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

项目摘要/总结 甲型流感病毒（IAV）通常被描述为具有近乎无限的进化能力，因为它们的 种群规模往往很大，突变率很高，世代时间很短。事实上， 全球范围内的进化的特征是获得和固定突变，这些突变有助于进化， 人类免疫的斗篷这些全球模式与全基因组测序的结果形成对比 对流感病毒在更局部范围内的研究，几乎没有发现自然选择的证据， 这表明，遗传漂变，等位基因频率的随机波动，是形成的主导力量， IAV在个体内和个体间的进化。群体遗传学理论预测，遗传漂变（ran- 在小种群中，自然选择的效率也相对较低。 IAV在宿主之间的传播涉及瓶颈，其中病毒群体大小显著减少， 因此，在IAV传播瓶颈期间，遗传漂变被放大是理所当然的。我假设- 遗传漂变是季节性IAV快速进化的一个未被充分认识的障碍， 瓶颈降低了自然选择的效率。为了验证这个假设，我将评估积云- 在细胞培养中，通过一系列精心控制的瓶颈事件，遗传漂变产生了积极的影响。我也会评估 这些体外实验的翻译相关性，通过表征天然IAV trans- 人类宿主的使命事件。该项目的目标是了解的影响和机制， 在体外系统和人类宿主中的遗传漂移约束IAV进化。 该提案将利用独特的分子工具集，并将采用进化假设检验- 为了理解（1）遗传漂变和（2）连续传递后有害突变棘轮的作用， 单个主机内部和之间的锡永瓶颈事件。 为了实现这一点，我提出了两个概念上相关但又不同的目标： 目标1将描述在中性（目标1a）和 选择性（目标1b）条件。 目标2将描述和量化流感在人类中传播的瓶颈。 成功完成拟议的实验将明确连接传输瓶颈，以控制 IAV病毒在个体宿主水平上的紧张进化，并将确定 在宿主中保存和传播有益的突变，这对改善当前的环境至关重要。 在种群水平上的IAV进化模型。此外，拟议的实验和分析将支持- 为我提供了有价值的培训，这些培训是专门为指导我实现我的总体职业目标而设计的-成为一名 独立的物理学家和科学家

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.