PRJNA169010
Sewage Viruses Metagenome
Analysis of sewage by deep sequencing provides an efficient method for large-scale viral discovery and for monitoring enteric viral infections in large populations. A metagenomics analysis was performed on viral particles purified from untreated sewage collected in the US, Nigeria, Thailand, and Nepal. Sequences related to 29 eukaryotic viral families infecting vertebrates, invertebrates, plants, and prokaryotes were identified (E score < 10-4) including known (>90% protein similarity) viral pathogens infecting human (Adenoviridae, Astroviridae, Caliciviridae, Hepeviridae, Parvoviridae, Picornaviridae, Picobirnaviridae, and Reoviridae), plants (Alphaflexiviridae, Betaflexiviridae, Partitiviridae, Sobemovirus, Secoviridae, Sobemovirus, Tombusviridae, Tymoviridae, Virgaviridae) and insects (Dicistroviridae, Nodaviridae, Densovirinae). The full and partial genomes of a novel kobuvirus, salivirus and sapovirus were described. A novel astrovirus, Casa astrovirus, basal to those infecting mammals and birds, potentially representing a third astrovirus genus, was identified. Multiple potential new genera and families of ssRNA viruses distantly related to members of the picornavirus-like superfamily were genetically characterized that we named Picalivirus, Secalivirus, Hepelivirus, Nedicistrovirus, Cadicistrovirus, and Niflavirus. Phylogenetic analysis placed these highly divergent genomes as diverging near the root of the picornavirus-like superfamily. Nucleotide composition indicated possible plant and arthropod tropisms. Highly divergent circular ssDNA genomes of the plant-infecting Geminiviridae family were identified. Two circular DNA genomes from Baminivirus and Niminivirus could be considered new genera of the plant infecting Geminiviridae. The generation of numerous long sequence assemblies without significant protein similarities to known viruses may reflect the presence of novel viral families. These results highlight the high viral genetic diversity found in a pervasive environmental pollutant and provide genetic information for future studies of these novel viruses.