Scientists have identified a new, highly mutated version of the coronavirus in white-tailed deer in southwestern Ontario, one that may have developed in animals since late 2020.
They also found a very similar viral sequence in one person in the area who had close contact with deer, the first evidence of possible transmission of the virus from deer to humans.
“The virus is evolving in deer and diverging in deer away from what we clearly see evolving in humans,” said Samira Mubareka, a virologist at the Sunnybrook Research Institute and the University of Toronto and an author of the new paper.
The report has not yet been published in a peer-reviewed journal, and there is no evidence that the deer lineage is spreading among humans, or poses an increased risk to humans. Preliminary lab experiments suggest that the lineage is unlikely to evade human antibodies.
But the paper went online just days after another team reported that the Alpha variant may continue to spread and evolve in Pennsylvania deer, even after it disappeared from human populations.
Together, the two studies suggest that the virus may have been circulating among deer for extended periods of time, increasing the risk that the animals could become a long-term reservoir of the virus and a source of future variants.
“There is certainly no need to panic,” said Arinjay Banerjee, a virologist at the University of Saskatchewan who was not involved in either study.
But, he added, “The more hosts you have, the more chances the virus has to evolve.”
Previous studies have shown that the virus is widespread in white-tailed deer. Research suggests that humans have repeatedly introduced the virus to deer, who then pass it on to each other. How humans spread the virus to deer remains a mystery, and so far there is no evidence that the animals return it to humans.
The Canadian study was a collaboration between more than two dozen researchers from institutions across Ontario. The scientists collected nasal swabs and samples of lymph node tissue from 300 white-tailed deer killed by hunters in Ontario between Nov. 1 and Dec. 31, 2021. Six percent of the animals, all from southwestern Ontario, tested positive for the virus. suggesting they were actively infected when they died.
The researchers sequenced the entire viral genomes of five infected deer and found a unique constellation of mutations that had not been documented before. A total of 76 mutations — some of which had previously been found in deer, mink and other infected animals — distinguish the lineage from the original version of the virus.
The deer samples were most closely related to viral samples taken from human patients in Michigan, not far from southwestern Ontario, in November and December 2020. They were also similar to samples taken from humans and minks in Michigan earlier that fall.
Those findings, as well as the rate at which the virus accumulates mutations, suggest that the new lineage may have diverged from known versions of the virus and developed undetected since late 2020.
But the exact path is unclear. One possibility is that humans passed the virus directly to deer and the virus then accumulated mutations as it spread among the deer. Alternatively, the lineage may have at least partially evolved into another, intermediate species — perhaps farmed or wild mink — which then somehow passed it on to deer.
“We don’t have all the pieces of the puzzle,” said Dr. Suresh Kuchipudi, a veterinary microbiologist at Penn State, who was not involved in the study, in an email. “We cannot rule out the involvement of an intermediate host.”
A viral sample collected from a human patient in southwestern Ontario in the fall of 2021 closely matched the deer samples. That individual is known to have had “close contact” with deer, the researchers said.
(They couldn’t release more details about the nature of this contact for privacy reasons, though Dr. Mubareka noted that people shouldn’t worry about occasional, indirect encounters, such as simply letting a deer roam their backyard.)
The sample size is small, scientists warned, and there’s no conclusive evidence that the person contracted the virus from deer. “We don’t have enough information yet to confirm that transmission to humans,” said Roderick Gagne, an ecologist in natural diseases at the University of Pennsylvania School of Veterinary Medicine.
But at the time the human sample was collected, Ontario sequenced samples of the virus from everyone in the region who tested positive on a PCR test. The researchers found no other people infected with similar versions of the virus, making it less likely to evolve independently in humans.
“If it had been widespread in humans, even to a limited extent in humans, we would have picked it up,” said Dr. mubareka.
There is also no evidence that the person infected with the lineage passed the virus on to anyone else.
And early data suggests that existing vaccines should still be able to protect against the lineage. Antibodies from vaccinated people were able to neutralize pseudoviruses — harmless, non-replicating viruses — designed to resemble the deer line, the scientists found.
In the second study, scientists at the University of Pennsylvania Veterinary and Medical Schools analyzed nasal swabs from 93 deer that died in Pennsylvania in the fall and winter of 2021. Nineteen percent were actively infected with the virus. When the researchers sequenced seven of the samples, they found that five of the deer were infected with the Delta variant, while two were infected with Alpha.
At the time the samples were collected, Delta was rife among the human population of the United States, but the alpha wave that hit Americans in the spring of 2021 had long faded.
“Alpha seems to persist in the white-tailed deer even when it’s not circulating in humans,” said Eman Anis, a microbiologist at the University of Pennsylvania School of Veterinary Medicine and an author of the study.
Indeed, the Delta samples in deer were genetically similar to those in humans, suggesting it had crossed species boundaries relatively recently. But the two alpha sequences were more significantly different from human lineages. (They also differed significantly from each other, suggesting that the variant had been introduced into the deer population at least twice.)
“The main implication would be that the deer support transmission and infections within their populations,” said Dr. Gagne, an author of the study in Pennsylvania. “So that’s not just, you know, a human overflow event, deer get infected and then it seeps out.”
Whether these genera will continue to circulate and evolve in deer is unknown, as is the risk they may pose to humans and other animals.
“Based on current information, I would say that the risk of wildlife, including deer, spreading the virus to humans is low,” said Jeff Bowman, a research scientist with the Ontario Ministry of Northern Development, Mines, Natural Resources. and Forestry and an author of the Canadian newspaper.
But ongoing surveillance is critical, scientists say. dr. Mubareka suggested officials should improve wastewater screening in Ontario and other nearby regions to look specifically for the deer line — and to make sure it doesn’t happen again.
Experts also urged people to continue to follow guidelines from public health authorities, which include not feeding deer or other wildlife and wearing gloves when slaughtering game.
“We would also need to shrink the largest reservoir for this virus, which is us,” said Dr. Mubareka, “to make sure we don’t run into deer all the time and create these new lineages.”
