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

J Vet Med Sci. 2015 Sep;77(9):1163-6. doi: 10.1292/jvms.14-0607. Epub 2015 Apr 6.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cattle
  • Cattle Diseases / diagnosis
  • Cattle Diseases / virology
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Nucleotide Sequencing / veterinary
  • RNA, Double-Stranded / genetics*
  • Rotavirus / genetics*
  • Rotavirus Infections / diagnosis
  • Rotavirus Infections / veterinary*
  • Rotavirus Infections / virology
  • Single-Strand Specific DNA and RNA Endonucleases / metabolism*
  • Swine
  • Swine Diseases / diagnosis
  • Swine Diseases / virology


  • RNA, Double-Stranded
  • Single-Strand Specific DNA and RNA Endonucleases