Korean Journal of Veterinary Service (한국동물위생학회지)

The Korean Society of Veterinary Service (한국동물위생학회)
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Application of next generation sequencing (NGS) system for whole-genome sequencing of porcine reproductive and respiratory syndrome virus (PRRSV)

돼지생식기호흡기증후군바이러스(PRRSV)의 전장 유전체 염기서열(whole-genome sequencing) 분석을 위한 차세대 염기서열 분석법의 활용

  • Moon, Sung-Hyun (College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University) ;
  • Khatun, Amina (College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University) ;
  • Kim, Won-Il (College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University) ;
  • Hossain, Md Mukter (Department of Medicine, Faculty of Veterinary & Animal Science, Sylhet Agricultural University) ;
  • Oh, Yeonsu (Department of Veterinary Pathology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University) ;
  • Cho, Ho-Seong (College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University)
  • 문성현 (전북대학교 수의과대학 수의학과 및 전북대학교 생체안전성연구소) ;
  • 아미나 카툰 (전북대학교 수의과대학 수의학과 및 전북대학교 생체안전성연구소) ;
  • 김원일 (전북대학교 수의과대학 수의학과 및 전북대학교 생체안전성연구소) ;
  • 후세인 엠디 묵터 (방글라데시 실렛농업대학교 수의동물자원과학과) ;
  • 오연수 (강원대학교 수의과대학 수의학과 수의병리학교실) ;
  • 조호성 (전북대학교 수의과대학 수의학과 및 전북대학교 생체안전성연구소)
  • Received : 2016.02.16
  • Accepted : 2016.03.17
  • Published : 2016.03.30
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Abstract

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.

Keywords

References

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