Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon

Simple Summary Numerous instances of SARS-CoV-2 transmission from humans to both domestic and wild animals have been reported globally. However, in Peru, natural infections in wild animals have not been documented, despite the high number of COVID-19 cases and deaths in humans, particularly in the Amazonian regions where interactions between humans and wildlife are frequent. In this study, we conducted SARS-CoV-2 surveillance using fecal samples from 76 captive and semi-captive monkeys in the Loreto, Ucayali, and Madre de Dios regions from August 2022 to February 2023. We identified a genetic segment of SARS-CoV-2 through metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins ( Cebus unicolor ) at a rescue center in Ucayali. Phylogenetic analysis further confirmed that the obtained sequence matched the SARS-CoV-2 genome. This study represents the initial report of molecular detection of SARS-CoV-2 in monkeys in the Peruvian Amazon, underscoring the adverse impact of human–wildlife interactions and emphasizing the importance of continuous surveillance for the early detection and anticipation of potential future emergencies involving new variants of SARS-CoV-2 in wildlife. Abstract Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human–wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins ( Cebus unicolor ) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human–NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.