HCV Genotype 6: A Model for HCV Genetics and Molecular Epidemiology Studies

HCV 基因型 6：HCV 遗传学和分子流行病学研究模型

• 批准号: 7886840
• 负责人: LING LU
• 金额: $ 36.6万
• 依托单位: UNIVERSITY OF KANSAS MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-15 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7886840
• 关键词: 5' Untranslated Regions; American; Antiviral Agents; Area; Asia; Basic Science; Behavior; Bioinformatics; Birth; Canada; Categories; Cell Culture System; Cell Culture Techniques; Cells; Cessation of life; Characteristics; Chimera organism; China; Cities; Classification; Clinical; Collection; Complementary DNA; Complex; Computer software; DNA; Data Set; Databases; Detection; Development; Diagnosis; Diagnostic; Epidemic; Epidemiology; Equilibrium; Event; Evolution; Fossils; Future; Gene Expression; Genetic; Genetic Recombination; Genetic Variation; Genome; Genomics; Genotype; Goals; Growth; Hepatitis C virus; Immunity; Infection; Knowledge; Length; Life; Life Cycle Stages; Link; Logistics; Markov Chains; Methods; Modeling; Molecular; Molecular Epidemiology; Mutation; Patient Care; Patients; Pattern; Phase; Population Growth; Preparation; Process; Property; Public Health; Qualifying; RNA; Recording of previous events; Recruitment Activity; Reporting; Research; Sampling; Serum; Southeastern Asia; System; Testing; Thailand; Time; Universities; Vaccines; Variant; Vietnam; Viral; Viral Proteins; Virion; Virus; Virus Assembly; Virus Replication; Walking; base; design; epidemiology study; expectation; experience; genetic epidemiology; improved; innovation; interferon therapy; novel; novel strategies; practical application; protein expression; public health relevance; research study; tool; transmission process; vaccine evaluation; vector; viral RNA; virology; virus genetics; virus host interaction

DESCRIPTION (provided by applicant): Among six genotypes, the genotype 6 represents the oldest, most diverse and genetically most complex viruses. This genotype currently has 22 subtypes, including 6r-6v we designated. We have sequenced the first complete genomes of 16 subtypes and 2 equivalents. We have also discovered 16 variants that may represent 14 new subtypes and 36 variants that show great genetic differences. The overall goal of this application is to define the genetic variation and virology properties of HCV by conducting detailed analyses on a full panel of genotype 6 complete sequences that will be determined from these variants. Based on the sequences, we will assemble full length HCV genomes and use for developing new HCV cell culture models. The rationale is that clarifying these HCV sequences will enable many bioinformatics analyses that have applications linking to basic research to patient care. The Specific Aims are to: (1) determine the complete genomes of 71 genotype 6 variants showing substantial genetic variations; (2) determine the epidemic dynamics of HCV that is represented by the oldest genotype 6 variants; and (3) develop HCV genotype 6 cell culture models using unique HCV genomes that are defined in (1). It is hypothesized that HCV genotype 6 represents a "living viral fossil" that will best reflect the past history of the virus and that, being the most complex among all HCV genotypes, the genotype 6 variants may have higher divergent properties that may make them more suitable for cell cultures. To accomplish these aims, we will employ an improved DNA walking strategy that can sequence a complete HCV genome from only 100 ¿l of serum. We will use the BEAST software that combines various coalescent methods. Novel strategies will be recruited to obtain the full length HCV genomes from the most infectious virus particles. In wild type or in chimeras with the JFH1 isolate, these genomes will be used to develop new HCV cell culture models that will have many applications. The successful completion of these studies will contribute the missing and fundamental knowledge to the epidemic dynamics of HCV, bioinformatic definition of its genetic variations, and the novel approaches in developing new HCV cell culture models. These models with the sequence will be vital for basic HCV research and for patient care and public health. PUBLIC HEALTH RELEVANCE: successful completion of these studies will contribute new viral sequences and cell culture models to understand the HCV genetic variation, epidemiology behavior, and virology mechanisms. This information and the derived models are vital for better strategies of HCV diagnosis and treatment, and the improved designs of antivirals and vaccines.

描述（由申请人提供）：在6个基因型中，基因型6代表了最古老、最多样化和遗传最复杂的病毒。该基因型目前有22个亚型，包括我们指定的6r-6v。我们已经对16个亚型和2个等价物的第一个完整基因组进行了测序。我们还发现了16个可能代表14个新亚型的变异和36个表现出巨大遗传差异的变异。该应用程序的总体目标是通过对从这些变异中确定的完整的6基因型完整序列进行详细分析来定义HCV的遗传变异和病毒学特性。基于这些序列，我们将组装全长HCV基因组并用于开发新的HCV细胞培养模型。其基本原理是，澄清这些HCV序列将使许多生物信息学分析能够应用于基础研究和患者护理。具体目的是：(1)确定71个具有显著遗传变异的基因6型变异的全基因组；(2)确定以最古老的基因6型变异为代表的HCV流行动态；(3)利用(1)中定义的独特HCV基因组开发HCV基因型6细胞培养模型。据推测，HCV基因型6代表了一种“活病毒化石”，它将最好地反映病毒的过去历史，并且作为所有HCV基因型中最复杂的基因型6变体可能具有更高的差异特性，这可能使它们更适合细胞培养。为了实现这些目标，我们将采用一种改进的DNA行走策略，仅从100 %的血清中就能测序出完整的HCV基因组。我们将使用BEAST软件，它结合了各种聚结方法。将采用新的策略从最具传染性的病毒颗粒中获得全长HCV基因组。在野生型或与JFH1分离物嵌合体中，这些基因组将用于开发具有许多应用价值的新型HCV细胞培养模型。这些研究的成功完成将为HCV的流行动态、遗传变异的生物信息学定义以及开发新的HCV细胞培养模型的新方法提供缺失的和基础的知识。这些具有序列的模型对于HCV基础研究以及患者护理和公共卫生至关重要。公共卫生相关性：这些研究的成功完成将为了解HCV遗传变异、流行病学行为和病毒学机制提供新的病毒序列和细胞培养模型。这些信息和推导出的模型对于HCV诊断和治疗的更好策略以及抗病毒药物和疫苗的改进设计至关重要。