Feasibility Study of Using Massively Parallel Pyrosequencing in Detecting Variation in Dengue Virus Genome
BackgroundDengue is a positive single-stranded RNA virus which causes Dengue hemorrhagic fever. Due to the lack of proof reading featare in RNA polymerasc, a collection of genetically-different but closely related viral population occurs during viral replication in a host; this is referred to as quasispecies 1. Quasispecies are believed to play an important role in the survival and evolution of dengue viruses as well as in the pathogenesis of disease. The study of Dengue quasispecies has been hampered technically by the sequencing technology. Most of the past investigations were carfled out by culturing the viruses or by RT-PCR amplification followed by cloning. Culture of the viruses is known to allow adaptations and selections to occur, putting artifacts into the studies.Massively parallel pyrosequeneing is a new high throughput sequencing system using emPCR instead of cloning technique This allows us to comprehensively study the quasispecies directly from patients sera/plasma without cloning or culture process. In this feasibility study, we tested whether Roche GS-FLX sequencer is suitable for studying quasispecies in Dengue virus. Two main questions were asked -whether we could cover the whole viral genome and whether we could detect variations at different allele frequencies.
Kwanrutai Chin-inmanu Aroonroong Jairungsri Duangjai Sangsrakru Sithichoke Tangphatsornruang Somvong Tragoonrung Prapat Suriyaphol
Bloinformatics and Data Management for Research Unit, Medical Molecular Biology Unit, Office for Res Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine, Siriraj Ho Genome Insitute, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Bloinformatics and Data Management for Research Unit Medical Molecular Biology Unit, Office for Rese
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
826
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）