Environmental RNA improves detection and surveillance of schistosomiasis transmission

Environmental diagnosis of schistosomiasis, a disease affecting over 250 million people globally, remains challenging, thereby limiting efficient eradication efforts. Current methods, including environmental DNA (eDNA), cannot distinguish between infectious parasite life stages present in the environment. Here, we develop and validate an environmental RNA (eRNA) approach that enables detection and quantification of Schistosoma mansoni miracidia (infective to snails) and cercariae (infective to humans) directly from water samples. We identified life stage-specific transcripts and designed ddPCR assays highly specific to S. mansoni and each life stage. Laboratory experiments demonstrate that stage-specific eRNA assays accurately detect and quantify the relative abundance of each life stage. While eRNA and eDNA assays showed similar analytical limits of detection (LOD), eRNA provided enhanced organism-level detectability due to higher target molecule availability per life stage, also resulting in longer signal persistence in water that may facilitate the detection of the highly transient free-living stages of S. mansoni in the environment, especially cercariae. Field validation at six endemic sites in Brazil confirms that eRNA outperforms eDNA and conventional snail surveys in detecting S. mansoni cercariae indicating local transmission risk to humans. By enabling living stage discrimination and improving detectability compared to eDNA, our study advances both fundamental understanding and environmental surveillance of schistosomiasis transmission, supporting elimination initiatives in affected regions.