Korean Journal of Veterinary Service (한국동물위생학회지)

The Korean Society of Veterinary Service (한국동물위생학회)
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Whole genome sequencing of foot-and-mouth disease virus using benchtop next generation sequencing (NGS) system

  • Moon, Sung-Hyun (Laboratory of Swine Diseases, College of Veterinary Medicine and Bio-Safety Research Institute, Jeonbuk National University) ;
  • Oh, Yeonsu (Department of Veterinary Pathology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University) ;
  • Tark, Dongseob (Korea Zoonosis Research Institute, Jeonbuk National University) ;
  • Cho, Ho-Seong (Laboratory of Swine Diseases, College of Veterinary Medicine and Bio-Safety Research Institute, Jeonbuk National University)
  • Received : 2019.12.08
  • Accepted : 2019.12.16
  • Published : 2019.12.30
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Abstract

In countries with FMD vaccination, as in Korea, typical clinical signs do not appear, and even in FMD positive cases, it is difficult to isolate the FMDV or obtain whole genome sequence. To overcome this problem, more rapid and simple NGS system is required to control FMD in Korea. FMDV (O/Boeun/ SKR/2017) RNA was extracted and sequenced using Ion Torrent's bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. The whole genome sequencing of raw data generated data of 1,839,864 (mean read length 283 bp) reads comprising a total of 521,641,058 (≥Q20 475,327,721). Compared with FMDV (GenBank accession No. MG983730), the FMDV sequences in this study showed 99.83% nucleotide identity. Further study is needed to identify these differences. In this study, fast and robust methods for benchtop next generation sequencing (NGS) system was developed for analysis of Foot-and-mouth disease virus (FMDV) whole genome sequences.

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References

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