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Deer may be a reservoir of ancient coronavirus variants, study finds

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A white-tailed deer at the Penn State Deer Research Center in State College, Pennsylvania on Feb. 2, 2022. (Hannah Yoon/The New York Times)

coronavirus variants

A white-tailed deer at the Penn State Deer Research Center in State College, Pennsylvania on Feb. 2, 2022. (Hannah Yoon/The New York Times)

Alpha and gamma variants of the coronavirus continued to circulate and evolve in white-tailed deer, even after ceasing to spread widely among humans, according to a new study.

It is not known if the variants still circulate in deer. “That’s the big question,” said Dr. Diego Diel, a virus expert at Cornell University and author of the study, which was published Tuesday in Proceedings of the National Academy of Sciences.

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 over into human populations.

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“This is a very large population of wildlife in North America that has constant and very intense contact with humans,” Diel said.

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Previous studies on deer have suggested that humans have repeatedly introduced the coronavirus to white-tailed deer populations in the United States and Canada and that deer can spread the virus to each other. Scientists don’t know how people transmit the virus to deer, but they have speculated that it could happen when people feed the deer or the deer encounter human trash or waste.

The magnitude of the risk that infected deer pose to humans remains unclear. Scientists have documented a 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.

For the new study, Diel and his colleagues analyzed about 5,500 tissue samples taken from deer killed by hunters in New York State from September to December 2020 and 2021.

In the 2020 season, only 0.6% of samples tested positive for the virus, a figure that rose to 21% in the 2021 season.

Genetic sequencing revealed that three variants of concern – alpha, gamma, and delta – were all present in deer during the 2021 season.

At the time, the delta was still prevalent among the human residents of New York. But alpha and gamma were all but gone, especially in 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 taken from humans. In deer, all three variants had novel mutations that distinguished them from human sequences. But the deer alpha and gamma samples diverged more significantly from the human sequences than the deer delta samples, the researchers found.

Together, the results suggest alpha and gamma likely circulated among deer and accumulated new mutations for months after spilling over from the human population, experts said.

“This supports the argument that deer may maintain lineages or variants that no longer circulate in humans,” said Dr. Suresh Kuchipudi, a veterinary microbiologist at Pennsylvania State University, who has no not participated in the new research.

The discovery not only raises concerns that deer could be a source of new coronavirus variants that could spread to humans; it also raises the possibility that the virus is evolving in a way that poses a greater risk to wild animals, he added. “It could end up becoming an animal health issue as well,” Kuchipudi said.

The study highlights the need for continued monitoring of wild deer populations, Kuchipudi and Diel said. Diel and his colleagues are preparing to analyze deer samples from the 2022 hunting season to determine if the virus remains prevalent among deer and what variants may be circulating.

The Centers for Disease Control and Prevention recommends deer hunters take a variety of basic precautions to reduce the risk of infection, including wearing masks when handling game and washing hands thoroughly afterward.

© 2023 The New York Times Company

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