Source: The Paper
An article published April 26 in the journal Nature recounts a series of studies scientists have conducted on deer colonies infected with the new coronavirus, including how the virus enters deer, what happens 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 from testing humans for nasopharyngeal swabs. Deer have long noses, and Andrew Bowman, a veterinary epidemiologist at Ohio State University in the United States, said: "Usually we run out of swabs before we get anything from [live deer]."
Hundreds of Odocoileus virginianus in North America tested positive for the coronavirus (SARS-CoV-2).
These deer often die behind hunter trucks, meat processing plants or butcher shops, waiting to be made into burgers, sausages, steaks and other foods. For decades, as part of routine wildlife surveillance, researchers have worked with hunters to manage deer populations and track the spread of infectious diseases. Recently, scientists have also been looking for new coronaviruses that infect humans in deer.
The researchers wore masks and gloves to wipe the mud and grass around the deer's nostrils and inserted cotton swabs to detect viral RNA. Blood is then collected to check for antibodies against the virus. Their work found that the North American white-tailed deer has been widely infected with the new coronavirus, 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 millions more live in Canada.
The viral variants that researchers found in deer are often consistent with viral variants that spread among people living nearby, but some studies suggest that the new coronavirus in the wild may have produced new evolutionary pathways through mutations.
It is unclear whether the virus will spread in deer in a long chain of infection, or whether deer-to-human transmission will trigger an outbreak. But researchers are increasingly concerned that these animals will become hosts for the virus, become the source of uncontrollable viral outbreaks, and potentially give birth to new variants. Some researchers believe that the highly contagious Omiljung variant stayed in the animal host for a period of time before appearing in the human body.
So far, infected deer have not shown great discomfort, but they could spread the coronavirus to livestock or other potentially more vulnerable wildlife. Marietjie Venter, a medical virologist at the University of Pretoria in South Africa, said: "Once the virus enters the wild animal, there is basically no way to control it at present."
Multifaceted outbreaks
Since the outbreak of covid-19, researchers have been concerned about wild animal infections. To do the surveillance, they started with the ACE2 receptor, a protein in host cells that the virus normally enters by binding to it. Animals with ACE2 receptors similar to those in humans are considered at risk of infection. Research teams around the world have conducted infection experiments on these animals to see if they are susceptible and can spread infection, including cats, deer mice (Peromyscus maniculatus), raccoons (Nyctereutes procyonoides) and white-tailed deer.
In early January 2021, researchers at the U.S. Department of Agriculture (USDA) discovered that fawns in captivity may be infected with the new coronavirus, excreting 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 illness was found in the deer herd.
William Karesh, president of the Paris-based OIE Wildlife Task Force, said the findings were "somewhat surprising" because other ungulates, such as cattle, sheep and goats, are fairly resistant to infection.
Thomas DeLiberto, coordinator of the Coronavirus Service program at the U.S. Department of Agriculture's Animal and Plant Health Inspection Service in Colorado, and colleagues collected 385 blood samples from deer between January and March 2021 and began research, about 40 percent of which contain antibodies to the new coronavirus. In a preprint of Nature last July, the team reported the finding for the first time, suggesting that deer had been exposed to the virus, but it was unclear whether it was a one-time contact or whether the virus had begun to spread among the animals. It is also possible that these antibodies are produced as a result of infection with other coronaviruses in deer.
These results prompted new sampling of deer across North America and urgently published the results of the 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, using polymerase chain reaction to detect the new coronavirus. 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 COVID-19 in about 360 animals sampled in Ohio.
Of the samples taken from infected Ohio deer, genome sequencing of more than half of the samples showed similar variants to the virus that was circulating in human communities across the state at the time. Since then, researchers have found positive deer in 24 of about 30 U.S. states reported sampling, as well as in Quebec, Ontario and other provinces in Canada, although the positivity rate in Canada is lower, at 1 to 6 percent.
In late December 2021, researchers discovered a highly contagious variant of the Olmikerron in white-tailed deer living on Staten Island in New York City. In March 2022, an Odocoileus hemionus in Utah tested positive for COVID-19.
However, the deer infection with the new crown virus seems to be limited to North America. Rachael Tarlinton, a veterinary virologist at the University of Nottingham in the United Kingdom, said: "So far, despite a large number of studies, no one has found the virus in European deer."
The researchers say biological differences don't seem to explain the differences. "All the data on the ACE2 receptor suggest that European deer species should be as susceptible as white-tailed deer," Tallington said. Instead, outbreaks in North American deer appear to be the result of a high density of deer and frequent interactions with them.
"In the Americas, deer basically walk in the wild or in people's backyards," Venter said. She added that where she works, there are far fewer interactions with large ungulates. "In Africa, most animals stay in wildlife sanctuaries."
How deer are infected by humans
How deer are infected remains a mystery. Humans transmit pathogens such as E. coli, measles viruses and the protozoan Giardia in the wild. But these "spillover" situations rarely lead to sustained transmission.
Scientists speculate that direct contact, such as people touching or feeding animals with their hands, may be to blame. In North American towns and cities, white-tailed deer live intimately with people — they live near human houses, walk the streets, and venture out on college campuses. In some U.S. states, people raise deer for food, and others have rehabilitation programs for fawns orphaned by car accidents. Captive deer may come into frequent contact with humans and wild deer, and they may also escape or be released back into the wild.
But Hale said there may not be enough direct contact in those cases to explain the hundreds of cases found so far, not to mention the myriad cases that have not been documented.
Another path might be through the environment. While there is no clear route for the virus to spread among humans through contaminated surfaces, deer may contract the virus by sticking their noses into discarded masks or swallowing flowers and vegetables in gardens that humans have sneezed on. Hunters also sometimes use corn or vegetables that may be contaminated with the virus as bait. But Hale noted that the deer must arrive at the right time, ingesting enough amount of virus to infect.
In addition, the researchers speculate that it may also be contaminated wastewater that has infiltrated the animal's water source. But many studies have found viral RNA in sewage, but have not yet isolated infectious viruses from them. And, it's not just urban deer that get infected, the researchers say, and some of the infected deer live in remote places.
According to other reports, other animals such as wild cats or wild mink may also act as a medium of communication.
"All of this seems far-fetched until we can prove it," Hale said. The researchers say there is not necessarily only one source of infection, but may involve multiple routes.
Whether the deer will re-infect people
Once a deer is infected with the virus, there are many opportunities for the virus to spread among the wider population. The white-tailed deer is a very social animal, and during the breeding season, that is, from October to February of the following year, the male can walk dozens of kilometers, moving back and forth between different deer herds, fighting with other males along the way. Occasionally, a female deer will travel up to 100 kilometers to "visit relatives and friends" and return to her usual territory after a few days or weeks. In some northern states, during heavy snowfalls, deer herds sometimes migrate to "deer parks," where there are dense trees where they may encounter other herds. During this time, the animals have been in contact with each other and may have transmitted the virus. Linda Saif, a virologist at Ohio State University in Worcester, said there was "a lot of face-to-face contact between deer."
All the possibilities of the virus spread have scientists worried that deer could become hosts — permanent hosts — and a recurrent source of outbreaks in other animals, including humans. Saif said that once it settles in deer, the new coronavirus may mutate, evolve and may recombine with other coronavirus genes. It could evolve to more easily infect other herbivores, such as sheep, goats and cattle, which share pasture with deer, she said. "Once you have a single wildlife host, you can imagine passing it on to other wildlife, even domestic livestock." She said.
A growing body of evidence supports such concerns. For example, the coronavirus is showing signs of long-term evolution in deer. In a February preprint of Nature, Samira Mubareka, a virologist at the Xinning Institute in Toronto, Canada, and her colleagues sequenced five coronavirus genomes from deer sampled in November and December 2021 in Ontario. These viruses have 76 mutations compared to the original coronavirus, and some mutations cause amino acid changes in the spike proteins that the virus uses to infect cells. This mutation is key to the success of highly contagious variants.
In the second Nature preprint dated Feb. 9, researchers discovered the alpha and Delta variants of the coronavirus in Pennsylvania deer in November 2021. The genomes of these alpha variants are different from those found in humans, and the alpha variants were found in deer a few months after the Delta variant became the dominant human infection variant, suggesting that alpha variants may have evolved independently in deer populations.
Mubareca and her colleagues made another unexpected discovery: A viral sequence in a human body from southwestern Ontario was very similar to the viral genome 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, the spread between deer and people will be a concern. From samples taken last December and January this year, the researchers also found a deer infected with the Omiljung variant virus, which also has antibodies against the Delta variant.
The researchers say there is not enough evidence to show whether deer are breeding grounds for dangerous mutations of the virus. Karesh said he needs to see more "spillover" events — from deer to humans — before he can call them hosts for human infections.
To truly understand this situation, more sampling of animals is needed. Some researchers have already started longitudinal studies, revisiting sampling sites during several hunting seasons.
In March 2021, the U.S. Department of Agriculture received a $300 million grant to investigate animals susceptible to covid-19, and during the 2022 hunting season, researchers sampled deer in at least 27 states. 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 taking more samples to determine which deer is at the highest risk — male or female, urban or suburban — could provide more clues.
Scientists also plan to conduct more experimental infection studies to see if variants like Omiljung and Delta behave differently in white-tailed deer and whether other wild animals are susceptible to infection. They may also try hybrid species studies, for example, to see if mink can spread the infection to rodents.
Mubareca said more needs to be done to track these rapidly spreading events. "These are just early chapters." She said.