High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage
Top Cited Papers
- 15 November 2012
- journal article
- Published by American Society for Microbiology in Journal of Virology
- Vol. 86 (22), 12161-12175
- https://doi.org/10.1128/jvi.00869-12
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, 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.This publication has 86 references indexed in Scilit:
- Molecular virology of hepatitis E virusVirus Research, 2011
- Human Bocaviruses Are Highly Diverse, Dispersed, Recombination Prone, and Prevalent in Enteric InfectionsThe Journal of Infectious Diseases, 2010
- Multiple novel astrovirus species in human stoolJournal of General Virology, 2009
- Viral agents associated with acute gastroenteritis in children hospitalized with diarrhea in Lanzhou, ChinaJournal of Clinical Virology, 2009
- A Newly Identified Bocavirus Species in Human StoolThe Journal of Infectious Diseases, 2009
- A highly prevalent and genetically diversified Picornaviridae genus in South Asian childrenProceedings of the National Academy of Sciences of the United States of America, 2008
- Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infectionsProceedings of the National Academy of Sciences of the United States of America, 2008
- RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics, 2006
- MAFFT version 5: improvement in accuracy of multiple sequence alignmentNucleic Acids Research, 2005
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004