High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage.

Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for high throughput viral discovery. A metagenomics analysis of purified viral particles in untreated sewage from the US (San Francisco), Nigeria (Maiduguri), Thailand (Bangkok), and Nepal (Kathmandu) revealed sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates and plants (BLASTx E score < 10-4) including known pathogens (>90% protein identities) in numerous viral families infecting humans (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Tombusviridae, Tymoviridae, Virgaviridae) and insects (Dicistroviridae, Nodaviridae and Parvoviridae). The full and partial genomes of a novel kobuvirus, salivirus and sapovirus are described. A novel astrovirus (Casa astrovirus) basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was partially characterized. Potential new genera and families of viruses distantly related to members of the ssRNA picornavirus-like superfamily were genetically characterized and named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes near the root of the picornavirus-like superfamily, with possible vertebrate, plant or arthropod hosts inferred from nucleotide composition analysis. Genomes from tentative new genera of circular ssDNA genomes of the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitoring shedding of viral pathogens, the high viral diversity found in this common medium, and provide genetic information to facilitate future studies of these newly characterized viruses.