Impact of intra-host population structure on influenza virus antigenic evolution

总结 在全球人群水平上，季节性甲型流感病毒（IAV）进化的特征是重复的选择性 新的抗原变异体逃避了抗体反应，取代了以前流行的病毒株。 尽管在群体水平上有这种明确的模式，但抗原变体的选择通常在群体中并不常见。 急性IAV感染者。这种明显的脱节，在人口的进化过程， 宿主内尺度有助于预测进化结果的挑战。阻碍的过程 IAV在宿主中的选择性及其效力尚未得到系统的研究。为了解决这个 知识差距，我们将测试中心假设，即宿主内病毒种群的遗传结构发挥作用， 在确定一个有益的突变成为固定的可能性方面起着重要作用。特别是，我们假设， 高度适合的变异病毒的命运是由其在接种物中的初始流行度（定量结构）决定的， 它重新出现的时间（时间结构），它在感染组织中的位置（空间结构） 以及竞争变体的存在或不存在（克隆干扰）。反过来，我们预测， 有益变体的传播将依赖于这些因素的组合和疫苗的严格性。 传输瓶颈我们还提出，瓶颈的严重程度是由预先存在的调制 宿主免疫力。为了验证这些假设，我们将监测混合病毒种群的动态 含有季节性IAV和其一种或两种HA抗原变体的豚鼠个体内和 传输伙伴。部分免疫将用疫苗接种诱导，以产生其中抗原性免疫的模型。 变体具有选择性优势。不同的序列条形码将被包括在重组人的HA和NA基因中。 每种病毒都能灵敏地检测出基因瓶颈。HA和NA中的跟踪条形码将允许 基因连锁有待评估。野生型和抗原性变体病毒将在体内与各种抗原性变体病毒组合。 定量、时间和空间结构，然后通过测序监测条形码动力学。与 通过这种方法，我们将对群体遗传结构的后果进行系统的评估， 病毒进化动力学这种控制良好的系统方法将允许识别过程 阻碍个体宿主内部和宿主之间的选择，提供了急需的洞察力， IAV进化的起点。

SUMMARY At the global population level, seasonal influenza A virus (IAV) evolution is characterized by repeated selective sweeps in which novel antigenic variants that escape antibody responses replace previously circulating strains. Despite this clear pattern at a population level, selection of antigenic variants is not typically seen within individuals with acute IAV infection. This apparent disconnect between evolutionary processes at population and within-host scales contributes to the challenge of predicting evolutionary outcomes. The processes that impede IAV selection within the host, and their potency, have not been examined systematically. To address this knowledge gap, we will test the central hypothesis that the genetic structure of within-host viral populations plays a major role in defining the likelihood that a beneficial mutation becomes fixed. In particular, we hypothesize that the fate of a highly fit variant virus is shaped by its initial prevalence in the inoculum (quantitative structure), the timing with which it arises de novo (temporal structure), its location within the infected tissue (spatial structure) and the presence or absence of competing variants (clonal interference). In turn, we predict that onward transmission of a beneficial variant will rely on a combination of these factors and the stringency of the transmission bottleneck. We furthermore propose that the severity of the bottleneck is modulated by pre-existing immunity in the host. To test these hypotheses, we will monitor the dynamics of mixed viral populations containing a seasonal IAV and one or two HA antigenic variants thereof within individual guinea pigs and between transmission partners. Partial immunity will be induced with vaccination to yield a model in which the antigenic variants have a selective advantage. Distinct sequence barcodes will be included in the HA and NA genes of each virus to allow sensitive detection of genetic bottlenecks. Tracking barcodes in both HA and NA will allow genetic linkage to be assessed. The wild type and antigenic variant viruses will be combined in vivo with various quantitative, temporal and spatial structures and then barcode dynamics will be monitored by sequencing. With this approach, we will perform a systematic evaluation of the consequences of population genetic structure for viral evolutionary dynamics. This well-controlled and systematic approach will allow identification of processes that impede selection within and between individual hosts, providing much needed insight into the forces shaping IAV evolution where it begins.