A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system

Mami Oba, Shinobu Tsuchiaka, Tsutomu Omatsu, Yukie Katayama, Konosuke Otomaru, Teppei Hirata, Hiroshi Aoki, Yoshiteru Murata, Shinji Makino, Makoto Nagai, Tetsuya Mizutani

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library. Furthermore, this method enabled us to determine nearly full-length genome sequence of porcine parainfluenza virus 1 and greatly increased Breadth, a value indicating the ratio of the mapping consensus length in the reference genome, in pig samples. Our data showed usefulness of SureSelect target enrichment system for comprehensive analysis of genomic information of various viruses in field samples.

Original languageEnglish (US)
Pages (from-to)1871-1877
Number of pages7
JournalBiochemical and Biophysical Research Communications
Volume495
Issue number2
DOIs
StatePublished - Jan 8 2018

Keywords

  • Comprehensive detection
  • Deep sequencing
  • Domestic animal
  • Porcine parainfluenza virus

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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  • Cite this

    Oba, M., Tsuchiaka, S., Omatsu, T., Katayama, Y., Otomaru, K., Hirata, T., Aoki, H., Murata, Y., Makino, S., Nagai, M., & Mizutani, T. (2018). A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system. Biochemical and Biophysical Research Communications, 495(2), 1871-1877. https://doi.org/10.1016/j.bbrc.2017.12.017