Viral pathogens in effluent samples collected from a swine slaughterhouse in Central Italy: a 1-year molecular surveillance

Introduction Molecular screening for zoonotic and species-specific viral pathogens in environmental samples is essential for obtaining epidemiological data to support risk-based assessments in the food industry, particularly in settings such as slaughterhouses. Methods This study screened 72 effluent specimens collected between January and December 2025 from two sites within a domestic pig slaughterhouse in Central Italy: the stocking yard (V1) and the wastewater treatment plant (WWTP; V2). The viruses investigated were astrovirus, hepatitis A virus, hepatitis E virus (HEV), norovirus (NoV), and rotavirus (RV). Viral detection was performed using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) and nested reverse transcription polymerase chain reaction (RT-PCR) assays, followed by phylogenetic analysis. Results The results showed that ribonucleic acid (RNA) from at least one of the target viruses was detected in 37.50% of the specimens, with HEV3-c detected in 26.39%, NoV-GII.3 in 12.50%, and NoV-GI.4 in 9.72%. Among the positive effluent samples, 62.96% were collected at V1 and 37.04% at V2. Samples from V1 exhibited higher viral loads, with HEV RNA levels reaching (105) genome equivalents per milliliter (GE/mL) and NoV-GI and NoV-GII RNA levels reaching (103) GE/mL, compared with (103) GE/mL for HEV RNA and (101) GE/mL for NoV-GI and NoV-GII RNA in samples from V2. Discussion The detection of viral RNA sequences both before and after WWTP treatment highlights scientific and regulatory concerns regarding the potential dissemination of zoonotic and species-specific viruses into the environment. Regulatory gaps in the management and monitoring of these environmental matrices underscore the importance of multidisciplinary approaches to addressing this One Health issue.