Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments

RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments—including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings — across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health. RNA viruses are well-known pathogens that can cause zoonotic spillover and threaten human health. Here, the authors have compiled samples collected from urban and surrounding environments across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas).