Wildlife exposure to SARS-CoV-2 across a human use gradient

ABSTRACT

The spillover of SARS-CoV-2 into humans has caused one of the most devastating pandemics in recorded history. Human-animal interactions have led to transmission events of SARS-CoV-2 from humans to wild and captive animals. However, many questions remain about how extensive SARS-CoV-2 exposure is in wildlife, the factors that influence wildlife transmission risk, and whether sylvatic cycles can generate novel variants with increased infectivity and virulence. We sampled 18 different wildlife species in the Eastern U.S. and detected widespread exposure to SARS-CoV-2 across wildlife species. Using quantitative reverse transcription polymerase chain reaction and whole genome sequencing, we conclusively detected SARS-CoV-2 in the Virginia opossum and had equivocal detections in six additional species. Species considered human commensals like squirrels, and raccoons had high seroprevalence, ranging between 62%-71%, and sites with high human use had three times higher seroprevalence than low human-use areas. SARS-CoV-2 genomic data from an infected opossum and molecular modeling exposed previously uncharacterized changes to amino acid residues observed in the receptor binding domain (RBD), which predicts improved binding between the spike protein and human angiotensin-converting enzyme (ACE2) compared to the dominant variant circulating at the time of isolation. These mutations were not identified in human samples at the time of collection. Overall, our results highlight widespread exposure to SARS-CoV-2 in wildlife and suggest that areas with high human activity may serve as important points of contact for cross-species transmission. Furthermore, this work highlights the potential role of wildlife in fueling de novo mutations that may eventually appear in humans.