Nature News: The new coronavirus is spreading among white-tailed deer in North America.

Testing deer for SARS-CoV-2 is slightly different than testing humans

These deer are usually found dead in the back of hunter's trucks, meatpacking plants or butcher shops, waiting to be made into burgers, sausages, steaks, ribs and more

For decades, researchers have worked with hunters to manage deer populations and track the spread of infectious diseases such as chronic wasting disease and bovine tuberculosis as part of routine wildlife surveillance

Between estimating the deer's age by examining the teeth and measuring the antlers, the researchers wore masks and gloves to wipe the mud and grass around the deer's nostrils, then inserted cotton swabs to detect viral RNA

Scientists want to understand how the virus gets into deer, what happens when it spreads between them, and what risks these infections might pose to other wildlife and humans

Samira Mubareka, a virologist at the Sunnybrook Research Institute in Toronto, Canada, said several research groups have cobbled together funds to investigate the deer

Coronavirus common in common American deer

"We mobilized a large number of students," Bowman said

The variants the researchers found in deer were often consistent with those circulating in humans who lived nearby, but some studies suggest that SARS-CoV-2 in the wild may already be exploring new evolutionary pathways through which mutations alter the virus

It is unclear whether the virus spreads in long chains in deer, or whether deer-to-human transmission could trigger an outbreak

Infected deer have so far not shown much discomfort, but they may spread the infection to domestic animals or other wild animals that may be more vulnerable

multiple outbreaks

Since the start of the COVID-19 pandemic, researchers have worried about wildlife infection, but tracking the movement of this promiscuous virus has been tricky

In early January 2021, U.

William Kareche, 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 fairly resistant to infection force
.

Find animals with coronavirus — and why it matters

The study was eye-opening, said Thomas Boto, SARS-CoV-2 coordinator for the USDA's Animal and Plant Health Inspection Service Wildlife Service in Fort Collins, Colorado
.
"We said, 'Okay, we'd better see if wild white-tailed deer had contact
.
'"

Shento and his colleagues began the study with 385 blood samples collected from deer from January to March 2021 as part of routine surveillance for wildlife disease in Illinois, Michigan, New York and Pennsylvania
.
About 40% of the samples contained SARS-CoV-2 antibodies
.
The finding, first reported in a preprint in July last year, suggested the deer had been exposed to the virus, but it was unclear if it was a one-time exposure or if the virus had spread among animals
.
It is also possible that these antibodies are the result of other coronavirus infections in the deer
.

The results have prompted new sampling of deer to begin across North America and a rush to publish the results of sampling projects already underway
.

During the first year of the pandemic, scientists began collecting nasal swabs and blood samples from deer to test for SARS-CoV-2 using polymerase chain reaction—a positive result would be direct evidence that the animals were infected
.
But until December 2020, "all we got were negative samples," said Vanessa Hale, an animal health researcher at Ohio State University
.
In the new year, everything changed
.
She and Bowman found 129 deer positive for SARS-CoV-2 viral RNA in about 360 animals sampled in Ohio between January and March 2021
.

Penn State virologist Suresh Kuchipudi and his colleagues got a similar positive test in Iowa
.
Of the 283 deer tested between April 2020 and January 2021, 33% were positive for SARS-CoV-2
.
Most of these cases occurred in November and December 2020, coinciding with the peak of human infections
.

Genome sequencing of more than half of the samples taken from infected Ohio deer revealed variants similar to those circulating in human communities across the state at the time (see "Deer Testing")
.
The virus appears to have spread from humans on 6 separate occasions
.
Mutations in the genetic sequence also confirmed that deer spread infections among them
.

Since then, researchers have reported sampling in 24 of about 30 U.
S.
states, as well as Canada's Quebec, Ontario, Saskatchewan, Manitoba, New Brunswick and British Columbia.
Positive deer have been found in the province, 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 SARS-CoV-2
.

Where did Omicron come from? Three key theories

The epidemic appears to be confined to North America
.
Rachel Tarrington, a veterinary virologist at the University of Nottingham, UK, said: "To date, despite extensive research, no one has detected the virus in European deer
.
" For example, Leibniz Zoo and Wildlife in Berlin Evolutionary virologist Alex Greenwood of the Institute of Zoology and his colleagues tested roe deer (Capreolus Capreolus), red deer (Cervus elaphus) and red deer (Dama Dama) in Austria and Germany, all of which did not Infection with SARS-CoV-2
.

Physiological 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, the prevalence in North America appears to be the result of the high density of deer and the frequent interaction of people with them
.

"In the Americas, deer are basically out in the wild, walking in people's backyards," Venter said,
adding that where she works, there are far fewer interactions with large ungulates
.
"In Africa, most animals are in wildlife reserves
.
"

manual intervention

How the deer got infected remains a mystery
.
"There's a window open somewhere, but we don't know what that is," Bowman said
.
Humans are known to transmit pathogens in the wild, such as E.
coli, the measles virus and the protozoan Giardia
.
But these human jumps or "spillovers" rarely, if ever, lead to sustained transmission
.

Direct contact, such as people keeping pets or hand-feeding animals, may be to blame
.
In North American towns and cities, white-tailed deer live with people—they live near houses, roam the streets, and explore college campuses
.
“They have adapted very well to human-dominated landscapes,” said Michael Tonkovich, who directs the deer project at the Ohio Department of Natural Resources in Athens
.

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, or they may 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 route of infection with SARS-CoV-2 may be the environment
.
Although there is no established route of transmission in humans through contaminated surfaces, deer may have contracted the virus by digging their noses into discarded masks, or by swallowing flowers and garden vegetables that humans have sneezed on
.
Hunters also sometimes feed and bait deer with corn or vegetables that may be covered in viruses
.
But Hale noted that the deer must arrive at the right time to ingest the infection
.
"Is it possible? Yes
.
Is it possible? Again, I don't know
.
"

Another route could be the trickle of contaminated wastewater into the animals' water sources
.
Although many studies have found viral RNA in sewage, no infectious SARS-CoV-2 has been isolated
.
And it's not just urban deer that get infected; some live in isolated areas, the researchers said
.

Some reports suggest that other animals such as feral cats or wild mink could act as vectors
.

"All of these things seem far-fetched until we can prove them," Hale said
.
But Mubareka said there is not necessarily just one source of infection
.
Multiple routes may be involved
.

face to face

Once a deer has contracted the virus, there are many opportunities for SARS-CoV-2 to spread among the wider population
.
White-tailed deer are very social animals, Tonkovich said
.
For most of the year, the bucks live in loose single groups of up to six, grooming and fighting each other
.
Matrilineal clans do live with generations of female offspring and fawns
.
The animal typically stays in a habitat of a few square kilometers, but during the breeding season -- the winter months of about October to February -- that all changes
.

Bucks can travel dozens of kilometers, moving back and forth between herds, locking antlers with other bucks along the way
.
Occasionally, a doe also makes trips of up to 100 kilometers, perhaps to "visit family or friends," returning to her usual territory after a few days or weeks, Tonkovich said
.
In some northern states, during heavy snowfalls, deer herds sometimes migrate to "deer parks," where dense trees prevent snow from accumulating on the ground, where they may encounter other deer herds
.
During this time, the animals have been interacting and potentially spreading the virus
.
"There's a lot of nose-to-nose 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 a reservoir for SARS-CoV-2 — a permanent reservoir for the virus and a frequent source of outbreaks in other animals, including humans
.
For example, camels are a natural host for the MERS-CoV coronavirus that causes Middle East respiratory syndrome, which is occasionally transmitted to humans
.
Saif said that once established in deer, SARS-CoV-2 could mutate, evolve and possibly recombine with other coronaviruses
.
It could have evolved to better infect other herbivores, such as sheep, goats and cattle, which share pastures with deer, she said
.
"Once you have a single wildlife host, it's conceivable that it will spread to other wildlife, even domestic livestock
.
"

There is growing evidence of this
.
For example, the virus shows signs of long-term evolution in deer
.
In a preprint in February, Mubareka and her colleagues sequenced five SARS-CoV-2 genomes from deer sampled in Ontario in November and December 2021
.
Compared to the original SARS-CoV-2 virus isolated in Wuhan, China, these viruses have 76 mutations, including some that 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
.

Beyond omega clones: what's next in the evolution of the new coronavirus

The closest relatives to the genomes of these viruses that the researchers could find were from Michiganders about a year ago
.
The results showed that the virus had been circulating in animals for a long time
.
"It's insane
.
Honestly, I can't believe it," Mubareka said, adding, "The fact that we found it in such a sparse sampling, you really wonder what else happened?"

A second preprint on February 9 found Alpha and Delta SARS-CoV-2 variants in Pennsylvania deer in November 2021
.
The Alpha genome differs from that found in humans, and was found in deer months after delta virus became the dominant human-infecting variant, suggesting that Alpha evolved independently in deer populations
.

Mubareka and her colleagues made another unexpected discovery: The sequence of a virus in a human from southwestern Ontario 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 confirmed, deer-to-human transmission would be a concern, as would reinfection from deer-to-human, as Kuchipudi may have observed
.
From samples taken in December and January, he found a deer infected with the omicron virus, which also had antibodies against delta 7
.
"If animals can re-infect like people, then the virus won't go away; it will continue to spread," he said
.

The researchers say there is not enough evidence yet to say whether deer are breeding grounds for the dangerous variant
.
Karesh said he needs to see more spillover events -- from deer to people -- to call them hosts of human infection
.

Brian Richards, a wildlife biologist and emerging diseases coordinator at the U.
S.
Geological Survey's National Wildlife Health Center in Madison, Wisconsin, agrees that deer don't appear to pose a danger yet
.
"Among the millions of people who came into contact with and hunted deer in the last year, we now know that one may have been infected," he said
.

To really understand the situation, more sampling of animals is needed
.
Some researchers have begun longitudinal studies where they revisit sampling sites over several hunting seasons
.

In March 2021, the USDA received a $300 million grant to investigate animals susceptible to SARS-CoV-2 and to sample deer during the 2022 hunting season in at least 27 states
.
Shento said his team plans to study footage of deer interacting with humans and other animals to quantify their interaction patterns
.
Richards said more sampling to determine which deer is at greatest risk -- stag or rural -- may provide more clues
.

The scientists also plan to conduct more experimental infection studies to see whether variants like Omicron and Delta behave differently in white-tailed deer, and whether other wild animals are susceptible
.
They found that red foxes (Vulpes Vulpes) were, but not coyotes (Canis latrans), and they wanted to observe mule deer and elk
.
They might also try mixed-species studies, for example, to see if mink could transmit infection to rodents
.

More work needs to be done to track these rapidly unfolding events, Mubareka said
.
"These are just early chapters
.
"