SARS-CoV-2 Has Already Spread Extensively In The Wildlife

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A new study by researchers from Virginia Tech, Blacksburg, Virginia – USA has shown that the SARS-CoV-2 coronavirus has already spread extensively among various wildlife including racoons, squirrels, possums, deer, foxes, skunks etc.

The study findings were published on a preprint server and are currently being peer reviewed.

 https://www.biorxiv.org/content/10.1101/2022.11.04.515237v1

We found that exposure to SARS-CoV-2 appears widespread among wildlife species. We detected positives in 6 species using RT-qPCR and neutralizing antibodies in an additional 4 species.

We found support for a relationship between human use and seroprevalence suggesting that areas with high human activity are potential hotspots for cross-species transmission.

Analysis of isolates collected from infected wildlife revealed novel mutations at the time of collection which have subsequently been found circulating in other regions. While some of these mutations likely increase binding affinity to the hACE2 receptor or confer some antibody resistance compared to ancestral BA.2 lineages, others appeared unique to the opossum.

Whether these mutations developed in humans not captured in surveillance at the time or in wildlife communities and were transmitted back to humans remains unknown but presents an important consideration for future variant surveillance.

Our combined results suggest that a high diversity of species are exposed to SARS-CoV-2 in the wild. Prevalence of active infections among wildlife was generally low and ranged from 1.6-20.0%. We found that 7.8% of opossums, a marsupial, were positive (including equivocal detections), similar to white-tailed deer (10.0%).

High seroprevalence (62%) and a single opossum with viral RNA levels at sufficient levels for WGS suggests this species may have high exposure to SARS-CoV-2 in natural settings. The SARS-CoV-2-positive opossum with two gene amplification was recaptured at the same site ∼30 days later, and was positive for antibodies (51.1 % neutralization), supporting that the serology data reflect previous infection with SARS-CoV-2.

The Eastern gray squirrel also had detections on both RT-qPCR (1.6%) and using serological tests (71.4%). Several other species that were examined for antibodies to SARS-CoV-2 suggested high levels of previous exposure, including raccoons (64%) and skunks (67%). All these species are considered human commensals and live in and around human settlements.

Many of these species’ range across large areas of North America and some have been introduced into Europe (gray squirrel and raccoon) and Asia (raccoon) and have close relatives across the globe. While it is unknown whether a sylvatic cycle has been established in any of these species, their close connection to human populations makes them important species for considering transmission to and from humans.

We found a relationship between human use, urbanization and seroprevalence among sites. This suggests that wildlife in areas with more human activity likely have higher exposure to SARS-CoV-2, leading to more wildlife infections. Interestingly, the site with the highest seroprevalence was a forested recreational trail that receives high human visitation but is less developed.

This suggests that recreational sites may be important points of contact between humans and wildlife and could be targeted for surveillance. Humans and wildlife rarely come into direct contact, but numerous indirect links likely exist. Wastewater has been proposed as a potential source for indirect exposure to SARS-CoV-2 (21), however, in rural areas where septic tanks are a dominant form of wastewater management, this is unlikely to be the only source. Instead, other forms of human waste, like trash receptacles, may serve as important sources of indirect exposure for wildlife (22, 23).

SARS-CoV-2 isolated from the opossum, showed unique mutations in the spike protein in the RBM and RBD of the spike protein. These previously uncharacterized amino acid changes are predicted to improve S-hACE2 binding and membrane fusion efficiencies compared to omicron BA.2, potentially providing a fitness advantage by either increasing the affinity of S for the ACE2 receptor or, alternatively, by evading the neutralizing activity of antibodies.

These mutations were not observed in human samples at the time of isolation from the opossum and have only recently been identified in a new Omicron sub-variant (BJ.1). These results highlight the role of wildlife in contributing unique mutations that may be more transmissible to humans as has been previously suggested with the emergence of the Omicron variant (6, 24

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