Assessment of viral pathogen removal across wastewater treatment stages in a swine processing facility

A swine abattoir wastewater treatment system in Queensland, Australia, was monitored over 6 months to assess the effectiveness of a pond-based treatment system for the removal of viruses prior to irrigation reuse. Four viruses were tracked through the facility, from points of entry to the final treated effluent, to identify major sources of viral contamination and quantify viral reductions across treatment stages. The truck wash contributed the highest viral loads overall, reflecting the accumulation of porcine faecal materials on transport vehicles and its release during washing. Substantial viral loads were also detected from the lairage area and slaughter floor, consistent with direct contact with live animals and carcase processing. In contrast, the boning room contributed the lowest viral loads among sampled locations. These findings identified priority locations for targeted hygiene interventions and drainage management. The three-pond system achieved substantial viral reductions, with concentrations decreasing consistently through the anaerobic, aerobic and storage ponds. By the final pond, viral concentrations were generally at or below detection limits. Overall reductions ranged from approximately 90%-99.9%, depending on virus type. Soil samples collected from irrigated areas tested negative for all viruses, consistent with non-detectable levels in the applied effluent, indicating no measurable viral presence in the soil following land application under the conditions studied. Viability-based quantitative polymerase chain reaction (qPCR) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays demonstrated that most detectable viral genomes in treated wastewater originated from non-intact, likely non-infectious particles. Intact viral particles were rarely detected following final treatment, even when viral genomes remained measurable, suggesting that conventional qPCR/RT-qPCR quantification alone may overestimate the presence of infectious viruses in treated effluent. Overall, the pond-based treatment system provided effective viral removal prior to irrigation reuse. Maintaining adequate retention times is recommended to sustain treatment performance and ensuring the safety of irrigation reuse. Strategic management of truck wash effluent was identified as an opportunity for further viral load reduction.