COVID-19: The Alpha variant persists in white-tailed deer long after it has disappeared from humans

A study reveals that the Alpha variant of SARS-CoV-2, which has not been detected in humans for over a year, is still actively circulating among white-tailed deer in Ohio, in the United States. This finding confirms that these animals could become a significant reservoir for older variants and accelerate their evolution.   Between January and March 2023, researchers at Ohio State University analyzed samples from 519 deer harvested as part of wildlife management programs. The result: more than 12% of the samples tested positive for the SARS-CoV-2 coronavirus! The biggest surprise came from the discovery of five confirmed cases of the Alpha variant, even though it had not been detected in humans in Ohio since August 2021. These cases, all from the same site and collected on the same day (January 2023), demonstrate viral persistence for more than a year and a half after the variant had disappeared from the human population.  

Deer Carrying Multiple Variants

The researchers also identified 31 sequences corresponding to Omicron subvariants circulating in humans at the time. Phylogenetic clusters between regions 10 km apart suggest transmission among deer, independent of human contact. Thus, two dynamics coexist within the wildlife population: the persistence of older variants such as Alpha and the arrival of recent variants via new episodes of human-to-animal transmission.  

Adaptive mutations in deer

Scientists have observed an acceleration in the virus’s evolutionary rate in deer. Mutations occur twice as fast in deer as in humans. While most are neutral, some recur repeatedly in the spike protein. These mutations may be associated with immune escape mechanisms, although their functional impact remains to be clarified.  

Transmission Across States and Species

Through data analysis, researchers have identified at least three independent introductions of the Alpha variant in deer in Ohio, probable deer-to-deer transmission between Pennsylvania and Ohio, and genetic links distinct from those observed in chronically infected human patients, which allowed them to rule out this hypothesis. The authors also note that SARS-CoV-2 is actively circulating among white-tailed deer in several U.S. states (New York, Illinois, Virginia…), and even among other species such as mink.  

A zoonotic risk

Although no cases of direct transmission from deer to humans have been documented in Ohio, a suspected case was observed in Canada in 2022. This raises a concerning question: what happens if these “forgotten” variants in humans return via animals? “If SARS-CoV-2 becomes endemic in deer, it could not only persist but also evolve independently,” the authors warn. “This could lead to the emergence of variants adapted to wildlife, posing a zoonotic risk of re-emergence in humans.”  

Essential veterinary and environmental surveillance

The study calls for systematic surveillance of SARS-CoV-2 in wild deer, as well as the development of experimental studies on modes of transmission (aerosols, contaminated soil) and multispezies serosurveillance campaigns across North America to detect the presence of antibodies. The white-tailed deer, already affected by chronic wasting disease, is once again at the center of public health concerns.