title: Viral detection by high-throughput sequencing.
abstract: We applied a high-throughput sequencing platform, Ion PGM, for viral detection in fecal samples from adult cows collected in Hokkaido, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.25 ml of fecal specimens (N = 8), and more than 5 μg of cDNA was synthesized. Unbiased high-throughput sequencing using the 318 v2 semiconductor chip of these eight samples yielded 57-580 K (average: 270 K, after data analysis) reads in a single run. As a result, viral genome sequences were detected in each specimen. In addition to bacteriophage, mammal- and insect-derived viruses, partial genome sequences of plant, algal, and protozoal viruses were detected. Thus, this metagenomic analysis of fecal specimens could be useful to comprehensively understand viral populations of the intestine and food sources in animals.
authors.affiliation: Department of Infection Metagenomics, Research Institute for Microbial Disease, Osaka University, Osaka, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Motooka
authors.forename: Shota
authors.initials: S
authors.lastname: Nakamura
authors.forename: Katsuro
authors.initials: K
authors.lastname: Hagiwara
authors.forename: Takaaki
authors.initials: T
authors.lastname: Nakaya
mesh_terms: D000818:Animals; D001435:Bacteriophages / Q000235:genetics / Q000302:isolation & purification; D002417:Cattle; D004247:DNA / Q000302:isolation & purification; D018076:DNA, Complementary; D005243:Feces / Q000821:virology*; D005260:Female; D015723:Gene Library; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D007304:Insect Viruses / Q000235:genetics / Q000302:isolation & purification; D012313:RNA / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D014780:Viruses / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D018076:DNA, Complementary; D012313:RNA; D004247:DNA