NEW YORK – A genetic surveillance study in Virginia and Washington, D.C., found evidence of apparent spillover of SARS-CoV-2 into wildlife, particularly among species and sites expected to have exposure to humans. The study appeared in Nature Communications on Monday.
"Our findings show that SARS-CoV-2 has spread more widely among wildlife than we thought, particularly in areas with a lot of human activity, making these spots likely points of repeated virus transfer between species," co-senior and co-corresponding author Carla Finkielstein, a biological sciences researcher at Virginia Tech's Fralin Biomedical Research Institute, said in an email.
While past research highlighted SARS-CoV-2 transmission from humans to white-tailed deer, she explained, a more comprehensive search for the virus had not been conducted in a wider range of wildlife species, prompting the team to evaluate wildlife samples collected across nearly two dozen species at sites with or without widespread human activity.
Using an RT-qPCR assay targeting the SARS-CoV-2 nucleocapsid, envelope, and spike genes, the investigators screened for SARS-CoV-2 in nearly 800 nasopharyngeal or oropharyngeal samples from 23 wildlife species tested at urban and rural sites in Virginia or Washington, D.C., from spring to mid-September 2023, and from animals at three wildlife rehabilitation centers.
They also searched for SARS-CoV-2 in more than 13,200 clinical samples from humans, following up on positive samples with SARS-CoV-2 sequence profiling by amplicon sequencing or whole-genome sequencing.
In the process, the team saw "extensive spread of SARS-CoV-2 among various wildlife species, highlighting the virus's ability to adapt and mutate within these species," Finkielstein explained. "This underscores several important implications for controlling future outbreaks of COVID-19 and other zoonotic diseases."
All told, the researchers tracked down SARS-CoV-2 sequences in half a dozen species — from deer mice, Virginia opossums, and groundhogs to raccoons, Eastern cottontail rabbits, and Eastern red bats. They also saw signs of past infections in rabbits, raccoons, the deer mouse, the white-footed mouse, and Eastern gray squirrels based on neutralizing antibody patterns in 126 blood serum samples from six species.
Consistent with potential spillover of the virus from humans to wildlife, the team noted that the viruses found in wildlife were similar to those circulating in humans at the time and that antibodies targeting SARS-CoV-2 turned up far more often in animals from urban sites or sites with high human use, including a frequently visited state park, compared to sites that humans are less likely to inhabit or visit.
Through sequencing nine viral isolates from six affected species, meanwhile, the team was able to parse out alterations that appeared to provide SARS-CoV-2 an advantage when infecting certain nonhuman animals.
For example, the researchers flagged — and modeled the possible consequences of — a new mutation that seems to have altered the receptor binding domain of the SARS-CoV-2 S protein after its jump into the opossum, pointing to a potential adaptation to that host.
"[S]tudying these mutations can offer insights into how the virus evolves and thus, can help in developing more effective vaccines and treatments that account for these evolutionary changes," Finkielstein said, noting that "[i]f certain wildlife species are significant reservoirs of the virus, developing and deploying vaccines for these animals could be a proactive measure to prevent the spread and mutation of the virus within wildlife populations."
Together, the results point to a "clear need" for enhanced wildlife surveillance of wildlife, Finkielstein explained, "not only for SARS-CoV-2 but also other viruses, especially in areas with high human activity."
"Curbing the spread of a virus, regardless of which one it is, is really a holistic endeavor that should consider all potential reservoirs and pathways of transmission," she added, noting that "educating the public and raising awareness about the risks of wildlife interactions and the importance of wildlife conservation can foster behaviors that reduce virus transmission risks."