Exploring the hepatitis C virus genome using single molecule realtime sequencing

作     者：Haruhiko Takeda Taiki Yamashita Yoshihide Ueda Akihiro Sekine 

作者机构：Department of Omics-based MedicineCenter for Preventive Medical ScienceChiba UniversityChiba 260-0856Japan Department of Gastroenterology and HepatologyGraduate School of MedicineKyoto UniversityKyoto 606-8507Japan 

出 版 物：《World Journal of Gastroenterology》 (世界胃肠病学杂志（英文版）)

年 卷 期：2019年第25卷第32期

页      面：4661-4672页

核心收录：

学科分类：10[医学] 

基　　金：Japan Society for the Promotion of Science, JSPS, (19K07520) Japan Society for the Promotion of Science, JSPS 

主　　题：Third generation sequencing PacBio RSII Single molecule real-time sequencing Hepatitis C virus Resistance-associated substitution Nanopore sequencer 

摘      要：Single molecular real-time(SMRT)sequencing,also called third-generation sequencing,is a novel sequencing technique capable of generating extremely long contiguous sequence *** conventional short-read sequencing cannot evaluate the linkage of nucleotide substitutions distant from one another,SMRT sequencing can directly demonstrate linkage of nucleotide changes over a span of more than 20 kbp,and thus can be applied to directly examine the haplotypes of viruses or bacteria whose genome structures are changing in real *** addition,an error correction method(circular consensus sequencing)has been established and repeated sequencing of a single-molecule DNA template can result in extremely high *** advantages of long read sequencing enable accurate determination of the haplotypes of individual viral *** sequencing has been applied in various studies of viral genomes including determination of the full-length contiguous genome sequence of hepatitis C virus(HCV),targeted deep sequencing of the HCV NS5A gene,and assessment of heterogeneity among viral ***,the emergence of multi-drug resistant HCV viruses has become a significant clinical issue and has been also demonstrated using SMRT *** this review,we introduce the novel third-generation PacBio RSII/Sequel systems,compare them with conventional next-generation sequencers,and summarize previous studies in which SMRT sequencing technology has been applied for HCV genome *** also refer to another long-read sequencing platform,nanopore sequencing technology,and discuss the advantages,limitations and future perspectives in using these thirdgeneration sequencers for HCV genome analysis.