Molecular detection of zoonotic RNA viruses in guinea pigs (Cavia porcellus) from small-scale family farming in the region of Cusco, Peru

Emerging zoonotic diseases are frequently associated with close human-animal interactions in small-scale farming systems. Guinea pigs (<i>Cavia porcellus</i>) are widely raised for food in the Andean region, often under poor sanitary conditions; however, little is known about their role as reservoirs of enteric viruses with zoonotic potential. This study aimed to detect zoonotic RNA viruses in intestinal samples from guinea pigs raised on small-scale family farms in the Cusco region of Peru. A total of 34 intestinal tissue samples from adult guinea pigs showing gastrointestinal lesions were analyzed by reverse transcription polymerase chain reaction (RT-PCR) and nested PCR for the molecular detection of Coronavirus (CoV), Rotavirus A (RVA), <i>Mammalian orthoreovirus</i> (MRV), and Kobuvirus (KoV). Positive amplicons were sequenced and analyzed phylogenetically to confirm the PCR assays. Overall, 91.18% (31/34) of samples tested positive for at least one virus. RVA was the most frequently detected (58.82%), followed by CoV (29.41%), MRV (23.53%), and KoV (23.53%). Single-virus infections accounted for 20 cases and co-infections were identified in 11 cases. RVA was the most frequently detected, both in single (<i>n</i> = 9) and co-infections (<i>n</i> = 11). KoV detection was predominantly associated with co-infections rather than single infections. These findings provide the first molecular evidence of multiple zoonotic RNA viruses in guinea pigs from small-scale farming in Peru, highlighting their potential role as reservoirs in zoonotic transmission cycles. Enhanced surveillance and improved farm-level biosecurity are essential to mitigate risks of viral emergence in these traditional farming systems.