Omicron-infected deer put scientists on high alert for spillover of new variants to humans

• Nearly 20 white-tailed deer in New York were infected with Omicron this winter, research suggests.
• The virus seems widespread among US deer, raising concerns about the spillover of new variants.

Vaughn Cooper sees white-tailed deer every day in his neighborhood outside Pittsburgh.

The species is common in most US states. Pennsylvania alone has around 1.5 million white-tailed deer — about 30 per square mile — while the US has around 30 million in total.

"My dog goes ripping after the deer every morning," Cooper, the director of the Center for Evolutionary Biology and Medicine at the University of Pittsburgh, told Insider.

Interactions between humans and deer — or deer and other animals — are a pressing concern among scientists, since the coronavirus now appears widespread in the US white-tailed deer population.

Researchers at Pennsylvania State University identified nearly 20 white-tailed deer in Staten Island, New York, that were infected with the Omicron variant between December 2021 and January 2022. Their findings, which haven't been peer reviewed, mark the first report of Omicron spilling over to wild animals. A spillover event occurs when a highly-infected population passes the virus to another species that hasn't encountered it (or that a particular variant) before.

The US Department of Agriculture has detected coronavirus infections among white-tailed deer in 15 states, a USDA spokesperson told The New York Times on Monday. In a study published last year, Penn State researchers identified the coronavirus in about one-third of white-tailed deer sampled in Iowa between September 2020 and January 2021. Another research group found the virus in one-third of sampled deer in Ohio from January to March 2021.

"We were not expecting to find this level of widespread infection," Suresh Kuchipudi, associate director of the Animal Diagnostic Laboratory at Penn State, told Insider. "It was quite surprising, and also quite concerning."

Scientists worry that deer could serve as a reservoir for the coronavirus, even after COVID-19 becomes endemic in humans. In the worst-case scenario, the virus might evolve in deer to become better at evading vaccine protection, then spill over into humans as a more lethal variant.

But such a phenomenon would be unprecedented, Cooper said. Most people in the US have some protection against the virus from vaccines or natural infection, making it tough for a new variant to override our existing immune defenses.

"Could deer become a host that gives rise to successful lineages in humans? I still think it's unlikely," Cooper said, adding, "We're actually becoming a harder population to invade because the leading virus is so prevalent."

A third animal could pass the virus between deer and humans

Deer aren't the only animals that can contract coronavirus infections.

Scientists have detected the virus in cats, dogs, ferrets, mink, pigs, and rabbits. But they're paying close attention to white-tailed deer for a few reasons: In addition to being highly vulnerable to infection, white-tailed deer are abundant in the US and live in close proximity to humans.

"There's no evidence that there's anything special about deer biology that makes them a more worrisome host," Cooper said, adding, "The major thing is that they're everywhere. They are the classic example of changes in human and animal populations brought on by civilization that promotes spillover."

For now, scientists don't know whether deer can spread the coronavirus to humans — they just know that the virus is quite good at infecting deer populations. The animals live in herds, making it easy for them to transmit the virus to one another through saliva or feces.

For deer to infect humans directly, "you'd basically need to be a hunter," Cooper said. It's also possible that deer could pass the virus to humans through an intermediate host, such as a rodent or household pet.

"Whenever you have an animal that is widely infected and virus is circulating, they always can be a source of infection in other susceptible animals — even sometimes humans, if the conditions are right," Kuchipudi said.

One deer in Staten Island showed evidence of reinfection

One of the most urgent mysteries is whether the same deer can be infected with multiple coronavirus variants. In that case, scientists wouldn't hold much hope for the virus dying out in deer populations.

"If we do find that deer can be reinfected, that signals clearly for the continued circulation of the virus in these animals," Kuchipudi said.

His preprint identified a single deer in Staten Island with high levels of coronavirus antibodies, which was also infected with Omicron. The study "hint[s] at the possibility that animals that are previously exposed could be reinfected," Kuchipudi said, but for now, "it's just one animal."

Even if the virus spilled over from deer to humans several years from now, Cooper said he's hopeful that genomic sampling and wastewater surveillance could detect it right away, before it "catches fire."

"It's legitimate to be concerned about the possibility of this, but the great news is that surveillance is so strong, generally, that we will see this when it happens," he said.

As far as historical patterns go, he added, it would be rare for a spillover variant to jump-start a new wave of the pandemic.

"I'm unaware of new lineages refueling an existing pandemic like this, except for flu," Cooper said. "Flu is clearly driven by continuing exchange back and forth between humans and pigs and fowl."

But Kuchipudi cautioned that scientists still have more to learn about whether white-tailed deer are strong reservoirs for mutations.

"We still haven't quite grasped the extent of the problem," he said, adding, "We need to be cautious about concluding if it's likely or unlikely. The honest answer is we don't know yet."