High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage

Abstract

g Deep sequencing of untreated sewage provides an opportunity to monitor enteric infections in large populations and for highthroughput 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 plantinfecting 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.

Genetic Variability and the Classification of Hepatitis E Virus

“…For example, a partial genome sequence that differs by an amino acid distance of Ͼ0.7 in the RNA-dependent RNA polymerase region of ORF1 was recently described from deep sequencing of untreated sewage from Nepal. Although awaiting further sequence data to confirm whether or not it possesses an HEV-like genome organization, its divergence potentially justifies its potential addition to the virus family as an additional new genus (39).…”

Diversity of picornaviruses in rural Bolivia

“…A single specimen was positive by 59NTR real-time reverse transcriptase (RT)-PCR targeting kobuvirus and salivirus except porcine and bovine kobuviruses (in silico analyses only) (Table 2 and Table S1, available in JGV Online), (Ng et al, 2012). Based on the partial VP1 sequence analyses, all three of these viruses are SALV A1.…”

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Many of these uncultivated viruses are related to members of the bacteriophage family Microviridae 9 , but perhaps even larger number encode RC-Reps displaying phylogenetic affinity to one of three families of eukaryotic ssDNA viruses-Circoviridae, Geminiviridae and Nanoviridae (for example, see refs [24][25][26][27]. Interestingly, instead of encoding genes for corresponding CPs (circo-, gemini-and nano-like), these viruses typically bear open-reading frames that do not share appreciable similarity with sequences in the databases.…”