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

doi:10.1016/j.bbrc.2017.12.017

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

Biochem Biophys Res Commun. 2018 Jan 8;495(2):1871-1877. doi: 10.1016/j.bbrc.2017.12.017. Epub 2017 Dec 6.

Authors

Affiliations

¹ Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.
² The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu 501-1193, Japan.
³ Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu 501-1193, Japan.
⁴ Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan.
⁵ Faculty of Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Nakagami District, Okinawa, 903-0129, Japan.
⁶ Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan.
⁷ Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; Murata Animal Hospital, 2016 Honnou, Mobara-shi, Chiba 299-4144, Japan.
⁸ Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555-1019, USA.
⁹ Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, 921-8836, Japan.
¹⁰ Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan. Electronic address: tmizutan@cc.tuat.ac.jp.

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.

Keywords: Comprehensive detection; Deep sequencing; Domestic animal; Porcine parainfluenza virus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle
Chromosome Mapping / methods
Chromosome Mapping / veterinary*
Cytopathogenic Effect, Viral / genetics*
Genome, Viral / genetics*
High-Throughput Nucleotide Sequencing / methods
High-Throughput Nucleotide Sequencing / veterinary*
Livestock / virology*
Swine
Viruses / genetics*
Viruses / isolation & purification*
Viruses / pathogenicity