title: High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage.
abstract: 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 United States (San Francisco, CA), 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 single-stranded RNA picorna-like virus 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 picorna-like virus superfamily, with possible vertebrate, plant, or arthropod hosts inferred from nucleotide composition analysis. Circular DNA genomes distantly related to the plant-infecting Geminiviridae family were named Baminivirus, Nimivirus, and Niminivirus. These results highlight the utility of analyzing sewage to monitor shedding of viral pathogens and the high viral diversity found in this common pollutant and provide genetic information to facilitate future studies of these newly characterized viruses.
authors.affiliation: Blood Systems Research Institute, San Francisco, California, USA.
authors.forename: Terry Fei Fan
authors.initials: TF
authors.lastname: Ng
authors.forename: Rachel
authors.initials: R
authors.lastname: Marine
authors.forename: Chunlin
authors.initials: C
authors.lastname: Wang
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
authors.forename: Beatrix
authors.initials: B
authors.lastname: Kapusinszky
authors.forename: Ladaporn
authors.initials: L
authors.lastname: Bodhidatta
authors.forename: Bamidele Soji
authors.initials: BS
authors.lastname: Oderinde
authors.forename: K Eric
authors.initials: KE
authors.lastname: Wommack
authors.forename: Eric
authors.initials: E
authors.lastname: Delwart
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D004267:DNA Viruses / Q000235:genetics*; D004270:DNA, Circular / Q000378:metabolism; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D009390:Nepal; D009549:Nigeria; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D012328:RNA Viruses / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid; D012722:Sewage / Q000821:virology*; D013785:Thailand; D014481:United States; D014773:Virology / Q000379:methods
chemical_list: D004270:DNA, Circular; D009711:Nucleotides; D012722:Sewage