Analysis of properties of HIV-1 subtype C envelope glycoprotein

描述(由申请人提供)：HIV-1疾病进展的许多重要生物学决定因素和包膜糖蛋白的传播图谱，包括抗体中和敏感性、病毒进入的趋向性和T细胞反应的表位。包膜基因的遗传和表型特征表明，病毒在传播到其他身体部分和传播过程中存在瓶颈效应，导致病毒种群主要是同质的。然而，目前在准确分配HIV-1辅助受体使用、区分遗传变异和检测患者体内和传播对之间的HIV准种中的微小变异方面的局限性导致了有争议的发现。此外，所研究的小患者样本量太小，无法对艾滋病毒传播和致病的机制做出广泛的概括。最后，包膜基因的这些不同特性主要在B亚型感染中被研究，而在艾滋病毒-1 C亚型感染中较少被清楚地阐明，C亚型是世界上传播最快和最流行的感染。我们假设，具有不同包膜序列和辅助受体使用的异源HIV-1群体在感染期间传播，但用我们目前可用的技术还没有完全表征和测量。我们建议使用新的和更灵敏的方法来确定辅助受体的使用，并对来自博茨瓦纳的一个大型C亚型临床队列的包膜基因进行深入的测序和遗传分析。C亚型感染的包膜基因将在纵向样本中以及血浆-母乳和母婴配对之间进行研究。我们计划更深入地研究HIV-1 C亚型包膜糖蛋白的特性，具体目的如下：1)确定辅助受体转换的临床和遗传决定因素；2)评估HIV-1母乳传播的相关性；3)使用超深测序方法检查母婴传播对中病毒通过不同途径的母婴传播。这项研究的结果将进一步了解病毒在传播和疾病进展的背景下的演变，确定传播和疾病进展的临床相关性，并最终为世界上受艾滋病毒影响最严重的地区的潜在预防、治疗和疫苗开发战略提供见解。

DESCRIPTION (provided by applicant): Many important biological determinants of HIV-1 disease progression and transmission map to the envelope glycoprotein, including antibody neutralization susceptibility, viral tropism for entry and epitopes for T cell response. Genetic and phenotypic characterizations of the envelope gene suggest a bottleneck effect in the spread of the virus to other body compartments and transmission, resulting in a predominantly homogenous viral population. However, the limitations in current methods to accurately assign HIV-1 coreceptor usage, distinguish genetic variations and detect minor variants in the HIV quasispecies within a patient and between transmission pairs have led to controversial findings. Furthermore, the small patient sample size studied has been too small to make broad generalization regarding mechanisms of HIV transmission and pathogensis. Lastly, these various properties of the envelope gene have been studied predominantly in subtype B infection and less clearly elucidated in HIV-1 subtype C, the most rapidly spreading and prevalent infection worldwide. We hypothesize that a heterogenous HIV-1 population with different envelope sequences and coreceptor usage are transmitted during infection but is not fully characterized and measured by our current available techniques. We propose to use novel and more sensitive methods to determine coreceptor usage and to perform in-depth sequencing and genetic analyses of the envelope gene from a large subtype C clinical cohort from Botswana. The envelope gene in subtype C infection will be studied in longitudinal samples, as well as between plasma-breast milk and mother-infant pairs. We plan to study in greater depth the properties of the HIV-1 subtype C envelope glycoprotein with the following specific aims: 1) identify clinical and genetic determinants of coreceptor switching, 2) assess for correlates of breastfeeding transmission of HIV-1 and 3) examine pattern of viral transmission among mother-to-child transmitting pairs occurring through different routes of MTCT using ultradeep sequencing. The results of this study will further the understanding of viral evolution in the context of transmission and disease progression, identify clinical correlates of transmission and disease progression, and ultimately give insights into potential strategies of prevention, treatment and vaccine development in those parts of the world most affected by HIV.