title: Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses.
abstract: Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5-28.4- and 10.1-208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.
authors.affiliation: Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Saya
authors.initials: S
authors.lastname: Shimada
authors.forename: Makoto
authors.initials: M
authors.lastname: Nagai
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Moriyama
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Fukuhara
authors.forename: Satoshi
authors.initials: S
authors.lastname: Koyama
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Omatsu
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Furuya
authors.forename: Junsuke
authors.initials: J
authors.lastname: Shirai
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Mizutani
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000175:diagnosis / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000662:veterinary; D012330:RNA, Double-Stranded / Q000235:genetics*; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000175:diagnosis / Q000662:veterinary* / Q000821:virology; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism*; D013552:Swine; D013553:Swine Diseases / Q000175:diagnosis / Q000821:virology
chemical_list: D012330:RNA, Double-Stranded; D015719:Single-Strand Specific DNA and RNA Endonucleases
references.citation: Curr Opin Virol. 2012 Feb;2(1):63-77
references.pmid: 22440968
references.citation: J Gen Virol. 2012 Sep;93(Pt 9):1853-68
references.pmid: 22647373
references.citation: Vet Microbiol. 2013 Aug 30;165(3-4):190-9
references.pmid: 23642647
references.citation: J Vet Med Sci. 2013 Dec 30;75(12):1651-5
references.pmid: 23912876
references.citation: J Virol. 2008 Apr;82(7):3204-19
references.pmid: 18216098
references.citation: FEMS Microbiol Rev. 2003 Jan;26(5):457-91
references.pmid: 12586391
references.citation: Future Microbiol. 2011 Sep;6(9):1049-65
references.pmid: 21958144
references.citation: Eur J Biochem. 1973 Feb 15;33(1):192-200
references.pmid: 4691350
references.citation: Cell. 1978 Jul;14(3):695-711
references.pmid: 688389
references.citation: Proc Natl Acad Sci U S A. 1979 Nov;76(11):5596-600
references.pmid: 230483
references.citation: Nat Methods. 2008 Jan;5(1):16-8
references.pmid: 18165802
references.citation: BMC Genomics. 2013;14:444
references.pmid: 23822119
references.citation: Vet Res Commun. 2009 Jan;33(1):1-23
references.pmid: 18622713
references.citation: Biochim Biophys Acta. 1966 Jan 18;114(1):158-68
references.pmid: 4287053