

@article {1742,
	title = {High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage},
	journal = {J Virol},
	volume = {86},
	number = {22},
	year = {2012},
	note = {Ng, Terry Fei Fan Marine, Rachel Wang, Chunlin Simmonds, Peter Kapusinszky, Beatrix Bodhidatta, Ladaporn Oderinde, Bamidele Soji Wommack, K Eric Delwart, Eric eng 095831/Wellcome Trust/United Kingdom R01 HL105770/HL/NHLBI NIH HHS/ R01HL083254/HL/NHLBI NIH HHS/ R01HL105770/HL/NHLBI NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t 2012/08/31 06:00 J Virol. 2012 Nov;86(22):12161-75. doi: 10.1128/JVI.00869-12. Epub 2012 Aug 29.},
	pages = {12161-75},
	type = {Journal Article},
	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.},
	keywords = {Amino Acid Motifs Amino Acid Sequence Computational Biology/methods Conserved Sequence DNA Viruses/*genetics DNA, Amino Acid Sewage/*virology Thailand United States Virology/methods, Circular/metabolism Genetic Variation Genome, DNA/methods Sequence Homology, Viral High-Throughput Nucleotide Sequencing/*methods Humans Likelihood Functions Molecular Sequence Data Nepal Nigeria Nucleotides/genetics Phylogeny RNA Viruses/*genetics Sequence Analysis},
	issn = {1098-5514 (Electronic) 0022-538X (Linking)},
	doi = {10.1128/JVI.00869-12},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22933275},
	author = {Ng, T. F. and Marine, R. and Wang, C. and Simmonds, P. and Kapusinszky, B. and Bodhidatta, L. and Oderinde, B. S. and Wommack, K. E. and Delwart, E.}
}
