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

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

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

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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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