Defining the role of genetic drift in within-host influenza evolution

项目摘要/摘要 甲型流感病毒(IAV)通常被描述为具有近乎无限的进化能力，因为它们 种群规模往往很大，突变率很高，世代时间很短。事实上，IAV 全球尺度上的进化的特征是获得和固定促进ES- 开普敦免于人类豁免权。这些全球模式与全基因组测序的结果进行了对比 在更多地方尺度上对流感病毒的研究，几乎没有发现自然选择的证据，而是 这表明，基因漂移，即等位基因频率的随机波动，是塑造 IAV在个体内和个体之间的进化。种群遗传学理论预测，遗传漂移(RAN-R) 多重性)对小种群的作用最强，在那里自然选择的效率也相对较低。 IAV在宿主之间的传播涉及一个瓶颈，其中病毒种群大小显著减少， 因此，遗传漂移在IAV传播瓶颈期间被放大是顺理成章的。我假设你是- 磁漂移是季节性IAV快速演变的一个被低估的障碍，因为传播 瓶颈降低了自然选择的效率。为了验证这一假设，我将评估积云- 基因漂移通过细胞培养中一系列精心控制的瓶颈事件产生的积极影响。我也会评估 这些体外实验的翻译相关性通过表征自然IAV反式病毒的大数据集。 在人类宿主中的任务事件。这个项目的目标是了解 体外系统和人类宿主中遗传漂移受限的IAV进化。 这项提议将利用一种独特的分子工具集，并将采用进化假说检验- 以了解(1)遗传漂移和(2)在序列传递后有害的突变棘轮的作用。 单个主机内部和之间的Sion瓶颈事件。 为了实现这一目标，我提出了两个概念上相关但截然不同的目标： 目标1将描述重复瓶颈对中性条件下IAV种群的影响(目标1a) 选择性(目标1b)条件。 目标2将描述和量化流感在人类中的传播瓶颈。 拟议中的实验的成功完成将明确地将传输瓶颈连接到CON-1。 IAV病毒在个体宿主水平上的紧张进化，并将确定支撑机制 有益突变在宿主中的保存和传递，这是改善电流的关键 种群水平上的IAV进化模型。此外，拟议的实验和分析将有助于 让我接受有价值的培训，专门指导我走向职业生涯的总体目标--成为一名 独立的医生兼科学家。

PROJECT ABSTRACT / SUMMARY Influenza A viruses (IAV) are typically described as having a near-limitless capacity to evolve because their population sizes are often large, their mutation rates are high, and their generation times are short. Indeed, IAV evolution on the global scale is characterized by the acquisition and fixation of mutations that facilitate es- cape from human immunity. These global patterns are contrasted by results from whole genome sequencing studies of influenza viruses on more local scales, which find little evidence for natural selection and instead suggest that genetic drift, the stochastic fluctuation of allele frequencies, is the dominant force shaping the evolution of IAV within and between individuals. Population genetics theory predicts that genetic drift (ran- domness) acts most strongly on small populations, where natural selection is also comparatively inefficient. Transmission of IAV between hosts involves a bottleneck in which viral population size is markedly reduced, so it stands to reason that genetic drift is amplified during IAV transmission bottlenecks. I hypothesize ge- netic drift is an underappreciated barrier to the rapid evolution of seasonal IAVs because transmission bottlenecks reduce the efficiency of natural selection. To test this hypothesis, I will evaluate the cumula- tive effects of genetic drift via a series of carefully controlled bottleneck events in cell culture. I will also assess the translational relevance of these in-vitro experiments by characterizing a large dataset of natural IAV trans- mission events in human hosts. The goal of this project is to understand the impact and mechanisms of genetic drift-constrained IAV evolution in an in-vitro system and in human hosts. This proposal will take advantage of a unique molecular toolset and will employ evolutionary hypothesis test- ing to understand the role of (1) genetic drift and (2) a deleterious mutational ratchet following serial transmis- sion bottleneck events within and between individual hosts. In order to accomplish this, I propose two conceptually related but distinct aims: Aim 1 will characterize the effects of repeated bottlenecks on IAV populations under neutral (Aim 1a) and selective (Aim 1b) conditions. Aim 2 will characterize and quantify influenza transmission bottlenecks in humans. Successful completion of the proposed experiments will definitively link transmission bottlenecks to con- strained evolution of IAV viruses at the level of the individual host and will identify mechanisms underpinning the preservation and transmission of beneficial mutations in hosts, which are essential to improve current models of IAV evolution at the population level. Additionally, the proposed experiments and analyses will pro- vide me with valuable training specifically designed to guide me toward my overall career goal – to become an independent physician-scientist.