farm system.

To prevent the next pandemic, the trick is the sh*t.

Specifically, it’s getting access to it. Pig excrement, produced by the metric ton, can be tricky to get a hold of. It means navigating a bio-secured industry and distrustful farmers, whose lives (and sometimes family legacies) balance on an economic and agricultural knife’s edge, as they pursue a calling most Americans barely understand.

But finding a way to get the whole community on board — with all the stakeholders in agreement, balancing the economic interests of farmers and local communities against the public health interest in disease surveillance — will all be worth it, if it can stop the next pig-decimating, pandemic-grade swine flu.

It is, unfortunately, a lot of sh*t to work through.

But a promising pilot study, run in the heat of North Carolina’s sticky, hurricane-lashed summer, shows potential. Slurry samples from pig farms proved capable of being tested for viruses, and farmers (at least at this one farm) were willing to embrace the mission.

The COVID-19 pandemic proves the urgency of establishing a serious surveillance program for zoonotic diseases that — like a pangolin or pig virus — can jump from animals to humans.

Pig Virus Problems

Large-scale farms are a necessity if the world’s demand for meat is to be met. Contact between humans and a legion of animals make farms potential hotspots for virus spillover. (The hypothetical coronavirus in Johns Hopkins’ pre-COVID-19 pandemic war game, Event 201, jumped in a pig farm in South America.)

Adenoviruses, enteroviruses, and, yes, coronaviruses, all have the potential to leap from pigs to people.

Despite being obvious zoonotic hot zones, there is little surveillance for infectious disease at these intersections. And massive pig and fowl farms are essentially witch’s cauldrons, the perfect places for viruses — especially influenza — to propagate and mutate, sometimes emerging as frighteningly ferocious avian or swine flu strains with the potential to unleash a pandemic.

“For influenza, they (pigs) have similar receptors that humans do,” says Jeff Bender, director of the Upper Midwest Agricultural Safety and Health Center at the University of Minnesota. “So that’s why the mixing between humans and pigs is much more prominent than, say, a dog, a cat, a cow.”

And influenza is not the only pig virus that can jump; adenoviruses, enteroviruses, and, yes, coronaviruses, all have the potential to leap from pigs to people.

One Health

As it stands, humanity is always on the back foot when it comes to outbreaks. A pig virus or bat virus or bird virus emerges, people get sick, people die, and we respond with reactionary measures: quarantines, ring vaccinations, masks and checkpoints and grinding society to a halt — with the albatross hung from the neck of those suffering most already.

Climate change and human encroachment on wild land all but guarantees more outbreaks. A virus is a perfect predator of people, and prey survives by being vigilant. To survive in a virus’s world, we will need to be meerkats, forever peering and peaking and ready to raise the alarm.

Virus spillover is a complex issue, and it’s not suited to humanity’s typical brute-force approaches (no, we shouldn’t kill all the bats). Instead, a more nuanced approach, called One Health, brings together specialists from any number of fields — ecology, biology, virology — to take a holistic approach to finding and stopping zoonotic diseases before it is too late.

The pig virus slurry is a microcosm of One Health in action.

One Farm

Emily Bailey, then at the Duke Global Health Institute, had an idea.

“All my research was focused on water,” Bailey, now an assistant professor in the Department of Public Health at the Texas Tech University Health Science Center, says.

Bailey realized that the presence of viruses in wastewater could provide an avenue for animal disease testing. It was an elegant solution to the problem of mass testing of millions of animals … but it rapidly ran into real world problems that have nothing to do with viruses.

Despite being well-known reservoirs of zoonoses, establishing a surveillance program for pigs has proven difficult. The pig industry is resistant to testing, as economic pressures and mistrust keeps us in the dark about what type of pig virus is circulating where.

“The margins for swine producers, especially now, is a little bit tight,” Bender says. It’s not that the industry is the mayor from Jaws — they do care about diseases like swine flu, which could decimate the pig industry even when it doesn’t jump into people. But, like any business, their main focus is staying in business.

Fear of lawsuits, regulations, and of losing their livelihood all makes farmers leery of letting folks on the farm. Add to this the biosecurity concerns of the industry, the pressure of the pork producers (who can take a hit that the farmers cannot), and the town/gown, Ivory Tower tensions between researchers and farmers — it becomes easy to see how testing for a pig virus becomes more a source of agitation or fear than a beneficial service against disease and economic exsanguination.

“Which is sad,” Annette G. Greer, an associate professor in the Department of Bioethics at East Carolina University, says in her honey-dripper drawl. “Because the work that we want to do is … looking at the health benefits to both animals and humans.”

In the case of Bailey’s slurry surveillance project, the cooperation of farmers was an absolute necessity: there’s no way the scientists could just pop in the barn and sample the swine.

Luckily, when it comes to pig farming, Greer knows what from. She has a family history in farming; indeed, she and her husband used to own a farm, and he still works on one. Greer helped Bailey’s team find a farm in eastern North Carolina willing to be part of the pilot.

“I think that those of us who come from the farm who have a relationship with science have a greater understanding of how the two are connected,” Greer says.

For her part, Bailey grew up in the rural Appalachians of western North Carolina.

“We have to be aware that this is their livelihood,” Bailey says.

“It’s not just science for them. This is their house, this is their farm, this is all of their money invested in this. It’s a different stake.”

Secrets in the Slurry

Beneath their snouts and curly tails, beneath their hooves, is a grate. Any discharge, from spit to snot to feces to urine — and any pig virus which may be in it — falls through this grate to a pit below. Periodically, in a biblical flushing, all of this waste will be washed away. This is the slurry.

The system Bailey’s team put in place was beautifully simple. After some training, farmers would collect two samples of slurry a week, freeze them, and mail them off to the lab in Durham for analysis — no prying researchers required. Along with the slurry was information denoting the date it was sampled, the sampling site and time, the number and weight of the pigs, ah, contributing to it, and the weather.

“It’s not a pretty medium to work with,” Bailey — whose work with human sewage for her dissertation inspired the idea — admits. “But it’s very rich in terms of diversity.”

Importantly, a slurry sample could be gathered without any contact with the animals. The pigs on the farm were what are called “finishing pigs”: they had been born and initially raised at a different farm, and were gathered at the finishing farm for their final fattening up before becoming food.

Those pigs, however, were not the property of the farmer. Depending on the arrangement, the pigs may actually belong to the pork producer, who is then contracting out their finishing. Since the producer owns the pigs, the hogs are off limits without their permission. (The producers don’t own the slurry, however, because why would they want to?)

We have to be aware that this is their livelihood. It’s not just science for them.

Emily Bailey

At the lab, Bailey ran RT-PCR and PCR tests to scan for a suite of DNA and RNA viruses. Among their targets were genes from influenza, senecavirus, adenovirus, enterovirus, encephalomyocarditis, and coronavirus.

Since anything that passed through the barn (perhaps a bird or bat flying overhead) could also drop waste into the slurry, Bailey looked only for the genetic signatures of pig-specific viruses — meaning she didn’t have to untangle the poop from its sources.

From spring through the fall of 2018, 105 samples were collected from two barns on the farm in eastern North Carolina. Of those, 86% tested positive for at least one zoonotic pig virus; enteroviruses, which can cause a common cold, led the way. (Despite likely being present, the tests could not find influenza.)

The samples were not just used to extract data on viruses; true to One Health’s emphasis on community cooperation, Bailey’s team looked to the farmers for other questions that could be investigated and insights that would be helpful to their work.

“They had excellent research questions,” Greer says. Farming is, after all, a science, learned on campus and on the farm.

The environment, a focus area for One Health, was a key concern for farmers; if it’s cold, the pigs may huddle together for warmth, increasing the chance of a respiratory pig virus burning through the barn.

The researchers found relationships between low pig weight and high pig density and an increase in enteroviruses and coronaviruses, while adenoviruses were associated with both lower weights and lower temperatures. (The weather, which had included Hurricane Florence, was not as strong a factor as Bailey had thought it may be).

Being able to tease out information that can help in the health and production of pigs will be a key to getting more farmers — and perhaps eventually Des Moines — on board.

Scientists will have to demonstrate that there is value in doing surveillance, the University of Minnesota’s Bender says. Setting up a surveillance system for, say, a coronavirus that is killing pigs could not only head off a potential spillover to humans but would help protect the animals and thus the bottom line.

Surveilling the Swine

Bailey’s vision of the future is a layer of wide-scale infectious disease surveillance built right into the farming process.

The finishing barns that hosted the pilot could be a good place in the chain, Bailey says. Piglets are more likely to get sick, and come from a whole host of places. By the time they are consolidated into finishing barns, the pigs should be hale and hearty; it’s also the last step before the abattoir.

“Ideally, you could say ‘this barn has H1N1,'” Bailey says. “And before it gets to the next barn, we can separate these two pigs who have H1N1.” If a swine flu were caught out early, the farmers could avoid a culling, and humanity could dodge a pig virus spillover.

(Still, if the pilot program is any indication, a better source than slurry may need to be found for influenza viruses — which will require yet more cooperation with farmers.)

Bender believes the approach modeled in the pilot program — particularly the focus on involving the farmers — is a strong one. By engaging the farmers and potentially, eventually, the pork producers, they could get the buy-in necessary for disease surveillance.

For Bailey, the study’s most important takeaway is that it is possible to look at slurry, to surveil the swine in a non-invasive way, and that the farmers can do it themselves — assuaging security concerns and distrust.

“I really think that the community engagement is important,” Bailey says. “That the buy-in really makes this special, because it’s just so much different when you have somebody that cares about the research.”

Looming over it all is the possibility that swine surveillance may not only prevent economic damage — the pork industry is currently being battered by COVID-19 in meat packing plants — but also save lives. Pandemic viruses need not come from parts unknown to wreak havoc.

There are, in Bailey’s slurry samples, multiple detections of viruses new to science.

Novel viruses in a barn in North Carolina.

Perhaps in a pig.

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