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Exploring the hepatitis C virus genome using single molecule realtime sequencing

World Journal of Gastroenterology 2019年第32期25卷 4661-4672页

作者： Haruhiko Takeda Taiki Yamashita Yoshihide Ueda akihiro sekine Department of Omics-based Medicine Center for Preventive Medical ScienceChiba UniversityChiba 260-0856Japan Department of Gastroenterology and Hepatology Graduate School of MedicineKyoto UniversityKyoto 606-8507Japan

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.

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

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