Deer harbor out-of-circulation SARS-CoV-2 strains, study finds

White-tailed buck

Hope Abrams / Flickr cc

Scientists analyzing samples collected from white-tailed deer in New York state have identified the Alpha, Gamma, and Delta SARS-CoV-2 variants well after they caused widespread COVID-19 in people, representing a reservoir for the strains and a potential future risk to humans.

The Cornell University researchers who conducted the study, published yesterday in Proceedings of the National Academy of Sciences, say it represents one of the most comprehensive approaches to date to assess the prevalence, genetic diversity, and evolution of SARS-CoV-2 in white-tailed deer.

A March 2022 study by some of the same investigators and their colleagues found SARS-CoV-2 in up to 40% of deer populations across five states. And a December 2021 study led by Ohio State researchers found a 36% incidence in Ohio. The United States is home to an estimated 30 million white-tailed deer, the most abundant large animal in the country.

Variants in deer well after human circulation

The Cornell scientists analyzed 5,462 samples collected from the lymph nodes in the throats of deer harvested in late 2020 and late 2021, during the hunting season. They detected SARS-CoV-2 RNA in 17 samples (0.6%) from 2020 and in 583 samples (21.1%) from 2021 and noted several hot spots of infection within the state.

The team compared the deer isolates with human isolates from March 2020 to April 2022.

[The] virus ... potentially, has now found a new wildlife reservoir in North America.

Sequencing of 164 deer samples revealed Alpha, Gamma, and Delta variants at a time when they had largely disappeared from the human population. "Notably, while the Alpha and Gamma variants were circulating in WTD [white-tailed deer] in NY in November and December 2021," the authors wrote, "detection of these [variants] in humans peaked between April and June 2021, with only sporadic detections after August.

"Three Alpha sequences were reported in NY in September 2021 based on data available at GISAID, with a single last detection occurring in February 2022, while the two last Gamma sequences were detected in NY in October 2021. All these latest Alpha and Gamma detections in humans in the state occurred in New York City, which was not included in the WTD sampling in this study."

GISAID (the Global Initiative on Sharing Avian Influenza Data) is a global database for sharing sequences of influenza viruses and SARS-CoV-2.

In a Cornell University news release, senior author Diego Diel, DVM, PhD, said, "A virus that emerged in humans in Asia, most likely after a spillover event from an animal reservoir into humans, apparently, or potentially, has now found a new wildlife reservoir in North America."

Dozens of mutations in deer viruses

Diel noted, "When we did sequence comparisons between those viruses recovered from white-tailed deer with the human sequences, we observed a significant number of mutations across the virus genome."

He said that some of the viruses had up to 80 mutations compared with the human sequences, providing further evidence that they had likely been circulating in the deer for some time. The mutations suggest the virus has adapted to deer, possibly making it more transmissible among them, Diel added.

It is very important to continue to monitor the virus in these animal populations.

"Because of the evidence obtained in our study, it is very important to continue to monitor the virus in these animal populations to really understand and track changes that could lead or favor spill back into humans and other wildlife," he added.

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