The Alpha and Gamma variants of the coronavirus continued to circulate and evolve in white-tailed deer, even after they stopped spreading widely among people, a new study suggests.
Whether the variants are still circulating in deer remains unknown. “That’s the big question,” said Dr. Diego Diel, a virologist at Cornell University and an author of the study, which was published in Proceedings of the National Academy of Sciences on Tuesday.
But the findings, which are based on samples collected through December 2021, provide more evidence that deer could be a reservoir of the virus and a potential source of future variants, which could spill back into human populations.
“It is a very large wildlife population in North America that has constant and very intense contact with humans,” Dr. Diel said.
Previous studies of deer have suggested humans have repeatedly introduced the coronavirus into white-tailed deer populations in the United States and Canada and that deer can spread the virus to one another. Scientists are not sure how people are passing the virus to deer, but they have speculated that it might happen when people feed deer or deer encounter human trash or waste.
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The scale of the risk that infected deer pose to humans remains unclear. Scientists have documented one case that most likely resulted from deer-to-human transmission in Ontario, and they note that hunters and others who have regular contact with the animals could potentially catch the virus from them.
For the new study, Dr. Diel and his colleagues analyzed about 5,500 tissue samples collected from deer killed by hunters in New York State from September through December in the years 2020 and 2021.
During the 2020 season, just 0.6 percent of the samples tested positive for the virus, a figure that rose to 21 percent during the 2021 season.
Genetic sequencing revealed that three different variants of concern — Alpha, Gamma and Delta — were all present in deer during the 2021 season.
At the time, Delta was still prevalent among New York’s human residents. But Alpha and Gamma had practically vanished, especially in the rural parts of the state where the infected deer were found.
The scientists also compared the genomic sequences of the viral samples they detected in deer to those that had been collected from humans. In the deer, all three variants had new mutations that set them apart from the human sequences. But the Alpha and Gamma samples from deer diverged more significantly from the human sequences than the Delta samples from deer did, the researchers found.
Together, the results suggested that Alpha and Gamma had likely been circulating among deer and accumulating new mutations for months after spilling over from the human population, experts said.
“It supports the argument that deer can sustain lineages or variants that are no longer circulating in humans,” said Dr. Suresh Kuchipudi, a veterinary microbiologist at Pennsylvania State University, who was not involved in the new research.
The finding not only raises concerns that deer could be a source of new coronavirus variants that could spread back to people; it also raises the possibility that the virus might evolve in ways that pose a greater risk to wild animals, he added. “It could also end up becoming an animal health problem,” Dr. Kuchipudi said.
The study highlights the need for ongoing surveillance of wild deer populations, Dr. Kuchipudi and Dr. Diel said. Dr. Diel and his colleagues are preparing to analyze deer samples from the 2022 hunting season to determine whether the virus remains widespread among deer and which variants may be circulating.
The Centers for Disease Control and Prevention recommends that deer hunters take a variety of basic precautions to reduce the risk of infection, including wearing masks while handling game and washing hands thoroughly afterward.