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

描述（由申请方提供）：在6种基因型中，基因型6代表最古老、最多样化和遗传最复杂的病毒。该基因型目前有22种亚型，包括我们指定的6 r-6v。我们已经测序了16个亚型和2个等价物的第一个完整的基因组。我们还发现了16种可能代表14种新亚型的变异体和36种表现出巨大遗传差异的变异体。本申请的总体目标是通过对基因型6的完整序列进行详细分析来确定HCV的遗传变异和病毒学特性，所述基因型6的完整序列将从这些变体中确定。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，有连接到基础研究的应用程序，病人护理。具体目标是：（1）确定71个基因型6变异体的完整基因组，这些变异体显示出显著的遗传变异;（2）确定由最古老的基因型6变异体代表的HCV的流行动力学;以及（3）使用（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趋异特性，这可能使它们更适合于细胞培养。为了实现这些目标，我们将采用一种改进的DNA步移策略，该策略仅需100微升血清即可对完整的HCV基因组进行测序。我们将使用结合了各种聚结方法的BEAST软件。将采用新的策略从最具感染性的病毒颗粒中获得全长HCV基因组。在野生型或与JFH 1分离的嵌合体中，这些基因组将用于开发新的HCV细胞培养模型，该模型将具有许多应用。这些研究的成功完成将有助于缺失和HCV的流行动力学，其遗传变异的生物信息学定义的基础知识，并在开发新的HCV细胞培养模型的新方法。这些具有该序列的模型对于基础HCV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理解HCV的遗传变异、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。这些信息和衍生的模型对于更好的HCV诊断和治疗策略以及改进抗病毒药物和疫苗的设计至关重要。

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.