Functional Profiles of Hepatitis C Virus Genome at Single Nucleotide Resolution

描述：丙型肝炎病毒已成为人类健康的主要问题，据估计，全世界有1.7亿人持续感染丙型肝炎病毒。丙型肝炎病毒感染导致肝脏疾病，包括慢性肝炎、肝硬变和肝细胞癌，特别是在艾滋病毒感染者中。病毒性肝炎在艾滋病患者中进展更快、更具破坏性，已成为非艾滋病相关死亡的主要原因。旨在评估消除丙型肝炎病毒对肝癌发病率的影响的研究表明，成功根除丙型肝炎病毒可以降低肝功能衰竭和肝癌发生的风险。然而，无论是预防性疫苗还是治疗性疫苗都不能用于丙型肝炎病毒感染。在最近批准这两种酶抑制剂之前，标准治疗一直是干扰素联合治疗(干扰素？)和利巴韦林，只提供有限的应答率。因此，有必要了解丙型肝炎病毒对干扰素的抗病毒作用产生抵抗的机制。已知的I型干扰素反应可以保护哺乳动物宿主免受病毒感染。然而，病毒已经进化到利用不同的策略来逃避多层免疫反应。结果，尽管诱导了干扰素应答，丙型肝炎病毒仍持续存在于宿主体内，因此约50%的丙型肝炎患者对干扰素？？产生抵抗力。治疗。为了研究丙型肝炎病毒对抗干扰素应答的机制，拟议的研究将利用高通量、定量、基因组规模的图谱平台系统地定位丙型肝炎病毒序列，这对于单一氨基酸分辨率的抗干扰素功能至关重要。这种方法背后的概念是随机突变病毒基因组上的每个碱基对，在存在或不存在干扰素-β的情况下为突变库进行选择，并进行大规模并行测序，以确定在选择中哪些突变被减少，这可能是由于它们失去了抗干扰素功能。研究的具体目标如下：(1)建立 高复杂性的单核苷酸突变丙型肝炎病毒文库；(2)用干扰素处理筛选文库。确定对对抗干扰素反应至关重要的病毒序列；(3) 确定单个突变体的特征，并验证丙型肝炎病毒与干扰素反应之间的相互作用。这项研究有望以系统和公正的方式绘制出整个丙型肝炎病毒基因组中导致其对干扰素治疗产生抵抗力的病毒序列。对这些序列的鉴定将为理解丙型肝炎病毒可以逃避干扰素反应并对治疗产生耐药性的原因提供知识。此外，这项研究将为疫苗开发提供深入的知识。在缺乏干扰素处理的情况下选择突变库也将揭示具有高遗传屏障的序列延伸，这将成为疫苗开发的新靶点。因此，它将为克服病毒耐药性提供新的抗病毒治疗策略。

DESCRIPTION: HCV has emerged as a major human health concern with an estimate of 170 million people who are persistently infected worldwide. HCV infections cause liver diseases including chronic hepatitis, cirrhosis, and hepatocellular carcinoma, especially in HIV- infected persons. Viral hepatitis progresses faster and more devastating among AIDS patients, which has become the leading cause of non AIDS-related deaths. Studies aiming to evaluate the effect of HCV elimination on the incidence of HCC indicate that successful eradication of HCV can reduce the risk for failure of liver function and HCC development. However, neither prophylactic nor therapeutic vaccine is available for HCV infection. Before the recent approval of the two protease inhibitors, the standard treatment has been combination therapy with interferon (IFN-?) and ribavirin which only offers limited response rate. Therefore, there is a need for understanding the mechanisms by which HCV develops resistance to the antiviral function of IFN. It's known that type I interferon (IFN) response can defend mammalian host from virus infection. However, viruses have evolved to utilize different strategies to evade from multiple layers of immune response. As a result, HCV persist in the host despite induction of IFN response and thereby approximately 50% of HCV patients are resistant to IFN-? treatment. To study the mechanisms by which HCV antagonizes the IFN response, the proposed study will systematically map HCV sequences, which is critical for anti-IFN function at single amino acid resolution with a high-throughput, quantitative, genome-scale profiling platform. The concept behind this approach is to randomly mutagenize every base pair on the virus genome, select for the mutant library in the presence or absence of IFN-?, and perform massively parallel sequencing to determine which mutations are diminished in the selection, which is presumably due to their loss of anti-IFN function. The research specific aims are the following: (1) Establish a single nucleotide mutant HCV library with high complexity; (2) Screen the library with treatment of IFN-? to identify the viral sequences critical for counteracting the IFN response; (3) Characterize individual mutants and verify the interaction between HCV with IFN response. The study is expected to map the viral sequences in the entire HCV genome responsible for its resistance to IFN therapy in a systemic and unbiased manner. Identification of these sequences will provide knowledge in understanding the reasons why HCV can evade the IFN response and establish resistance to the treatment. Additionally, this study will provide a depth of knowledge for vaccine development. Selection of the mutant library in the absence of IFN treatment will also reveal the sequence stretches with high genetic barrier to mutate, which will serve as novel targets for vaccine development. Therefore, it will offer novel antiviral treatment strategies to overcome viral resistance.