NEF GENE EVOLUTION FROM A SINGLE TRANSMITTED STRAIN IN ACUTE SIV INFECTION

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 目的：利用HIV-1/AIDS的非人灵长类动物模型，检验我们的主要HIV-1感染模型的有效性。 为了研究SIV感染急性期单个传播株的nef基因的进化，我们采用单基因组扩增的方法进行了全长nef基因的纵向测序。免疫缺陷病毒感染的急性期在决定人类和非人类灵长类动物的稳态病毒载量和随后的疾病进展方面发挥着至关重要的作用。最近，我们开发了一种蒙特卡罗模拟方法，对初次感染HIV-1期间的病毒进化进行数学分析，从而能够对来自多个传播病毒株和单个传播病毒株的新HIV-1感染进行分类，并估计感染后的时间。 结果：用SIVmac239克隆感染两只恒河猴后的前3周，共收集了207个SIV nef SIV序列，其遗传多样性水平与急性HIV-1感染的基因多样性水平相当，为0%~0.053%，为0.005%~0.127%。我们证实，急性HIV-1感染模型正确地将实验中的SIV感染识别为由单个创立者菌株引发的“同源”感染。样本菌株的一致序列与模型预测的传播序列相对应。然而，在感染后第7天、第11天和第18天测得的多样性顺序减少违反了模型假设，没有任何选择地中性进化。虽然来自单一传播毒株的SIV感染前3周的nef基因进化速度与急性HIV-1感染时观察到的序列进化速度相当，但在实验感染非人灵长类动物的早期阶段观察到了对创始人nef基因的纯化选择。 这项研究使用了WNPRC模仿学和病毒学和遗传学服务。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Objective: To test the validity of our primary HIV-1 infection model using a non-human primate model for HIV-1/AIDS. To examine evolution of the viral nef genes from a single transmitted strain during the acute phase of SIV infection, we sequenced full-length nef genes longitudinally using the method of single genome amplification. The acute phase of immunodeficiency virus infection plays a crucial role in determining steady-state virus load and subsequent progression of disease in both humans and nonhuman primates. Recently we developed a Monte-Carlo simulation with mathematical analysis of viral evolution during primary HIV-1 infection that enables classification of new HIV-1 infections originating from multiple versus single transmitted viral strains and the estimation of time elapsed following infection. Results: A total of 207 SIV nef SIV sequences, collected during the first 3 weeks following experimental infection of two rhesus macaques with the SIVmac239 clone, were analyzed and found to display a comparable level of genetic diversity, 0% to 0.053%, with that of env sequences from acute HIV-1 infection, 0.005% to 0.127%. We confirmed that the acute HIV-1 infection model correctly identified the experimental SIV infections in rhesus macaques as "homogenous" infections, initiated by a single founder strain. The consensus sequence of the sampled strains corresponded to the transmitted sequence as the model predicted. However, measured sequential decrease in diversity at day 7, 11, and 18 post infection violated the model assumption, neutral evolution without any selection. While nef gene evolution over the first 3 weeks of SIV infection originating from a single transmitted strain showed a comparable rate of sequence evolution to that observed during acute HIV-1 infection, a purifying selection for the founder nef gene was observed during the early phase of experimental infection of a nonhuman primate. This research used WNPRC Immulogy & Virology and Genetics Services.