COVID-19 is more widespread in animals than we thought
From lions and tigers to big hairy armadillos, a growing number of animals have been infected with the coronavirus. Here’s what we’ve learned.
We think of COVID-19 as a human pandemic, but it’s much more than that. The virus that causes the disease, SARS-CoV-2, can infect a wide and growing range of animals, both captive and wild.
So far, the virus has been detected in more than a hundred domestic cats and dogs, as well as captive tigers, lions, gorillas, snow leopards, otters, and spotted hyenas, according to the U.S. Department of Agriculture. Zoo staff in the U.S. have recorded a single positive case in a binturong, coati, cougar, domestic ferret, fishing cat, lynx, mandrill, and squirrel monkey.
In the United States, only three wild species—mink, mule deer, and white-tailed deer—have tested positive, according to the USDA. Cases have been detected elsewhere in the world in wild black-tailed marmosets, big hairy armadillos, and a leopard.
But testing of wild animals is infrequent, and COVID-19 has likely impacted many more species, which emerging research is beginning to show. “I think the spread to wildlife animals is much wider than previously thought,” says Joseph Hoyt, a disease ecologist at Virginia Tech.
How does SARS-CoV-2 infect such a big range of species, and what are the impacts?
The receptor connection
A major reason lies in a complicated receptor found in all mammals, called ACE-2. This receptor plays an important role in regulating blood pressure and other physiological functions.
Once the spike protein of SARS-CoV-2 enters the body, it begins infecting host cells by binding to the ACE-2 receptor, which is widespread in the upper airways and sinuses of humans and many other mammals.
The ACE-2 receptor’s physical structure varies relatively little across vertebrate species compared with other similar proteins, says Craig Wilen, a virologist at Yale University. Even so, there are enough small variations that scientists initially thought some mammals would be very unlikely to be infected.
But that thinking has changed as animals initially thought to be less susceptible have proven anything but. It now appears that many if not most mammalian ACE-2 receptors are susceptible and don’t represent a limiting factor for the virus.
“It seems like it’s good enough… even if it isn’t a perfect match,” says Rick Bushman, a professor at University of Pennsylvania’s School of Medicine who studies host-microbe interactions.
Instead, there are likely many other factors at play that determine vulnerability, the details of which remain almost totally unknown.
A vast range
We already know that the virus can infect and spread within wild mink and white-tailed deer—and for both species, there is at least one verified instance in which the virus has gone from humans to the animals and back again to humans. Besides mink, domestic ferrets and golden hamsters also appear to easily spread the virus to one another in captive settings.
Aside from the previously listed animals, an upcoming study published ahead of print in BioRxiv identified probable cases of SARS-CoV-2 infection in wild deer mice, raccoons, opossums, gray squirrels, white-footed mice, striped skunks, and more.
Carla Finkielstein, a co-author of the paper, along with Hoyt and conservation biologist Amanda Goldberg, were surprised when they first found evidence of SARS-CoV-2 infection in Virginia opossums.
“We were worried, because that means it’s jumping” to distantly related mammals, Finkielstein says. “Opossums are very different from us biologically,” Goldberg adds.
Opossums are marsupials that give birth to honeybee-size young, which suckle on teats in their mothers’ pouches. Marsupials diverged from placental mammals—which includes many common mammals—more than 150 million years ago.
If SARS-CoV-2 can infect opossums, they reasoned, it’s likely that it could infect a massive variety of mammals. Indeed, the team found signs of antibodies against SARS-CoV-2 in significant percentages of six urban wildlife species in southwestern Virginia. They also obtained positive PCR hits—which are indicative of but don’t prove infection—in two of these species and in another four others, including red foxes and bobcats.
Another recently submitted paper also found signs of the pathogen infecting 17 percent of New York City sewer rats tested. And a small percentage of wild white-footed mice in Connecticut have also become infected, according to research by Rebecca Earnest, a doctoral student at Yale University.
Infection questions
But how are wild animals such as deer becoming exposed to the virus?
The question has yet to be answered, but there are theories. Wildlife could become infected by coming into close contact with human trash or wastewater, or by inhaling the virus when near people. Exposure could also occur following interactions with pets such as cats and dogs—or captive deer—which can carry the virus.
But “I think everybody agrees… that nobody knows,” Bushman says.
However white-tailed deer are being exposed, it is happening often. One 2021 study suggested that more than one-third of deer in the U.S. Northeast and Midwest had been exposed. Another paper found that the virus had entered into deer at least four separate times from humans, and yet a third study found the virus passed back into a single human in Canada. (Read more: Wild U.S. deer found with coronavirus antibodies.)
One reason animal infections matter is because they represent new reservoirs for the virus, where it can be sustained and acquire new mutations that could theoretically help it spread better if it finds its way back to humans.
“More transmission across more species is not something we want to see,” Earnest says.
Overlooked problem
The ability of SARS-CoV-2 to infect wildlife amounts to a hidden panzootic—the animal version of an epidemic—with almost entirely unknown effects, says Finkielstein.
Infected animals often appear to have mild symptoms, but experts know almost nothing about how the various variants of the virus affect most animals. Sometimes, infections are deadly. The virus appears to kill a small percentage of infected mink, and three snow leopards died due to complications from COVID-19 at the Lincoln Children’s Zoo in Nebraska.
Wilen cautions that we don’t really know how sick animals may be getting in the wild. He cites the example of chimpanzee simian immunodeficiency virus (SIVcpz), which jumped into humans and turned into HIV-1. It was long thought SIV caused only mild symptoms in chimpanzees, but research eventually determined that the virus can lead to a condition similar to AIDS in the animals, which usually shortens their life spans.
Effects of viruses are particularly hard to study in wild animals, particularly at the ecological level, Hoyt adds.
“We don’t know the consequences of this for the wildlife,” Finkielstein agrees. “That’s another aspect that has been largely ignored.”
SARS-CoV-2 could be lurking in animal hidey-holes
Many animals besides humans look as if they can catch the virus, too
In the field of epidemiology, a “spillover” is a virus that has made the leap from one host species to another. The spillovers of most concern to people are those from other animals to Homo sapiens. These may then go on to create “zoonotic” human diseases—of which covid-19 is believed to be one (the original host of sars-cov-2 is thought to have been an as-yet-undetermined species of bat).
Such traffic can, however, run in two directions. For example, in 2020 the World Health Organisation reported that says-cov-2 had spilled over in Denmark from human beings into farmed mink, and was thereafter transmitted from animal to animal to create a separate veterinary epidemic. And, earlier this month, a paper posted on BioRxiv, an electronic host for work that has not yet been peer-reviewed, presented evidence that the virus is also circulating in white-tailed deer in North America, having presumably spilled over from people there. All of which is on top of reports suggesting that domestic pets, especially cats and dogs, can also pick up sars-cov-2 and in the case of cats at least, can then pass it on to others of their kind.
These, though, are reactive approaches. A proactive one would try to establish which species are at greatest risk of becoming reservoirs for sars-cov-2 before they actually do so. That would permit the monitoring of threats before they got out of hand. And, as she reports this week in the Proceedings of the Royal Society, Barbara Han of the Cary Institute of Ecosystem Studies, an independent environmental research organisation based in Millbrook, New York, thinks she has worked out a way to achieve this.
Hidden ACEs
Starting early in 2020, just after covid emerged, Dr Han and her colleagues focused their attention on ace2, a cell-membrane protein that had been identified almost immediately as the virus’s point of entry. ace2’s day job is to help regulate blood pressure, and most vertebrates have it in one form or another. The researchers wanted to determine in which other vertebrate species sars–cov-2 might be expected to bind as strongly to the local ace2 receptors as it does to those in human beings. These would be candidates for the role of reservoirs.
To this end, they gathered molecular information about every version of ace2 that they could get their hands on. Mostly, these were from mammals—142 species of them. They then used computer modeling of the interatomic forces involved to work out the strengths of the bonds likely to develop between sars-cov-2’s spike protein and each version of ace2. As they expected, based on news that broke while they were conducting their work, the bond with mink ace2 was particularly strong. They found a similarly strong affinity with ace2 from white-tailed deer, long before reports of infections in that species emerged. Cats and dogs also showed up as being at risk—which reports then confirmed that they were. And gorillas and macaques, which have suffered a few cases in zoos, looked susceptible as well.
The researchers studied everything they could—from breadth of diet, metabolic rate and age of sexual maturity to litter size, lifespan, geographical range and phylogenetic relationships—about more than 5,000 mammals for which little or no ace2-receptor information was available. This enormous database completed, they fed the outcome into a machine-learning system that had been trained on the characteristics of the 142 species they had already examined. The result was the revelation of 540 species which seemed likely to have vulnerable ace2 receptors and thus the potential to function as covid reservoirs.
Most primates were on this list—which, considering that people are primates too, was expected. Nor, given suspicions about sars–cov-2’s origins, was the inclusion of 35 types of bat a surprise. Surprises, however, there were. Though the common house mouse does not look to be a risk, which is good news, two of its fellow rodents, the ricefield rat and the Malayan field rat, both do. Since these species are often preyed on by domestic cats, themselves now known to be covid-susceptible, that provides a route by which people might become infected.
Dozens of other species were also flagged up as potential reservoirs. These included red foxes and raccoon dogs—two creatures which, like mink, are sometimes farmed for fur—and white-lipped peccaries (pig-like creatures found in South and Central America) and nilgai (a large Asian antelope), both of which are farmed occasionally, and also hunted and eaten.
Among more widespread livestock, the species of most concern is the water buffalo. There are reckoned to be over 200m of these around the world, acting as both beasts of burden and sources of milk. And other frequently hunted animals, such as the duiker (another antelope), the warty pig and the mule deer were also reckoned vulnerable, together with some rarities, including two critically endangered antelopes, the addax and the scimitar-horned oryx (pictured below), which was once extinct in the wild and is only now being reintroduced. In these cases the threat is less to human beings than to the survival of the species concerned.
Paying the buffalo bill
The sheer range of species involved staggers Dr. Han. “I never imagined that we would ever see a virus with such a high cross-species infection potential,” she says. “It appears that there is at least an order of magnitude more species that are susceptible to sars-cov-2 infection than any other zoonotic virus I can think of.”
Forewarned, however, is forearmed. And here there is perhaps a lesson on keeping the weapons in the arsenal sharp. One reason Dr. Han’s study took so long from inception to publication is the disparate nature of the sources she needed to draw on. Scattered as they were around the world’s natural-history collections, assembling them took time. Many museums are now in the business of making their collections available electronically. To some, that might sound a low priority. Work like this suggests it is not.
A deer may have passed COVID-19 to a person, study suggests
The virus is widely circulating in white-tailed deer. Until now, no humans are known to have been infected by deer.
MARCH 4, 2022 National Geographic
A white-tailed deer in Canada likely infected a human with coronavirus, according to new research. The case, reported in a preprint journal, would be the first known instance of a COVID-19 spillover from a white-tailed deer—a common species throughout North America—into another species.
Previous work has shown that the virus is circulating widely in U.S. white-tailed deer populations. Before this latest report, however, the virus appeared to be very similar to that found in nearby humans, suggesting that the deer likely were sickened by us—not the other way around.
Now, a team of 32 government and academic researchers in Canada has concluded in a new work posted in BioRxiv that in late 2021, more than a dozen white-tailed deer in Canada had been infected with coronavirus that had a constellation of “mutations that had not been previously observed among SARS-CoV-2 lineages.”
What’s more, further analysis revealed that a person who had close contact with white-tailed deer in Ontario was infected with the same variant of coronavirus. (It was detected as part of Canada’s standard genomic sampling of all COVID-19 cases in the area at the time.)
Together, those factors suggest that the virus had been circulating among deer and accumulated mutations as it hopped from one animal to the next, before ultimately being passed to a person. It’s possible the virus was transmitted first through another host species, such as a mink, though the genomic analysis suggests that direct transmission from deer to human is “the most likely scenario,” the authors write.
The preliminary research, which has not yet been peer-reviewed, is not a cause for alarm, experts say.
The chances of transmitting coronavirus between people remains much higher than contracting the virus from a deer, says Jüergen Richt, a veterinarian and director of the Center on Emerging and Zoonotic Infectious Diseases at Kansas State University, who was not involved with the work.
Deer nose swabs
For the research, scientists took nose and tissue samples from 300 dead white-tailed deer in southwestern and eastern Ontario between November and December 2021. All the animals had been killed by hunters and were already being tested as part of an annual surveillance program for chronic wasting disease, which kills deer and their relatives. A few samples tested weren’t usable, but the researchers found that 17 of 298 deer—6 percent of the animals—tested positive for a “new and highly divergent lineage” of the coronavirus.
Their results also showed that the variant is an older version of COVID, one that predated Delta and Omicron, suggesting that coronavirus has been circulating among deer for a long time.
After discovering the coronavirus cases, the study authors analyzed whether the deer virus would likely be able to evade an existing COVID vaccine and concluded it would likely still provide robust coverage.
That’s good news, says Richt, who agrees that deer-to-human infection appears to be the most likely explanation for the human case in Ontario.
But he notes that there likely are other virus variants in people and animals that haven’t yet been recorded, possibly making the picture more complex than we realize.
“As a scientist, you always have to discuss what else could be happening if you aren’t 100 percent sure,” he says.
It remains unknown if there are other human cases of the Ontario deer-related virus or if there have been other spillover events from deer to people, the Canadian team emphasizes.
“The emergence of Omicron and the end of deer-hunting season has meant both human and [white-tailed deer] testing and genomic surveillance in this region has been limited since these samples were collected,” they wrote in the paper.
Mink and hamster cases
During the pandemic, there have been documented cases of humans sickened with COVID from farmed mink and also an incident in which a Hong Kong pet shop employee contracted the virus from a hamster—leading to the killing of the hamsters in that shop and the city government’s request for owners of recently acquired pet hamsters to surrender them to be euthanized. In contrast to those isolated instances with domestic animals, it’s far more challenging to control—as well as detect—transmission between white-tailed deer and humans, the researchers note.
Exactly how deer may have acquired coronavirus remains unknown too. As National Geographic reported in August 2021, deer may be in contact with people for research, conservation efforts, tourism, and hunting.
At the time, U.S. Department of Agriculture researchers theorized that deer could have encountered the virus through contaminated wastewater or from exposure to other infected species, such as mink.
The USDA did not respond to a request for comment for this article.
COVID antibodies were first detected by USDA researchers in 40 percent of tested white-tailed deer in Michigan, Illinois, New York, and Pennsylvania early in 2021. That work suggested that the animals had encountered the virus, but none of the deer appeared symptomatic. In Iowa, among other states, later studies detected COVID virus in deer. Richt says it’s now plausible that the virus is “circulating widely” in the animals in the U.S.
Boosting surveillance of humans and animal populations, especially deer, is of “particular importance” the Canadian team writes.
“At this time, there is no evidence of recurrent deer-to-human or sustained human-to- human transmission” of the virus found in deer and one person in Ontario, they wrote.
But identifying reservoir hosts capable of driving sustained transmission of the virus or passing it from one species to the next, they say, is essential.
“I think this is going to be a landmark study,” says Tracey McNamara, a veterinary pathologist at Western University of Health Sciences, in Pomona, California. She hopes “this will be the future of biosurveillance, where we will have to look across the spectrum of the animal kingdom—not just humans in isolation, not just animals in isolation, but doing that work jointly—which is what this group did, and that was pretty remarkable.”