Metatranscriptomic Compendium of 55900 RNA Viruses Deciphers Human Health Implication and Ecological roles of RNA Virome in Global Wastewater Treatment Plants

RNA viruses play diverse functional roles in engineered ecosystems, influencing biotechnological process and serving as indicators of human health. Comprehending the ecological and health significance of RNA viruses in wastewater treatment plants (WWTPs) can derive their valuable implications on microbial community control and wastewater-based epidemiology. This study delved into an extensive analysis of RNA sequencing data, totally over 3.8 Tb, sourced from 557 metatranscriptomes across global WWTPs, to scrutinize the diversity, host associations, and auxiliary metabolic functions of RNA viruses. We identified 11414 RNA virus operational taxonomic units from the WWTPs, doubling the current known diversity of the RNA viruses in global engineered systems. Phylogenetic analysis of RNA-dependent RNA polymerases supported the establishment of the five established RNA virus phyla while also advocating for taxonomy revisions due to our discovery of novel clades. Notably, the RNA viral community within the WWTPs was predominated by prokaryotic viruses, encompassing both previously identified RNA phage lineages ( Leviviricetes and Cystoviridae ) and potential prokaryotic viruses from newly-identified clades. Detections of prevalent human RNA viruses such as Astrovirus , Respirovirus , Rotavirus , and Norovirus , alongside high-risk human RNA viruses like SARS-Cov-2 and Zika virus, highlighted the potential of leveraging wastewater-based surveillance for human health protection. Moreover, the presence of auxiliary metabolic genes encoded by RNA viruses suggested their involvement in diverse host metabolic processes, including enhancing translation efficiency, cellular respiration, nitrogen metabolism, and even antibiotic resistance. Collectively, our findings unveil the previously hidden diversity, health implications, and biochemical impacts of RNA viruses within WWTPs, underscoring their multifaceted roles in engineered environmental systems.