Detection of Japanese Encephalitis (JE) Virus in Piggery effluent from an Australian Farm Prior to Outbreaks of JE

Japanese encephalitis virus (JEV), a mosquito-borne orthoflavivirus, raises concerns about its seasonal re-emergence. Pigs are a major amplifying host and JEV infection can manifest as significant reproductive disease and losses, necessitating robust surveillance. This study evaluated effluent surveillance for early JEV detection in piggery effluent from a Victorian farm between December 2024 and March 2025. Effluent samples were tested using JEV-specific real-time reverse transcription (RT)-PCR, with positive detections found on four separate sampling days, despite an absence of clinical signs in livestock through the testing period. Subsequent veterinary investigations for JEV in litters born on 17/05/2025 (suspect cases only) aligned with a positive effluent sample collected during the estimated JEV infection exposure periods of the sows. With the single clinically confirmed JEV case (which farrowed on 1/06/2025) collection of the same positive effluent sample fell just outside, but near, the estimated exposure period for the affected sow. These findings highlight ability of effluent monitoring to detect JEV infection 2 to 4 months before clinical manifestations present, offering potential for a non-invasive, herd-level early warning system. Intermittent detections may suggest limitations in grab sampling and low viral loads in effluent samples. Integrating effluent surveillance with veterinary clinical testing of litters suspected of being exposed to JEV or during high-risk periods could enhance JEV management in Australia’s enzootic regions, supporting One Health strategies.