Use of S1 nuclease in deep sequencing for detection of double-stranded RNA          viruses

Saya SHIMADA; Makoto NAGAI; Hiromitsu MORIYAMA; Toshiyuki FUKUHARA; Satoshi KOYAMA; Tsutomu OMATSU; Tetsuya FURUYA; Junsuke SHIRAI; Tetsuya MIZUTANI

doi:10.1292/jvms.14-0607

Virology

Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses

Saya SHIMADA, Makoto NAGAI, Hiromitsu MORIYAMA, Toshiyuki FUKUHARA, Satoshi KOYAMA, Tsutomu OMATSU, Tetsuya FURUYA, Junsuke SHIRAI, Tetsuya MIZUTANI

Author information

Saya SHIMADA
Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Makoto NAGAI
Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Research and Education Center for Prevention of Global Infectious Diseases of Animal, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Hiromitsu MORIYAMA
Laboratory of Molecular and Cellular Biology, Department of Applied Biological Science Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Toshiyuki FUKUHARA
Laboratory of Molecular and Cellular Biology, Department of Applied Biological Science Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Satoshi KOYAMA
Laboratory of Ethology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Tsutomu OMATSU
Research and Education Center for Prevention of Global Infectious Diseases of Animal, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Tetsuya FURUYA
Research and Education Center for Prevention of Global Infectious Diseases of Animal, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Laboratory of Microbiology, Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Junsuke SHIRAI
Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Research and Education Center for Prevention of Global Infectious Diseases of Animal, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan
Tetsuya MIZUTANI
Research and Education Center for Prevention of Global Infectious Diseases of Animal, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183–8509, Japan

Keywords: deep sequencing, double-stranded RNA viruses, group a rotavirus, next-generation sequencer, S1 nuclease

JOURNAL FREE ACCESS

2015 Volume 77 Issue 9 Pages 1163-1166

DOI https://doi.org/10.1292/jvms.14-0607

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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.

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