“I’m not sure exactly how we’re going to pay for this, to be honest,” said Samira Mubareka, a microbiologist at Sunnybrook Health Sciences Centre in Toronto, about the work she’s doing monitoring COVID-19 in wildlife. “I just heard we’re getting another set of samples. I don’t want to say no, because if we’re finding things like this, we can’t just say no. We’ll have to scrape together some funding somehow.”

By “things like this,” Mubareka means the presence of SARS-CoV-2, the virus that causes COVID-19, in white-tailed deer in Canada. In December, Environment and Climate Change Canada announced positive tests in deer in Quebec, followed by cases confirmed in Ontario, Saskatchewan and, just last week, Manitoba

Deer all over the United States are positive too, and the U.S. Department of Agriculture has reported that over 30 per cent of white-tailed deer in some northeastern states have antibodies suggesting a previous COVID-19 infection. It’s not as bad here: antibody tests have been positive in about six per cent of Canadian deer. The animals are almost certainly getting the virus from humans — directly, via an intermediary like an indoor-outdoor cat or, least likely, from wastewater — and our population is less dense and more vaccinated. 

That doesn’t mean we can let our guard down. The day after deer in Manitoba were declared positive, Mubareka and a team of researchers led by the Canadian Food Inspection Agency released research announcing the discovery of a new lineage of SARS-CoV-2 in Ontario deer. A lineage isn’t a variant, but it’s divergent enough to take notice of, especially since there was also possible evidence that the lineage had been transmitted from deer to a human. Though not yet peer-reviewed, the study shows that consistent monitoring is crucial.

Samira Mubareka
Early in the pandemic, microbiologist Samira Mubareka isolated the genetic sequence of the SARS-CoV-2 virus in a lab. She said genomic surveillance was underfunded then, and that monitoring the virus in animals still suffers from lack of money and organization. Photo: Sunnybrook Health Sciences Centre

Which is why Mubareka isn’t going to say no to samples from provincial ministries, zoos or universities, even if it’s not always clear how she’ll pay her researchers. “It’s definitely been a patchwork we’ve kind of cobbled together, like ‘okay, I’ll take one person’s salary line from this grant,’ ” she said. 

Two years in, one of Canada’s most important COVID-19 researchers still doesn’t know when or even if she’ll have stable funding for a key pillar of her work. It’s the same situation she faced at the beginning of the pandemic, when she kicked off her human genomic sequencing program. In March 2020, when there were just 74 known cases of COVID-19 in the country, Mubareka and colleagues at Sunnybrook and the University of Toronto isolated the genetic sequence of the SARS-CoV-2 virus in a lab, a crucial step in developing treatments and vaccines. 

“There was no funding program for it, we just did it, because it just had to be done,” said Mubareka. Eventually, Ontario developed a formal, funded human genomic surveillance program for SARS-CoV-2. 

“One thing I’ve learned in the pandemic, if you wait for the funding to do anything, then it’s too late. You almost have to do it first and really, really, really hope that the value is recognized. But I don’t know if that will happen with this. I hope it does.” 

The federal department at the top of the wildlife monitoring chain is Environment and Climate Change Canada. In an email, a spokesperson said that “non-government organizations involved in wildlife health surveillance … obtain funding from governments and other agencies, and pool those resources to support wildlife health programs throughout the country.” The email also said that wildlife testing “will continue into the spring of 2022 after which a decision will be made by all partners on (a) possible extension .…” 

With the spring of 2022 just weeks away, this sort of uncertainty is stressful. It’s an issue Mubareka shares with researchers in Canada and around the world. They say not enough public health attention — or money — is directed towards figuring out how widespread the virus is in both wildlife and domestic animals. That’s even though the World Organisation for Animal Health has recorded the virus in 17 species in 34 countries, including deer, dogs, mink, otters, ferrets, gorillas and all sorts of cats, big and small.

The good news is, there’s no need to panic about catching COVID-19 from your puppy: putting aside the latest deer findings, mink are the only animal known to infect humans. It’s also a positive that most animals don’t get very sick from the disease. But as with humans, widespread infection is a risk in any population that can’t be isolated, vaccinated or in dire situations, culled. The worst case scenario for an animal population is a wave of deaths. For humans it would be a viral mutation that jumps back to us, especially one that makes COVID-19 more dangerous. 

With luck, the spread of COVID-19 in animals won’t ever explode or affect humans. Even then, researchers wish more time and money were directed towards understanding zoonotic diseases —  infections passed from animals to humans. There also needs to be more attention paid to the environmental factors at play, such as habitat loss and climate change. One barrier to that is painfully Canadian: the jurisdictional hot potato played between government departments about just whose problem this is, exactly. 

All sorts of cats, big and small, have gotten COVID-19. In South Africa, virologist Maritjie Venter has found positive cases in three lions and a puma, the only recorded animal cases on the entire African continent. Photo: Gary Whyte / Unsplash

Climate change, urban expansion, demand for meat: human behaviour makes zoonotic illnesses more likely

Over the past 20 years or so, a model known as One Health has become increasingly important in the global field of public health. It’s an approach that aims to go beyond treating today’s illness with today’s cure, instead considering complex issues through a multidisciplinary lens that encompasses not just treatments, but prevention. Mubareka is currently working with the Royal Society of Canada to define what One Health policy should look like here  — “if you ask three people, you’ll get 10 different opinions on what One Health is” — but an understanding that human health is intertwined with the health of the environment and ecosystem we live in is core to the concept. 

As COVID-19 gripped the world, One Health researchers knew animal cases were inevitable. It didn’t take long for them to show up. Domestic cats and dogs in multiple countries were diagnosed early on: in March 2020, the Hong Kong government advised people to stop kissing their pets. In April, tigers at the Bronx Zoo in New York City developed respiratory illness symptoms. One tested positive, then a few more, followed by a group of lions. 

“That sort of rang the first alarm bells,” said Marietjie Venter, a virologist and professor at the University of Pretoria in South Africa, whose specialty is respiratory diseases and zoonotic viruses. Her One Health program has long studied respiratory illness in animals, so when COVID-19 showed up, she registered with the national and provincial departments of agriculture to test any wildlife with possible symptoms for the virus. 

In the past two years, her team has identified the virus or its antibodies in one puma, in July 2020, and three lions, in July 2021, all at the same zoo in Johannesburg. Those are the only cases that the World Organisation for Animal Health, an international body of 182 member countries monitoring animal diseases, has recorded for the entire African continent. 

“We think it is highly unlikely that these are the only cases,” Venter said during a February phone call. “We just think this zoo is really good, that they would actually work with us to identify these cases.” It’s mandatory for countries to report positive results to the World Health Organisation for Animals, but testing is voluntary. While there are over 25 million genomic sequences recorded for SARS-CoV-2 in humans, there are only about 1,500 recorded for animals.  

Computational biologist Darren Martin, left, and virologist Marietjie Venter, right, are both in South Africa. They said surveillance of COVID-19 in animals is critical in Africa, a continent with abundant wildlife and multiple countries with vulnerable healthcare systems, but so far it’s not happening on a wide scale. Photos: supplied by Darren Martin and Marietjie Venter

Surveillance is crucial on a continent with abundant wildlife and multiple countries with vulnerable healthcare systems, but so far it’s not happening on a wide scale. Venter’s colleague, Darren Martin, a professor at the Institute of Infectious Diseases and Molecular Medicine at the University of Cape Town, doesn’t think testing wild animals would necessarily be difficult. Testing can be done with fecal swabs and, as he put it during a video call, “the coronavirus is just sitting on leaves because animals are walking around and peeing and shitting on everything.”

A high level of circulating virus could turn an animal population into a reservoir, where SARS-CoV-2 lies in wait for humans’ antibodies from vaccines or previous infections to wane. Martin particularly wants to know which animals might support long-term infections, which make mutations more likely. 

“It’s a crucial thing for figuring out whether these other species are suitable hosts for the accelerated evolution of coronaviruses,” he said. Venter found that some big cats tested positive for seven weeks, though they didn’t necessarily have a high enough viral load to be infectious the whole time. 

A silver mink in a cage
Millions of mink have been culled worldwide because of COVID-19 outbreaks on farms. All of Canada’s mink farm outbreaks have been in B.C. and in the fall of 2021, the provincial government announced a plan to phase out the industry, with an immediate ban on breeding. Photo: Gregory Golovin / iStock

Other than humans, the animal that has suffered the most from COVID-19 is farmed mink. From early on, rapid spread through mink farms sent panicked shockwaves through the industry, health researchers and governments, not least because the small animals are prone to escaping, which could introduce viruses to other species. In November 2020, outbreaks on 200 mink farms in Denmark led to the culling of about 17 million of the animals and a ban on breeding. 

Canada’s three mink farm outbreaks have all been in B.C., where four animals escaped from their cages last summer. Though the Ministry of Agriculture, Food and Fisheries reported all as re-captured, COVID-19 seems to have ended the province’s industry. Last November, the ministry announced a plan to phase out mink farms by 2025, with an immediate ban on breeding; in February, breeders announced a court challenge, citing lack of consultation. 

While it’s a tragedy for mink, rampant spread in an animal population is not great for humans either. First, SARS-CoV-2 jumped to humans from an animal. Then, through “reverse zoonosis,” it moved from humans to other animals. After spreading quickly through tightly packed farmed mink, it came back to us again. One fear is that the animals could incubate a new variant that infects us, especially a particularly ferocious one that kickstarts a fresh wave of severe illness. 

Claire Jardine, left, is the regional director for Ontario and Nunavut at the Canadian Wildlife Health Cooperative. J. Scott Weese, right, is the director of the University of Guelph Centre for Public Health and Zoonoses. Both are on the team looking into a possible new lineage of SARS-CoV-2 in Ontario deer, which may have been passed on to a human. Photos: supplied by Claire Jardine and J. Scott Weese.

The leading theory of the origins of SARS-CoV-2 is that it came from a Chinese horseshoe bat, probably with another animal acting as intermediary. At this point, we’ll never know for sure, said J. Scott Weese, a professor at the Ontario Veterinary College and director of the University of Guelph Centre for Public Health and Zoonoses. What we do know is that zoonoses are exacerbated by human behaviour.

“It’s been said that we’re in a pandemic era because we’re creating a lot of situations for increased risk,” said Weese. “Climate change changes geographic ranges of animals. Anything that brings us in closer contact with animals, especially animals we haven’t had contact with before, increases our risk of being exposed to their pathogens.”

“Urban expansion, armed conflict, population displacements, increasing wealth with an increase in demand for meat protein, which can include changes with farming, it can include bush meat, wet markets — all those things kind of come together.” 

Animals have always incubated new viruses and humans have always been exposed to them, but most don’t make us sick. Even if they did, Weese said, a virus that emerged a century or two ago might hit a family or a small community and then have nowhere else to go. Now, the human population is increasingly dense and mobile, giving viruses a chance to spread far, wide and fast. “We’re increasing the risk of us encountering new diseases and we’re increasing the risk of spreading them when we do encounter them.” 

Weese is another researcher who knew early on that it was important to look at SARS-CoV-2 in animals, and who had trouble getting government attention. By January 2020, he was sending emails to Ontario’s Ministry of Health pointing out that the 2003 SARS virus infected cats and spread among them, just one reason he thought it was important to figure out which animals were susceptible to SARS-CoV-2, and whether they could infect each other or people. 

“We basically got crickets,” he said. “We had a hard time getting buy-in.” A cross-country working group of researchers came together fairly quickly, he said, but “while there are people with strong understanding of the need for a One Health approach, that’s not always reflected by actions,” especially at “higher levels.” (Ontario’s health ministry did not respond to a request for comment.)

And that disinterest seemed international. “[Centers for Disease Control] in the U.S., they kept coming out with statements saying ‘okay, well, there’s no evidence that this virus can infect animals,’ which is true — because nobody looked,” Weese said. The New York Times just asked U.S. researchers about animal surveillance there: “I am ripping my hair out” in frustration, one replied. 

Weese and his team took it upon themselves to set up a program for pets, donning protective equipment to test dogs and cats in homes with confirmed cases. The results were both startling and reassuring. About 35 per cent of dogs were positive, but almost none got sick. And while over 50 per cent of cats got the virus, they weren’t much worse off, symptom-wise. Best of all, neither seemed to be infecting humans. “We got lucky to some degree that animals aren’t playing a major role,” said Weese.

And truly, we have mostly lucked out. No Canadian pets have definitively died from COVID-19. Other than deer, researchers have tested and ruled out 16 wild animal species in Ontario and Quebec. 

Globally, mink and hamsters are the only farmed animals that have tested positive in large numbers. The Canadian Food Inspection Agency, which oversees COVID-19 monitoring in livestock, pets and zoo animals, has done its own tests of turkeys, chickens and pigs and found that none of them had high susceptibility to SARS-CoV-2 or the ability to spread the virus. In an email, an agency spokesperson said that there are no international reports of cows, sheep or goats being infected with SARS-CoV-2, or of the virus being found in cattle “tissues used for human consumption.” Because of these findings, there is no ongoing monitoring of these animals.

A photo illustration of a gorilla over a background of viruses.
Dossi, a gorilla at the Calgary Zoo, is pregnant. In February, the zoo asked visitors to continue masking in the gorilla pavilion to protect her. Photo: Calgary Zoo. Illustration: Shawn Parkinson / The Narwhal

Zoo animals in Canada have been spared too. The Calgary Zoo is eagerly awaiting Canadian Food Inspection Agency approval of an animal vaccine, said Jamie Dorgan, director of animal care, health and welfare. It’s already being used by zoos in countries including Chile and the United States: the Associated Press reported that 18 gorillas at the Atlanta zoo developed COVID-19 last fall while waiting for vaccine delivery. 

“We are obviously keeping our eyes very, very open with our primates, specifically, and our large cats,” said Dorgan. In February, the zoo asked people visiting the gorilla pavilion to continue masking after the provincial mandate lifts, since Dossi, one of the primates, is pregnant. 

In Calgary, rapid tests using fecal swabs are done when an animal has symptoms, and so far none have been positive. Weese, who advises the Toronto Zoo, agrees testing is only needed after a known exposure. The chance of a random positive is low and testing can be stressful for the animal, sometimes requiring sedation. “Collecting nasal swabs from a pet cat is hard enough,” he wrote in an email. 

He believes that animal surveillance is most important “early in a pandemic, and late in a pandemic.” In the beginning, containment will be much harder if a new virus affects animals other than humans, who can be told to isolate and will (mostly) listen. Then, “as things start to wane, you get to the point where very few people are having infections hopefully, but then animals might be your biggest source of exposure,” said Weese. 

Which is, perhaps, where we are, at least in places where vaccines are plentiful and uptake is high. With less ability to hook into humans, SARS-CoV-2 will find other hosts. Scientists would like to keep an eye on rodents, which have tested positive after inoculation in labs but not in the wild: in New York City, researchers are trying to figure out if a mysterious variant in wastewater that hasn’t been seen in humans is being carried and spread by the urban rat population

Rodents are key to one of three leading theories on the origins of Omicron. The first is that the variant came from an under-surveilled population, such as a country with limited access to tests. The second is that it popped up in an immunocompromised population living in tight quarters, perhaps a hospital or long-term care home: there, SARS-CoV-2 would have a chance to stick around in a body that had a hard time ridding itself of the virus, mutate, get passed on to another vulnerable body, on and on until something strong enough to infect healthier people emerged. 

The last theory is rodents which are social, reproductive creatures with lots of interaction with humans — exactly why the Canadian Wildlife Health Cooperative was already monitoring pathogens in Ontario’s urban rat population pre-pandemic. 

“We were able to sort of piggyback on that particular project to monitor for SARS-CoV-2,” said Claire Jardine. She’s regional director for Ontario and Nunavut at the cooperative, which is a national partnership between five veterinary schools and a lab in Abbotsford, B.C.

Much COVID-19 wildlife surveillance is done via what Environment Canada called “ongoing research and monitoring programs” like that one. Throughout the country, samples have long been collected to test for another deer illness, chronic wasting disease, and the provinces of Saskatchewan and Ontario confirmed their existing programs have been adapted during the pandemic. 

In Ontario, hunters can voluntarily take deer heads to drop-off sites to be tested for chronic wasting disease, which is neurological. Now, samples are also taken from the animals’ noses or thoracic cavities, which are sent to labs like the one at Sunnybrook Health Sciences Centre for SARS-CoV-2 assessment. 

In 2020, 742 Ontario deer were sampled for chronic wasting disease out of over 50,000 hunted, or less than two per cent. A spokesperson for the Ministry of Northern Development, Mines, Natural Resources and Forestry said in an email that there will be drop-off locations in more areas of the province this year, and a ministry scientist said that SARS-CoV-2 samples are collected in other ways as well. 

Jardine was also on the team that just identified a possible new lineage of SARS-CoV-2 in deer, and said there’s currently no reason to panic. Although the potential transmission to a human is unsettling, it looks like existing vaccines “effectively neutralized” the altered virus, preventing it from spreading person-to-person. 

While she’s glad existing programs can be adapted, Jardine said the ability of the Canadian Wildlife Health Cooperative to monitor animal diseases was already maxed out before the pandemic. It’s a non-governmental organization with multiple funders, and could definitely benefit from a government commitment to COVID-19 monitoring. 

“We don’t have a lot of surge capacity to deal with these new issues, and it kind of limits our ability to respond,” she said. “We’re trying, and everyone’s sort of playing catch-up, but wouldn’t it be nice if we didn’t have to do that?”

A photo illustration of a deer over a background of viruses.
Vaccinating deer would be tricky, requiring catching and releasing thousands of animals, or administering an oral vaccine at bait stations. Photo: Unsplash. Illustration: Shawn Parkinson / The Narwhal

‘Who should pay for it?’ Two years in, Canada’s monitoring of COVID-19 in animals still lacks structure

Ultimate responsibility for all of this lies with Environment and Climate Change Canada, which oversees wildlife, and the Canadian Food Inspection Agency, which is in charge of livestock, zoo animals and pets. Both liaise with the Public Health Agency of Canada. 

Test results are collected from, well, everyone: multiple provincial and territorial ministries that oversee natural resources and the environment; Parks Canada; the Canadian Wildlife Health Cooperative; and various other academic labs, like the one run by Weese.

Analysis is done by Sunnybrook, the National Microbiology Laboratory in Winnipeg or the Prairie and Northern Wildlife Research Centre and Western College of Veterinary Medicine in Saskatoon. All “non-negative” tests are sent via the Canadian Food Inspection Agency to the National Centre for Foreign Animal Disease in Winnipeg for confirmation and sequencing. After that, the public and Canada’s delegate to the World Organisation for Animal Health are informed of any positive results. 

“It’s hard to really pinpoint who’s responsible,” said Mubareka. “At least for humans, [monitoring] SARS, coronavirus, genomics, that’s clearly public health, right? In this situation, you have multiple federal agencies, you have multiple provincial agencies, and then you have multiple academic content experts that are all contributing. So who should pay for it? There’s kind of no one.” 

Along with stable funding, she said, there’s a need for a standardized framework that would make it easier to compare data across jurisdictions.

“The question is, what can we anticipate in the next few years in terms of setting up a more formal screening program?” she said. Asked about data consistency, Environment Canada’s spokesperson said in an email that “co-ordination of data collection activities is achieved through collaborative mechanisms and sample and data sharing agreements.” 

The department said that Canada is taking a One Health approach to monitoring COVID-19 in animals. And it’s true that such a big undertaking requires a multidisciplinary approach, which by definition will have numerous participants. But two years in, the lack of structure is concerning. 

Weese attributes the holes to “lack of awareness and lack of uptake.” 

“Anytime you’re in a pandemic, there are things that are higher priority and lower priority, and animals are lower priority,” he said. Though things are looking better now, “it took them a long time, and a series of changing messages before they really acknowledged potential animal issues. …”

In South Africa, Venter and Martin have seen firsthand what happens when proactive research unearths an unpleasant finding: the wave of international scapegoating that happened after Lancet Laboratories identified the Omicron variant in November 2021. Governments across the world, including Canada, banned flights from multiple African countries even though most hadn’t had definitive Omicron cases yet, many had low transmission rates overall and there was no evidence that just because the variant was found on the continent that it had originated there. 

“What it says is if you have the capability to do genomic sequencing and have a high level of efficiency … those capabilities must be driven underground,” South African health minister Joe Phaahla said at the time, adding that researchers might “feel that it is a risk to disclose” new discoveries. 

“People don’t actually want to know,” Martin said, about the reality of just how many animals are infected with SARS-CoV-2. He imagines the thought process of a government official: “So you want us to give you a quarter billion dollars so that you can go and exhaustedly sample all the species that SARS-CoV-2 can infect and work out which of them are the ones where this viral evolution is happening? Cool. That’s fine. That’s a good idea. But what are you going to do when you find those species?” 

It’s a worthwhile question, one to consider in the case of white-tailed deer, whose infections are starting to get close attention just as many humans declare the pandemic over, whether that’s scientific fact or not. Restrictions are being lifted worldwide, and more virus circulating among us means more virus capable of spillover into animal populations. 

Vaccinating a wild population would be tricky at best, requiring either catching and releasing thousands of animals, or an oral vaccine administered through bait stations. “I suspect these would be major limitations,” said Weese, who was also on the team that just identified the possible new lineage.

Culls are distasteful and won’t work anyway, if the practice that causes the virus to spread continues. “You just can’t cull enough deer to prevent a disease that gets transmitted really easily,” he said. “We know that from dogs and rabies, culling doesn’t work, you have to use other control measures. If this virus is actually circulating in deer and you went through and culled a lot of them, you’d still leave some infected ones behind.” 

“Or even if we got rid of all the infected deer, they’d still be susceptible to getting infected from us.” While other animals do present a COVID-19 risk to humans, it’s largely because of the threat we pose to them. 

Updated March 5, 2022 at 2:25 p.m. ET: This story was updated to clarify that J. Scott Weese occasionally advises the Toronto Zoo, but is not affiliated with the zoo in an official capacity.

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