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) |
|---|---|
| Journal | Biochemical and Biophysical Research Communications |
| DOIs | |
| State | Accepted/In press - Jan 1 2017 |
Fingerprint
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
}
TY - JOUR
T1 - A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system
AU - Oba, Mami
AU - Tsuchiaka, Shinobu
AU - Omatsu, Tsutomu
AU - Katayama, Yukie
AU - Otomaru, Konosuke
AU - Hirata, Teppei
AU - Aoki, Hiroshi
AU - Murata, Yoshiteru
AU - Makino, Shinji
AU - Nagai, Makoto
AU - Mizutani, Tetsuya
PY - 2017/1/1
Y1 - 2017/1/1
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.
KW - Comprehensive detection
KW - Deep sequencing
KW - Domestic animal
KW - Porcine parainfluenza virus
UR - http://www.scopus.com/inward/record.url?scp=85039076929&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85039076929&partnerID=8YFLogxK
U2 - 10.1016/j.bbrc.2017.12.017
DO - 10.1016/j.bbrc.2017.12.017
M3 - Article
C2 - 29223400
AN - SCOPUS:85039076929
JO - Biochemical and Biophysical Research Communications
JF - Biochemical and Biophysical Research Communications
SN - 0006-291X
ER -