It is well known that SARS-CoV-2 can be transmitted to animals. Some infected animals have even made headlines, like the tigers in the Bronx Zoo that tested positive for COVID-19 in 2020. In addition to captive animals, other documented animal infections have been noted in a few wildlife species, notably the white-tailed deer and feral mink. But SARS-CoV-2 has the potential for a broad host range, and little is known about other animals that may be infected.

Now, a new study significantly expands the number of species examined and the understanding of SARS-CoV-2’s transmission to and among wildlife. Investigators tested animals from 23 common Virginia species for both active infections and antibodies indicating previous infections. The findings suggest that SARS-CoV-2 is widespread among wildlife species, with positive detections of SARS-CoV-2 RNA in six common backyard species: the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022–September 2023 across Virginia and Washington, D.C. In addition, the data suggest that areas with high human activity may serve as points of contact for cross-species transmission.

This work is published in Nature Communications in the paper, “Widespread exposure to SARS-CoV-2 in wildlife communities.

“This study was really motivated by seeing a large, important gap in our knowledge about SARS-CoV-2 transmission in a broader wildlife community,” said Joseph Hoyt, PhD, assistant professor of biological sciences in Virginia Tech’s College of Science. “A lot of studies to date have focused on white-tailed deer, while what is happening in much of our common backyard wildlife remains unknown.”

The research team collected 798 nasal and oral swabs across Virginia from animals either live-trapped in the field and released, or being treated by wildlife rehabilitation centers. The team also obtained 126 blood samples from six species.

The highest exposure to SARS CoV-2 was found in animals near hiking trails and high-traffic public areas, suggesting the virus passed from humans to wildlife. More specifically, the team found that sites with high human activity had three times higher seroprevalence than low human-use areas.

In addition, the team obtained SARS-CoV-2 genomic sequences from nine individual animals (from six species) which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time, they write, “suggests at least seven recent human-to-animal transmission events.”

Researchers are not certain about the means of transmission from humans to animals. One possibility is wastewater, but the Virginia Tech scientists believe trash receptacles and discarded food are more likely sources.

The scientists stressed, however, that they found no evidence of the virus being transmitted from animals to humans, and people should not fear typical interactions with wildlife.

Genomic interpretation 

Genetic analysis in wild animals confirmed both the presence of SARS-CoV-2 and the existence of unique viral mutations with lineages closely matching variants circulating in humans at the time. This work further supports human-to-animal transmission.

“The virus is indifferent to whether its host walks on two legs or four. Its primary objective is survival,” noted Carla Finkielstein, PhD, professor of biological sciences at the Fralin Biomedical Research Institute at VTC. “Mutations that do not confer a survival or replication advantage to the virus will not persist and will eventually disappear.”

The virus isolated from one opossum showed viral mutations that were previously unreported and can potentially impact how the virus affects humans and their immune response. The study also identified two mice at the same site on the same day with the exact same variant, indicating they either both got it from the same human, or one infected the other.

The findings highlight the identification of novel mutations in SARS-CoV-2 in wildlife and the need for broad surveillance, the researchers say. These mutations could be more harmful and transmissible, creating challenges for vaccine development.

“I think the big take-home message is the virus is pretty ubiquitous,” said Amanda Goldberg, PhD, a former postdoctoral associate in Hoyt’s lab. “We found positives in a large suite of common backyard animals. There is a lot of work to be done to understand which species of wildlife, if any, will be important in the long-term maintenance of SARS-CoV-2 in humans.”

SARS-C0V-2
Despite the genetic diversity of the SARS-CoV-2 virus, this “evolutionary tree” shows there are clear connections between strains found in wild animals and humans. The viral genetic sequences of nine wild animals shown in red represent opossum, raccoon, deer mouse, groundhog, and Eastern cottontail. The tree also includes 90 virus sequences colored from yellow to purple to represent different strains of the virus that have appeared in humans since the appearance of the Omicron variant. Meanwhile, the “root” in black is the original SARS-CoV-2 sequence from Wuhan, China, in 2019. The structure illustrates the genetic connections between the virus strains, suggesting potential cross-species transmission from people to animals. Finally, the 3D image in the background represents a key protein that acquired at least two mutations to create an evolutionary path for the virus to jump and transmit to other species. [Finkielstein/Virginia Tech]
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