Coronavirus Spreads Among North American Deer Herds

An article published in the April 26 issue of the journal Nature describes a series of studies by scientists on deer herds infected with the novel coronavirus, including how the virus enters the deer and occurs when the virus spreads between deer herds. and what risks these infections may pose to other wildlife and humans.
Testing deer for COVID-19 is slightly different than testing humans with nasopharyngeal swabs. Deer have long nasal passages, says Andrew Bowman, a veterinary epidemiologist at Ohio State University. “Usually we run out of cotton swabs before we get anything on [a live deer].”
These problem deer often die in the back of hunter’s trucks, in meatpacking plants or in butcher shops, waiting to be made into burgers, sausages, steaks and more. For decades, researchers have worked with hunters to manage deer populations and track the spread of infectious diseases as part of routine wildlife surveillance. Recently, scientists have also looked for the novel coronavirus that infects humans in deer.
Wearing masks and gloves, the researchers wiped the mud and grass around the deer’s nostrils and inserted cotton swabs to test for viral RNA. Blood is then collected to check for antibodies against the virus. Their work found widespread infection of North American white-tailed deer with the virus, with hundreds of infected animals in 24 U.S. states and several Canadian provinces.
Deer are widely distributed in North America. Nearly 30 million deer live in the United States, and several million live in Canada.
Variations in the virus that researchers find in deer are often consistent with those circulating in people who live nearby, but some studies suggest that SARS-CoV-2 in the wild may have mutated into new evolutionary pathways. It is unclear whether the virus spreads in long chains in deer, or whether deer-to-human transmission could trigger an outbreak. But researchers are increasingly concerned that these animals could serve as reservoirs for the virus, the source of unmanageable outbreaks that could breed new variants. Some researchers believe that highly contagious variants of Omicron linger in animal hosts for a while before appearing in humans.
Infected deer have so far not been terribly ill, but they could spread the virus to domestic animals or other potentially more vulnerable wild animals. “Once a virus enters a wild animal, there is basically no way to control it,” said Marietjie Venter, a medical virologist at the University of Pretoria in South Africa.
multifaceted outbreak
Since the outbreak of the covid, researchers have been worried about wildlife infection. To carry out their surveillance work, they started with the ACE2 receptor, a protein in host cells to which viruses normally bind to enter cells. Animals with ACE2 receptors similar to those in humans are considered at risk of infection. Teams around the world are experimenting with infection in these animals, including cats, deer mice (Peromyscus maniculatus), raccoon dogs (Nyctereutes procyonoides), and white-tailed deer, to see if they are susceptible and spread the infection.

In early January 2021, U.S. Department of Agriculture (USDA) researchers found that fawns in captivity could be infected with the novel coronavirus, shedding the virus through nasal mucus and feces, spreading the infection to other fawns in adjacent enclosures. Within a week, the animals began to develop antibodies against the virus, but no severe disease was found in the herd.
William Karesh, chair of the Paris-based OIE wildlife working group, said the findings were “somewhat surprising” because other ungulates, such as cattle, sheep and goats, are highly susceptible to infection. quite strong resistance.
Thomas DeLiberto, the coronavirus coordinator for the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service Wildlife Service in Colorado, and colleagues collected 385 samples from deer between January and March 2021. About 40% of the samples contained antibodies to the novel coronavirus. In a preprint in Nature last July, the team first reported the finding, suggesting that deer had been exposed to the virus, but it was unclear if it was a one-time exposure or if the virus had already started spreading in the animals. It is also possible that these antibody production is the result of infection with other coronaviruses in the deer.
The results have prompted new deer sampling across North America to begin, and an urgent release of the results of sampling projects that have been undertaken.
In 2020, the first year of the COVID-19 outbreak, scientists began collecting nasal swabs and blood samples from deer to test for the virus using polymerase chain reaction. Until December 2020, “all we got were negative samples,” said Vanessa Hale, an animal health researcher at Ohio State University. However, between January and March 2021, she and Bowman found 129 deer that tested positive for SARS-CoV-2 RNA among about 360 animals sampled in Ohio.
Genome sequencing of more than half of the samples taken from infected Ohio deer showed similar mutations to the virus circulating in human communities across the state at the time. Since then, researchers have found positive deer in 24 of the roughly 30 U.S. states that reported sampling, as well as in the Canadian provinces of Quebec and Ontario, although Canada has a lower positivity rate of 1%-6%.
In late December 2021, researchers found a highly contagious variant of Omicron in a white-tailed deer living on Staten Island in New York City. In March 2022, a mule deer (Odocoileus hemionus) in Utah tested positive for the novel coronavirus.
However, the infection of deer with the covid virus appears to be limited to North America. “To date, despite extensive research, no one has found the virus in European deer,” said Rachael Tarlinton, a veterinary virologist at the University of Nottingham, UK.
Biological differences do not appear to explain the differences, the researchers said. “All the data on the ACE2 receptor suggest that European deer species should be as susceptible as white-tailed deer,” Tarrington said. Instead, outbreaks in North American deer appear to be the result of high deer densities and frequent human interaction with them.
“In the Americas, deer are basically in the wild or in people’s backyards,” Venter said, adding that where she works, there is much less interaction with large ungulates. “In Africa, most animals stay in wildlife reserves.”
How deer are infected by humans
How the deer got infected remains a mystery. Humans transmit pathogens in the wild, such as E. coli, the measles virus, and the protozoan Giardia. But these “spillover” situations rarely lead to sustained transmission.
Scientists speculate that direct contact, such as people petting or feeding animals with their hands, may be to blame. In North American towns and cities, white-tailed deer live close to people—living near human houses, walking the streets, and exploring college campuses. In some U.S. states, deer are raised for food, and others have rehabilitation programs for deer orphaned by car accidents. Deer in captivity may have frequent contact with humans and wild deer, and they may also escape or be released back into the wild.
But Hale said that in these cases, there may not be enough direct contact to explain the hundreds of cases identified so far, let alone the countless undocumented cases.
Another path might be via the environment. While there is no clear route for the virus to spread in humans through contaminated surfaces, deer may have contracted the virus by sticking their noses into discarded masks or by swallowing flowers and garden vegetables from which humans have sneezed. Hunters also sometimes use corn or vegetables that may be infected with the virus as bait. But Hale noted that the deer had to arrive at the right time to ingest enough virus to infect them.
In addition, the researchers speculate that contaminated wastewater may also have infiltrated the animals’ water sources. However, although many studies have found viral RNA in sewage, no infectious virus has been isolated from it. And it’s not just urban deer that get infected, the researchers say, some infected deer live in isolated areas.
According to some reports, other animals such as wild cats or wild mink may also act as vectors.
“All of these seem far-fetched until we can prove them,” Hale said. The source of infection does not have to be just one, the researchers said, and may involve multiple routes.
Can deer reinfect people?
Once a deer is infected with the novel coronavirus, there are many opportunities for the virus to spread among the wider population. White-tailed deer are very social animals, and during the breeding season, from October to February each year, bucks can walk dozens of kilometers, moving back and forth between different herds, fighting other bucks along the way. Occasionally, a female deer will also travel up to 100 kilometers to “visit relatives and friends,” returning to her usual territory in a few days or weeks. In some northern states, during periods of heavy snowfall, deer herds sometimes migrate to “deer parks” with dense trees where they may encounter other herds. During this time, the animals have been in contact with each other and may spread the virus. “There’s a lot of face-to-face contact between deer,” said Linda Saif, a virologist at Ohio State University in Worcester.
All the potential for the virus to spread has scientists concerned that deer could be the reservoir of the novel coronavirus — a permanent reservoir and a recurring source of outbreaks in other animals, including humans. Saif said that once settled in the deer, the novel coronavirus may mutate, evolve, and possibly recombine with other coronavirus genes. It could have evolved to more easily infect other herbivores, such as sheep, goats and cattle, which share pastures with deer, she said. “Once you have a single wild animal host, conceivably it’s passed on to other wild animals, even domestic livestock,” she said.
Mounting evidence supports such concerns. For example, the novel coronavirus shows signs of long-term evolution in deer. In a February Nature preprint, Samira Mubareka, a virologist at the Sunnybrook Institute in Toronto, Canada, and her colleagues report on the November and December 2021 events in Ontario. Five SARS-CoV-2 genomes of deer sampled in the province were sequenced. Compared with the original novel coronavirus, these viruses have 76 mutations, some of which lead to amino acid changes in the spike protein the virus uses to infect cells. This mutation is the key to the success of the highly infectious mutation.
In the second Nature preprint on February 9, researchers discovered the novel coronavirus alpha and delta variants in Pennsylvania deer in November 2021. The genomes of these alpha variants are different from those found in humans, and these alpha variants were found in deer months after delta variants became the dominant human-infecting variant, suggesting that alpha variants may have evolved independently in deer populations .
Mubareka and her colleagues made another unexpected discovery: a human from southwestern Ontario had a viral sequence that closely resembled the genome of the virus found in deer. Although the evidence is unclear, scientists suspect that the person may have contracted the virus from a deer.
If this is confirmed, deer-to-human transmission would be a concern. From samples taken in December and January, the researchers also found a deer infected with the Omicron variant, which also had antibodies against the delta variant.
The researchers say there is not enough evidence yet to say whether deer are breeding grounds for dangerous mutations in the virus. Karesh said he needs to see more “spillover” events — from deer to people — to call them hosts of human infection.
To really understand the situation, more sampling of animals is needed. Some researchers have begun longitudinal studies that revisit sampling sites over several hunting seasons.
In March 2021, the U.S. Department of Agriculture received a $300 million grant to investigate animals susceptible to the novel coronavirus, and researchers sampled deer in at least 27 states during the 2022 hunting season. Boto said his team plans to study footage of deer interacting with humans and other animals to quantify their interaction patterns. Another researcher said that more sampling to determine which deer are at the highest risk — bucks or females, urban or suburban deer — may provide more clues.
The scientists also plan to conduct more experimental infection studies to see if variants like Omicron and Delta behave differently in white-tailed deer, and whether other wild animals are susceptible. They might also try mixed-species studies, for example, to see if minks can transmit infections to rodents.
Mubareka said more needs to be done to track these fast-spreading incidents. “These are just early chapters,” she said.