White-tailed deer ­– the most abundant large mammal in North America – are harboring SARS-CoV-2 variants that were once widely circulated but no longer found in humans.

The study, “White-tailed Deer (Odocoileus virginianus) May Serve as a Wildlife Reservoir for Nearly Extinct SARS-CoV-2 Variants of Concern,” which was published Jan. 31 in the journal Proceedings of the National Academy of Sciences, represents one of the most comprehensive studies to date to assess the prevalence, genetic diversity and evolution of SARS-CoV-2 in white-tailed deer. The study focused on the white-tailed deer population in New York.

“One of the most striking findings of this study was the detection of co-circulation of three variants of concern – alpha, gamma and delta – in this wild animal population,” said Dr. Diego Diel, associate professor of population medicine and diagnostic sciences and director of the Virology Laboratory at the Cornell University College of Veterinary Medicine’s (CVM) Animal Health Diagnostic Center. 

Although the exact cause remains unknown, research indicates that over the course of the pandemic, deer have become infected with SARS-CoV-2 through ongoing contact with humans, possibly from hunting, wildlife rehabilitations, feeding of wild animals or through wastewater or water sources.

This study was made possible thanks to a program co-designed by Dr. Krysten Schuler, assistant research professor of public and ecosystem health at CVM and a senior author of the study. As director of the Cornell Wildlife Health Lab, Schuler has worked with the New York State Department of Environmental Conservation to design a statewide surveillance program for chronic wasting disease in white-tailed deer. The program collected thousands of samples of deer lymph tissues taken from deer killed by participating hunters.

“We were able to leverage those samples that had already been collected and then test them for SARS-CoV-2, so we had a good statewide representation,” Schuler said.

The testing revealed potential hotspots of infection across the state, including seven clusters where samples from a defined geographic area all contained the same variant. Samples from one cluster, for example, confined to one county, all tested positive for the gamma variant. Similar clusters were also found for alpha and delta variants in different locations in the state.

When researchers compared the genomic sequences of the variants found in deer with sequences of the same variants taken from humans across New York, they found the viruses had mutated in the deer, suggesting the variants had likely been circulating in deer for many months. By the time alpha and gamma variants were detected in deer, for example, there was no evidence of these viral strains still circulating in humans. In fact, when they were found in deer, neither variant had been detected in humans in New York for four to six months.

In future work, Diel and colleagues hope to assess the effect of the viruses’ mutations, including whether these changes make the virus more or less capable of binding to human receptors. Currently, only one study published in Canada has documented a case of a human being infected by SARS-CoV-2 that originated in deer.   

“Obviously, humans are still the primary reservoir and the likelihood of anybody getting SARS-CoV-2 is from another human rather than a deer,” Schuler said.

More research is needed to confirm whether white-tailed deer have truly become a reservoir for these variants now extinct in humans or whether the variants will disappear over time in the wild. Other questions include whether the deer might spread SARS-CoV-2 to other wildlife animals, including predators.  

Written by Krishna Ramanujan; the full version of this story appears in the Cornell Chronicle.

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