In November 2020, Covid-19 cases in Iowa surged to 32,081 cases in a single week — at the time, a record high. And that was only among the humans. As scientists would learn, an epidemic was also beginning to rage among the state’s many white-tailed deer.
A shockingly high number of deer — 80 out of 97 — tested positive for SARS-CoV-2, the virus that causes Covid-19, in a seven-week survey that followed the Iowa surge. “We were gobsmacked, completely bowled over,” says Vivek Kapur, a Penn State veterinary microbiologist who recently, with co-authors, published an analysis of the shadow deer epidemic in PNAS. “We had no clue.”
It’s not just in Iowa. Evidence is mounting that deer infections have been widespread across the country. A separate study in Nature found infections in a third of deer surveyed in Ohio, and the USDA has reported coronavirus antibodies in Illinois, Michigan, New York, and Pennsylvania deer. Tens of millions of deer live across the United States. It’s unknown how many total have been infected, but these studies suggest the numbers are high.
The deer themselves don’t appear to get very sick from the virus — lab studies show them developing asymptomatic infections when exposed — but that’s not the top concern here. Veterinary infectious disease experts are describing these outbreaks in deer as a possible Pandora’s box — and now that it’s open, there’s a small but real chance it could lead to future variants that infect humans, or spread to other wildlife that could get sick.
Before starting the study, Kapur and his colleagues thought that deer would be highly unlikely to test positive for Covid-19. “We thought it would be a long shot,” Kapur says, to find even one positive test in a survey of deer that were killed by hunters or road accidents.
There’s only a limited window of time when a deer’s infection would show up on a PCR test before it clears their system. That’s what made the results so shocking: “Our studies suggest that there were more deer, in terms of percentage of their population, than humans infected with this virus.”
Despite the potential risks to animals and humans, the future of the coronavirus in animals may be largely outside of our control. “We can’t even control it in people,” Sarah Olson, an epidemiologist at the Wildlife Conservation Society, says. “There’s hardly a chance we’re going to be able to control it in the wild. It creates a hugely chaotic space. And we don’t have a lot of eyes on that space.”
How the virus spreads among wildlife is a black box that scientists try to peer into through the tiniest of pinpricks. But what they do know is that when the coronavirus establishes itself in wildlife, it creates for itself a sort of insurance policy. We may be able to get the pandemic among humans under control, but the virus is likely to lurk in other species, making it that much harder to monitor and defeat.
The spread of SARS-CoV-2 in wildlife is not the most pressing issue of the pandemic right now. Humans are still catching the virus from each other and dying from it. Still, these wildlife risks, if they are realized, could have serious consequences. Scientists want to be vigilant about dangers that could emerge from the wilderness.
Covid-19 may be pretty widespread among deer
The fact that SARS-CoV-2 can infect animals is not new. The virus probably originated in an animal species and then jumped to humans, a process that scientists call spillover. Since the pandemic began, there have been documented cases of many animals getting the virus, with various degrees of illness.
Infections have turned up in cats, dogs, lions, tigers, pumas, ferrets, mink, certain rodents, snow leopards, and others. The CDC even has guidelines to protect pets from Covid-19. When a virus jumps from animals to humans and then back to animals, scientists call that spillback.
Most of these infections in animals appeared to be self-contained. An infected house cat presumably stays in the house when infected — it doesn’t start a chain of transmission. “They were all isolated cases,” Suresh Kuchipudi, a Penn State infectious disease researcher who collaborated with Kapur, says of known cases in animals.
The deer infections were different. “This is first time that a completely free-living animal species in the wild has been found to be infected, and that infection is widespread,” Kuchipudi says.
How the deer got infected in the first place remains a mystery, but researchers believe the outbreak came from humans. The virus circulating in the deer had similar genetic sequences to the virus circulating in humans at the time that they got it.
“I don’t believe that there’s much direct human-to-deer interaction,” says Andrew Bowman, a professor of veterinary preventive medicine at the Ohio State University. He co-authored a separate study of infections in deer in Ohio, which also found widespread infection. It’s not like deer and people are hanging out in bars and restaurants together. Instead, Bowman suspects the deer might be picking it up from some source of environmental contamination, like garbage or sewage.
Whatever happened to start the deer outbreaks, it appears to have happened many times. The genetic analysis in the PNAS paper finds evidence of several separate jumps from humans into animals. Further research needs to be done to identify the exact pathway, and hopefully to prevent the next leap.
Once the virus jumps into the deer, they are also spreading it to each other, the studies find. “There was not just human-to-deer spillover, but there was also deer-to-deer transmission, as evidenced by genomic changes that would confirm that,” Kuchipudi says.
Viruses can mutate in animals, just as they do in people
There are two main reasons to be concerned about deer that spread the virus among themselves.
1. Viruses are always evolving
As viruses copy themselves in the human body, they slowly acquire genetic changes, which can lead to variants such as alpha and delta. Now imagine that “a similar parallel trajectory was also happening in some animal populations,” Kuchipudi says. When the virus becomes established in a new species, “the evolution of the virus becomes twice as complicated.”
This is the virus’s so-called insurance policy. In theory, it’s possible that long after the pandemic dies down in humans — maybe even 10 years from now — deer could reinfect humans with a new variant that our immune system isn’t as good at fighting off. (There’s even some speculation that the omicron variant emerged from an animal population.)
“Then it comes back, and we’re fighting a whole new battle,” Olson says.
So far, the scientists don’t have any indication that a new dangerous variant is brewing within deer. Also reassuring: “Right now, we don’t have any evidence that any of these animals are transmitting back to people,” says Angela Bosco-Lauth, who studies infectious disease and veterinary medicine at Colorado State University. “I don’t really see that as much of a threat.”
But if a person were to catch the virus from an animal, it would be hard to prove it, Bosco-Lauth says. Scientists have only tested several hundred of the roughly 25 million deer in the United States, and many other species haven’t been studied.
“If you had a group of animals that all had the same virus, that had the same genetic sequence, and then you found people downstream from that who had interacted with those animals and had the same sequence as the animal, that, to me, would be pretty solid proof that that’s where it came from,” she says. But that solid proof would be really hard to get. Scientists just don’t do a lot of testing in animals.
2. There are a lot of animals out there
The next concern is that the outbreak may not stop at the deer. Olson says the deer could potentially spread the virus to other animals.
Let’s say a deer infected with the coronavirus comes into contact with other mammals — for example, a predator like a mountain lion that kills a deer, or a scavenger like an ermine that nibbles away at a deer’s carcass. Olson says she’s not aware of any documented cases of SARS-CoV-2 spreading from one species’ remains to a new species. But she says it’s “plausible.”
If those other species pick up the virus and start an outbreak among their kind, many different species could perhaps end up with Covid-19. “Then you can think about almost like a complex network of animals passing the virus back and forth, right?” Kuchipudi says. “What is unsettling is that we have absolutely no clue if it’s happening or not.”
All of this is hypothetical. But if it were to happen, we wouldn’t necessarily find out. Contact tracing is hard enough in humans — it’s even more daunting when you consider the size and scope of the animal kingdom. “We have to approach this with humility,” Kuchipudi says.
While researchers don’t have evidence that Covid-19 is killing deer, it can be lethal for mustelids — think weasels, mink, and ferrets — and endangered snow leopards. Considering how much the coronavirus has evolved in people, it could potentially evolve in a way that hurts some animals. “There’s conservation threats there,” Olson says.
What can we do about it?
The pandemic in humans is much more urgent than Covid-19 in animals. All of the scientists I spoke to agreed about that. The coronavirus is still killing thousands of people every day, and that’s the problem that should get the bulk of our attention and resources.
“Humans are doing such a great job at spreading Covid between each other,” Bosco-Lauth says. “I don’t particularly worry about any animals maintaining this pandemic — I think we’re going to do that just fine on our own.”
On the other hand, the scientists say they want more visibility into what’s happening in the animal world. “We need wildlife surveillance,” Olson says, meaning more testing of animals for coronavirus antibodies — a sign they have been exposed — or active infections. “We just don’t have the tools to begin to understand the system, to even start mapping what’s going to happen here, because our ability to see it is so opaque right now.”
Scientists still have a lot to learn about how viruses jump between species, Olson says, and what factors make these jumps more or less likely.
Could scientists vaccinate deer or other wildlife? Not really. “There’s nothing to be done,” Olson says. While some vaccines are formulated for animals and routinely administered to pets, we don’t know enough about the immune system of the deer to know how it would respond to vaccines made for humans. Then come the logistical problems: Inoculations would need to be mixed with bait somehow, delivered via dart, or administered directly to captured animals. To top it off, one dose might not be enough.
“How are you going to capture the same animal four times?” Olson says. “There’s just no toolbox for this.”
For all these reasons, Covid-19 outbreaks in animals are not situations we can plausibly control. Rather, they’re something to monitor in case they start to look like pressing problems.
“We have been focusing predominantly on humans because there is a global pandemic going,” Kuchipudi says. “But at the same time, we can’t be ignoring this problem. The danger is then if we don’t address it, we could be completely blindsided and caught by surprise when a new variant emerges.”
The course of the pandemic continues to be impossible to predict, even in humans. The addition of it spreading in wildlife just makes it even harder. If there’s a lesson here, it’s this: “This virus never ceases to surprise us,” Kapur says.