[논문]Whole genome sequencing of foot-and-mouth disease virus using benchtop next generation sequencing (NGS) system

Moon, Sung-Hyun; Oh, Yeonsu; Tark, Dongseob; Cho, Ho-Seong

doi:10.7853/kjvs.2019.42.4.297

Whole genome sequencing of foot-and-mouth disease virus using benchtop next generation sequencing (NGS) system 원문보기

韓國家畜衛生學會誌 = Korean journal of veterinary service, v.42 no.4, 2019년, pp.297 - 300

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)

Abstract ▼ AI-Helper

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.

주제어

표/그림 (2)

그림 Fig. 1. (A) Workflow of Ion torrent PGM system; (B) Sensor, well and chip architecture. Ions get released when DNA bases are matched. Sequence output is generated by the detection system (Rothberg et al, 2011).
그림 Fig. 2. The map represents the circular view of the genome sequence of Foot-and-mouth disease (FMD) virus. The circle was made by BRIG software version 0.95. The chromosome outermost circular ring shows FMD virus, followed by the second ring from reference strain (GenBank accession No. MG983730). The third circular ring towards the center represents the GC skew information in the (+) strand (green) and (−) strand (dark pink).

AI 본문요약
AI-Helper

* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.

문제 정의

1). The purpose of this study is to develop simple and rapid sequencing system for FMDV isolated from Korea (O/Boeun/SKR/2017) using the benchtop NGS system.

제안 방법

Amplification was performed in a VeritiTM 96-Well Thermal Cycler (Applied Biosystems, CA, USA), the program consisting of an initial denaturation of 5 min at 95°C was, 15s of denaturation at 95°C, 60s of annealing at 58°C and 1 min of extension at 70°C for 8 cycles.

대상 데이터

FMDV isolate (O/Boeun/SKR/2017) was used in this study. Viral RNA was extracted using the QIAamp Viral RNA Mini Kit (Qiagen, USA) as per the manufacturer’s instructions.
2. The raw sequence data were assembled with CLC Genomics Workbench version 8.5.1 (CLC Bio, Qiagen, USA) using Foot-and-mouth disease virus (O type, GenBank accession No. MG983730). The assembly visualization was performed using BLAST Ring Image Generator (BRIG) software which allowed comparative genome analysis (Alikhan et al, 2011).

이론/모형

MG983730). The assembly visualization was performed using BLAST Ring Image Generator (BRIG) software which allowed comparative genome analysis (Alikhan et al, 2011).

성능/효과

2. Compared with FMDV (GenBank accession No. MG983730), the FMDV sequences in this study showed 99.83% nucleotide identity. However, the comparative analysis between MG983730 and sequenced FMDV reveals deletion and mutation in the FMDV.

후속연구

However, the comparative analysis between MG983730 and sequenced FMDV reveals deletion and mutation in the FMDV. Further study is needed to identify these differences.

참고문헌 (8)

Alexandersen S, Zhang Z, Donaldson AI, Garland AJ. 2003. The pathogenesis and diagnosis of foot-and-mouth disease. J Comp Path 129: 1-36.

상세보기
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. 2011. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12: 402.

상세보기
Brito BP, Rodriguez LL, Hammond JM, Pinto J, Perez AM. 2017. Review of the global distribution of foot-and-mouth disease virus from 2007 to 2014. Transbound Emerg Dis 64: 316-332.

상세보기
Daum LT, Rodriguez JD, Worthy SA, Ismail NA, Omar SV, Dreyer AW, Fourie PB, Hoosen AA, Chambers JP, Fischer GW. 2012. Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol 50: 3831-3837.

상세보기
Knowles NJ, Samuel AR. 2003. Molecular epidemiology of footand-mouth disease virus. Virus Res 91:65-80.

상세보기
Lee YJ, Chu JQ, Lee SY, Kim SM, Lee KN, Ko YJ, Lee HS, Cho IS, Nam SH, Park JH. 2011. Analysis of complete genome sequence of foot-and-mouth disease (FMD) Aisa1 vaccine strain. Korean J Vet Serv 34: 95-102.

원문보기 상세보기
Moon SH, Khatun A, Kim WI, Hossain MM, Oh Y, Cho HS. 2016. Application of next generation sequencing (NGS) system for whole-genome sequencing of porcine reproductive and respiratory syndrome virus (PRRSV). Korean J Vet Serv 39: 41-49.

원문보기 상세보기
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.

상세보기

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증