HCV diversity and resistance analyzed by DNA bar coding and pyrosequencing

通过 DNA 条形码和焦磷酸测序分析 HCV 多样性和耐药性

• 批准号: 7989329
• 负责人: GARY P. WANG
• 金额: $ 11.02万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-01 至 2013-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7989329
• 关键词: Antiviral Therapy; Area; Bar Codes; Biochemistry; Bioinformatics; Chronic; Chronic Hepatitis C; Clinical; Cloning; Combined Modality Therapy; Communicable Diseases; Complex; DNA; Data; Data Analyses; Development; Dideoxy Chain Termination DNA Sequencing; Disease; Drug resistance; Drug resistance pathway; Enzymatic Biochemistry; Enzymes; FDA approved; Fellowship; Future; Genetic; Genetic Heterogeneity; Genetic Variation; Genomics; Genotype; HIV; Hepatitis C; Hepatitis C virus; Human Genome; Individual; Interferons; Internal Medicine; Investigation; Knowledge; Laboratories; Lead; Liver diseases; Mediating; Mentors; Methods; Minor; Molecular; Mutation; Nature; New Agents; Pathogenesis; Pathway interactions; Patients; Pennsylvania; Pharmaceutical Preparations; Phase; Population; Proteins; Research; Research Personnel; Research Training; Residencies; Resistance; Running; Sampling; Scientist; Sequence Analysis; Site; Structure; Techniques; Technology; Training; Training Programs; Treatment Protocols; Treatment outcome; Universities; Variant; Viral; Viral Pathogenesis; Virus; Work; anti-hepatitis C; antiretroviral therapy; base; career; career development; experience; in vivo; innovation; insight; interferon therapy; lentiviral integration; novel; novel therapeutics; resistance mutation; response; skills; viral resistance; virology; virus genetics; virus host interaction; virus infection mechanism; virus pathogenesis

DESCRIPTION (provided by applicant): This application outlines a 5 year plan to train the candidate for an academic career investigating the pathogenesis of hepatitis C virus (HCV) infection and mechanism of drug resistance. Dr. Wang has completed residency training in Internal Medicine at Yale University and a Clinical Fellowship in Infectious Diseases at University of Pennsylvania. He has a strong background in mechanistic enzymology, having received a Ph.D. in biochemistry under Dr. Charles Grubmeyer at Temple University, and is now working in the laboratory of his sponsor, Dr. Frederic Bushman, studying the function of lentiviral vectors in gene therapy patients using DMA bar coding and pyrosequencing. Dr. Wang has established a comprehensive research and training program so that he can gain the expertise to independently attack questions of HCV pathogenesis and resistance. Dr. Bushman, a world authority in the field of virology, and Dr. Kyong-Mi Chang, an expert in HCV pathogenesis, will jointly mentor the candidate's scientific development. An advisory board of prominent scientists and clinicians will mentor his career development. HCV is a leading cause of chronic liver disease in the U.S. The only FDA approved treatment using interferon is often ineffective, yet the basic mechanisms of resistance are largely unknown. Several compounds targeting viral-encoded enzymes are currently in clinical development. However, their use will almost certainly be complicated by the highly diverse viral populations in vivo, which may result in complex drug resistance pathways. Recently, the application of genome sequencing techniques to such problems in viral resistance has allowed mass identification of viral variants. In published work, we have utilized DNA bar coding and pyrosequencing to identify rare drug resistant mutations in HIV and to monitor locations of retroviral integration sites in vivo. We will combine these powerful tools with bioinformatics and a variety of molecular techniques to advance understanding of HCV evolution and resistance in vivo. We propose the following Aims: 1) establish methods for efficient amplification and high-throughput pyrosequencing of HCV; 2) investigate the selective pressures on viral populations resulting from interferon therapy; 3) define the population structure of HCV. The proposed in-depth laboratory and didactic training will guide the candidate in becoming an independent investigator in viral pathogenesis and resistance.

描述（由申请人提供）：本申请概述了一个5年计划，以培养候选人的学术生涯调查丙型肝炎病毒（HCV）感染的发病机制和耐药机制。王医生在耶鲁大学完成了内科住院医师培训，并在宾夕法尼亚大学获得了传染病临床奖学金。他在机械酶学方面有很强的背景，曾获得博士学位。他在坦普尔大学的Charles Grubmeyer博士的指导下从事生物化学研究，现在在他的赞助人Frederic Bushman博士的实验室工作，使用DMA条形码和焦磷酸测序研究慢病毒载体在基因治疗患者中的功能。王博士已建立了一个全面的研究和培训计划，使他能够获得专业知识，独立攻击丙型肝炎病毒的发病机制和耐药性的问题。病毒学领域的世界权威Bushman博士和HCV发病机制专家Kyong-Mi Chang博士将共同指导候选人的科学发展。一个由杰出科学家和临床医生组成的顾问委员会将指导他的职业发展。HCV是美国慢性肝病的主要原因，FDA批准的唯一使用干扰素的治疗通常无效，但耐药的基本机制在很大程度上是未知的。几种靶向病毒编码酶的化合物目前正在临床开发中。然而，它们的使用几乎肯定会因体内高度多样化的病毒群体而复杂化，这可能导致复杂的耐药途径。最近，基因组测序技术在病毒抗性中的这些问题的应用已经允许大量鉴定病毒变体。在已发表的工作中，我们利用DNA条形码和焦磷酸测序来鉴定HIV中罕见的耐药突变，并监测体内逆转录病毒整合位点的位置。我们将联合收割机这些强大的工具与生物信息学和各种分子技术相结合，以促进对HCV体内进化和耐药性的理解。我们提出以下目标：1）建立HCV的高效扩增和高通量焦磷酸测序方法; 2）研究干扰素治疗对病毒群体的选择性压力; 3）确定HCV的群体结构。拟议的深入实验室和教学培训将指导候选人成为病毒发病机制和耐药性的独立研究者。