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

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

Microbiology And Immunology

Research output: Contribution to journal › Article › peer-review

6 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 language	English (US)
Pages (from-to)	1871-1877
Number of pages	7
Journal	Biochemical and Biophysical Research Communications
Volume	495
Issue number	2
DOIs	https://doi.org/10.1016/j.bbrc.2017.12.017
State	Published - 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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10.1016/j.bbrc.2017.12.017

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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

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, vol. 495, no. 2, pp. 1871-1877. https://doi.org/10.1016/j.bbrc.2017.12.017

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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.",

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

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AU - Hirata, Teppei

AU - Aoki, Hiroshi

AU - Murata, Yoshiteru

AU - Makino, Shinji

AU - Nagai, Makoto

AU - Mizutani, Tetsuya

N1 - Funding Information: This study was supported by the Research Project for Improving Food Safety and Animal Health of the Ministry of Agriculture, Forestry and Fisheries of Japan ( 716057223 ). Publisher Copyright: © 2017 Elsevier Inc.

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N2 - 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.

AB - 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.

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

Abstract

Keywords

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