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 journal › Article

2 Citations (Scopus)

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)
JournalBiochemical and Biophysical Research Communications
DOIs
StateAccepted/In press - Jan 1 2017

Fingerprint

Livestock
Viruses
Agriculture
Nucleic Acids
Swine
Genes
Genome
RNA
Paramyxoviridae Infections
Pathogens
Goats
Feces
Libraries
Polymerase Chain Reaction

Keywords

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

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system. / Oba, Mami; Tsuchiaka, Shinobu; Omatsu, Tsutomu; Katayama, Yukie; Otomaru, Konosuke; Hirata, Teppei; Aoki, Hiroshi; Murata, Yoshiteru; Makino, Shinji; Nagai, Makoto; Mizutani, Tetsuya.

In: Biochemical and Biophysical Research Communications, 01.01.2017.

Research output: Contribution to journal › Article

Oba, M, Tsuchiaka, S, Omatsu, T, Katayama, Y, Otomaru, K, Hirata, T, Aoki, H, Murata, Y, Makino, S, Nagai, M & Mizutani, T 2017, 'A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system', Biochemical and Biophysical Research Communications. https://doi.org/10.1016/j.bbrc.2017.12.017
Oba M, Tsuchiaka S, Omatsu T, Katayama Y, Otomaru K, Hirata T et al. A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system. Biochemical and Biophysical Research Communications. 2017 Jan 1. https://doi.org/10.1016/j.bbrc.2017.12.017
Oba, Mami ; Tsuchiaka, Shinobu ; Omatsu, Tsutomu ; Katayama, Yukie ; Otomaru, Konosuke ; Hirata, Teppei ; Aoki, Hiroshi ; Murata, Yoshiteru ; Makino, Shinji ; Nagai, Makoto ; Mizutani, Tetsuya. / A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system. In: Biochemical and Biophysical Research Communications. 2017.
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