Is the Coronavirus in Your Backyard?
Emily Anthes and Sabrina Imbler
Mon, February 7, 2022
Suresh Kuchipudi, a veterinary microbiologist at Penn State University, with Cashew, a young white-tailed deer in the university's deer research center in State College, Pa., on Feb. 2, 2022. (Hannah Yoon/The New York Times)
In late 2020, the coronavirus silently stalked Iowa’s white-tailed deer. The virus infected large bucks and leggy yearlings. It infiltrated a game preserve in the southeastern corner of the state and popped up in free-ranging deer from Sioux City to Dubuque.
When scientists sifted through bits of frozen lymph node tissue — harvested from unlucky deer killed by hunters or cars — they found that more than 60% of the deer sampled in December 2020 were infected.
“It was stunning,” said Vivek Kapur, a microbiologist and infectious disease expert at Penn State, who led the research.
Kapur and his colleagues have now analyzed samples from more than 4,000 dead Iowa deer, diligently marking the location of each infected animal on a map of the state. “It’s completely mad,” he said. “It looks like it’s everywhere.”
From the start of the pandemic, experts were aware that a virus that emerged from animals, as scientists believe SARS-CoV-2 did, could theoretically spread back to animals. Mink have garnered much attention after the virus spread through mink farms in Europe and North America, leading to massive culls of the animals. But white-tailed deer, which may wander into urban and rural backyards, are also easily infected.
Infections in free-ranging deer, which display few signs of illness, are tricky to detect and difficult to contain. Deer also live alongside us in dizzying numbers; about 30 million white-tailed deer roam the continental United States.
If white-tailed deer become a reservoir for the virus, the pathogen could mutate and spread to other animals or back to us. Adaptation in animals is one route by which new variants are likely to emerge.
“This is a top concern right now for the United States,” said Dr. Casey Barton Behravesh, who directs the One Health Office — which focuses on connections between human, animal and environmental health — at the Centers for Disease Control and Prevention.
“If deer were to become established as a North American wildlife reservoir, and we do think they’re at risk of that, there are real concerns for the health of other wildlife species, livestock, pets and even people,” she added.
The virus is likely to continue circulating in deer, many experts predicted. But crucial questions remain unanswered: How are deer catching the virus? How might the pathogen mutate inside its cervid hosts? And could the animals pass it back to us?
White-tailed deer are a “black box” for the virus, said Stephanie Seifert, an expert on zoonotic diseases at Washington State University: “We know that the virus has been introduced multiple times, we know that there’s onward transmission. But we don’t know how the virus is adapting or how it will continue to adapt.”
Cervid surge
The coronavirus enters human cells by attaching to what are known as ACE2 receptors. Many mammals have similar versions of these receptors, making them susceptible to infection.
Early in the pandemic, scientists analyzed the genetic sequences for ACE2 receptors in hundreds of species to predict which animals might be at risk. Deer ranked high on the list, and laboratory experiments later confirmed that the animals could become infected with the virus as well as transmit it to other deer.
The U.S. Department of Agriculture’s Animal and Plant Health Inspection Service began looking for coronavirus antibodies in blood samples from deer in Illinois, Michigan, New York and Pennsylvania. In July, the agency reported that 40% of the animals in those areas had antibodies, suggesting that they had already been infected by the virus.
Some months later, Kapur’s team, which partnered with the Iowa Department of Natural Resources, reported that active coronavirus infections were common in Iowa deer, and another group announced that more than one-third of the deer they had swabbed in northeastern Ohio were infected. Genomic analysis suggested that in both Iowa and Ohio, humans had passed the virus to deer multiple times and then the deer readily passed it to one another.
“The early detections in companion animals, in mink farms, in zoological collections — those were all different because those were confined populations,” said Dr. Andrew Bowman, a veterinary epidemiologist at Ohio State University, who led the Ohio research. “We didn’t really have a natural setting where the virus could run free.”
Whether the virus makes deer sick remains unknown. There is no evidence that infected deer become seriously ill, but humans might not notice if a wild animal was feeling slightly under the weather.
And these early studies — which have largely relied on preexisting disease surveillance or population control projects in deer — provided only a snapshot of what could be a sprawling problem. “I wouldn’t be surprised if more sampling uncovers the fact that these are not necessarily sporadic events,” said Dr. Samira Mubareka, a virologist at Sunnybrook Research Institute and the University of Toronto.
In Canada, reports of infected deer are beginning to trickle in from Ontario, Quebec and Saskatchewan. When Mubareka’s team sequenced virus recovered from Canadian deer, the researchers found it closely matched sequences in Vermont. “Deer don’t respect borders,” said Arinjay Banerjee, a virologist at the University of Saskatchewan.
‘No masking, no social distancing’
How humans are transmitting the virus to deer remains an open question. “It’s definitely a mystery to me how they’re getting it,” said Dr. Angela Bosco-Lauth, a zoonotic disease expert at Colorado State University.
There are many theories, none entirely satisfying. An infectious hunter might encounter a deer, Mubareka noted, but “if they’re good at hunting,” she added, “it’s a terminal event for the deer.”
If an infected hiker “sneezes and the wind is blowing in the right direction, it could cause an unlucky event,” said Dr. Tony Goldberg, a veterinary epidemiologist at the University of Wisconsin-Madison. Or if people feed deer from their porch, they could be sharing more than just food.
And white-tailed deer are expert leapers, reaching heights of 8 feet. “If you want to fence deer out of a place, you have to be trying very hard,” said Scott Creel, an ecologist at Montana State University. Deer would have no trouble jumping into alfalfa fields to graze alongside cattle, perhaps inviting a close encounter with a farmer, Creel said.
Transmission could also happen indirectly, through wastewater or discarded food or other human-generated trash. “Deer, like most other animals, will sniff before they eat,” Kapur said. And deer release their feces as they feed, creating conditions where other deer might forage in areas contaminated with waste, or snuffle around waste that has feed mixed in, experts say.
But it’s not clear how long the virus would remain viable in a polluted water source or on the surface of a half-eaten apple, or whether enough of it would be present to pose a transmission risk.
An intermediate host, such as an itinerant cat, might ferry the virus from humans to deer. Farmed deer, which have frequent contact with humans, might also pass the virus to their wild counterparts through an escapee or their feces, Seifert said. (More than 94% of the deer in one captive site in Texas carried antibodies for the virus, researchers found — more than double the rate found in free-ranging deer in the state.)
It may not require many spillovers for the virus to take off in a herd. Infected deer, which shed virus in nasal secretions and feces and have an infectious period of five to six days, can readily spread the virus to others, said Dr. Diego Diel, a virologist at Cornell University.
Wild deer are social — traveling in herds, frequently nuzzling noses and engaging in polygamy — and swap saliva through shared salt licks.
And unlike humans, deer have no tools for flattening the curve. “They don’t have rapid antigen tests,” Banerjee said.
Kapur added, “No masking, no social distancing.”
Dr. Sarah Hamer, a veterinary epidemiologist at Texas A&M University, is seeking funding to start contact tracing of deer to understand how their social interactions influence viral transmission. She hopes to use proximity loggers to record the time and duration of the animals’ interactions with one another. “What deer are hanging out with what deer?” Hamer said. “Are there deer superspreaders?”
Research is still in early stages, but understanding how the virus is spreading is essential both for slowing transmission in deer and for protecting other vulnerable wildlife. Deer may graze alongside other cervids, such as boreal woodland caribou, which are endangered in Canada and are a traditional food source of First Nations peoples.
And if humans are contaminating the wilderness with the virus, it could threaten other, highly endangered species, such as the black-footed ferret, which experts fear may be vulnerable to the virus. “If it’s in the environment, and we don’t know exactly how it’s in the environment or how it’s spreading, all of a sudden we have these endangered animals that are at even higher risk,” said Kaitlin Sawatzki, a virologist at Tufts University.
Knowing how we are giving the virus to deer is also crucial for assessing the risk that they may pass it back to us. “The metaphorical window is open, and we don’t know where,” Bowman said.
Herd immunity
The virus is clearly spreading in deer. But what happens next, and how worried should we be?
Many experts said they expected the virus to become established in deer and circulate indefinitely. “If it’s not already established, it’s heading in that direction,” Mubareka said.
Still, scientists said they needed longer-term data to be sure, and the outcome was not a given. Currently, people appear to be reintroducing the virus to deer frequently; but if human case rates fell substantially, and people stopped spreading the virus, it could disappear from deer populations.
Moreover, deer do develop antibodies to the virus; if the antibodies are strong enough and enough deer develop them, literal herd immunity could squelch the spread. But scientists know very little about deer immunity. “Does exposure to one variant protect the deer population from subsequent variants?” Banerjee asked.
If the virus does establish itself in deer, it is likely to evolve in ways that help it thrive in its new hosts.
A deer-optimized version of the virus would not necessarily be more dangerous for people; the virus might adapt in ways that make humans less hospitable hosts. “If this became ‘Deervid,’ then that would be great,” Goldberg said. (“Hopefully it would stay benign in deer,” he added.)
But the virus could retain its ability to easily infect humans while picking up more worrisome mutations, including ones that might allow it to evade our existing immune defenses.
“Even if you got the human population immune and fully vaccinated, if there’s still a reservoir persisting in the animals, then that can allow the virus to continue to evolve,” said Linda Saif, a virologist and immunologist at Ohio State University.
There is not yet any evidence that deer are infecting people, and for the foreseeable future, experts agreed, humans are far more likely to catch the virus from one another than from anything with hooves.
“Even if deer were infecting people, it’s largely inconsequential in the grand scheme, because millions of people are getting infected from human-to-human transmission,” said Dr. Scott Weese, an infectious diseases veterinarian at the University of Guelph in Ontario. “But it becomes more of a risk as we start to control it.”
Hunters, who handle deer carcasses extensively, could be at higher risk for contracting the virus from deer, scientists said. (There is no evidence that people can be infected by eating deer meat cooked to an internal temperature of 165 degrees Fahrenheit.) People who hand-feed their local deer — a practice experts warn against — could also be at risk.
An abundance of ungulates
Other animals, too, may be at risk from infection from deer. Predators such as mountain lions which kill deer by biting into their trachea or over their nose and mouth, could be infected while feasting.
Scientists were relieved when early research suggested that cattle and pigs were minimally susceptible to the virus. But inside the bodies of white-tailed deer, the virus could morph into a pathogen capable of infecting such livestock.
“That could be a big problem for food production stability,” Seifert said.
Health officials must stay vigilant, experts said.
The USDA is now working with state agencies to collect blood samples and nasal swabs from dead deer in more than two dozen states. The work should help experts estimate how many deer have already been infected and whether certain characteristics, from age to habitat type, put some deer at elevated risk.
“As we learn more, we will continue to refine and target our surveillance,” said Dr. Tracey Dutcher, the science and biodefense coordinator for the Animal and Plant Health Inspection Service at the USDA.
Long-term genomic surveillance is also needed, experts said. “If we start to see some really divergent viral variants popping up in deer in certain places, that would be a red flag,” Goldberg said.
Depending on what scientists learn in the near future, officials could consider a variety of potential mitigation measures, including vaccinating captive deer, thinning infected herds or cleaning up whatever environmental viral contamination is giving the deer the virus in the first place.
“I think we’ve got to get our hands around the situation before we really make plans on where to go,” Bowman said.
For now, scientists also advise keeping a close eye on other wildlife. If the virus is so prevalent in deer, which are relatively easy to sample, it could be silently spreading in other species, too.
After all, the only reason scientists found the virus in deer is because they thought to look. “We hadn’t realized it was spread in deer at all,” Kapur said. “We had no clue.”
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