Global RNA Virome in Wastewater Treatment Plants Reveals Ecological Insights and Human Health Implications

RNA viruses are widely recognized for their roles in causing human diseases and shaping Earth’s biodiversity. Wastewater treatment plants (WWTPs) are eco-friendly biotechnological systems where the roles of RNA viruses in process engineering and sanitation remain unclear. This study analyzed RNA sequencing dataset (> 3.8 Tb) from global WWTPs to examine the diversity, host associations, and auxiliary metabolic functions of RNA viruses. We identified 11,414 RNA virus operational taxonomic units (vOTUs), expanding the known diversity of RNA viruses in WWTPs by 67%. The RNA viral community in WWTPs was dominated by prokaryotic viruses, including both established RNA phage lineages and novel clades with broad ecological distributions, highlighting their underestimated diversity and broad niche breadths. Notably, a vOTU from the base -Howeltoviricetes phage clade was associated with the pathogenic bacterium Aliarcobacter cryaerophilus , suggesting potential applications in RNA phage therapy. Furthermore, the examined distribution and fate of human RNA viruses emphasized the utility of quantitative metatranscriptomics-based wastewater surveillance for public health monitoring. The discovery of auxiliary metabolic genes encoded by RNA viruses further revealed their involvement in critical host metabolic pathways such as translation and cellular respiration. These findings underscore the multifaceted roles of RNA viruses in the critical engineered systems.