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

摘要 在全球人口水平上，季节性甲型流感病毒(IAV)的演变具有反复选择性 逃避抗体反应的新的抗原变异体取代以前流行的菌株的扫描。 尽管在种群水平上有这种明显的模式，但抗原变异的选择通常不会在 患有急性IAV感染的个人。这种明显的种群进化过程和进化过程之间的脱节 宿主内部的尺度增加了预测进化结果的挑战。阻碍进程的进程 寄主内的IAV选择及其效力还没有得到系统的检验。要解决这个问题 知识鸿沟，我们将检验宿主内病毒种群的遗传结构起作用的中心假设 在定义有益突变变得固定的可能性方面起着重要作用。特别是，我们假设 高度匹配的变异病毒的命运取决于它在接种物中的初始流行(数量结构)， 它产生的时间(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，我们预测未来 有利变种的传播将取决于这些因素和严格的 传输瓶颈。我们进一步提出，瓶颈的严重性是由预先存在的 宿主的豁免权。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及其一个或两个HA抗原变异体的豚鼠个体内和之间 传输伙伴。将通过接种疫苗诱导部分免疫，以产生一种模型，在该模型中，抗原 变种有选择性的优势。不同的序列条码将包括在HA和NA基因中 每种病毒都能灵敏地检测到遗传瓶颈。跟踪HA和NA中的条形码将允许 基因连锁有待评估。野生型和抗原性变异病毒将在体内与各种 数量、时间和空间结构，然后条形码的动态将通过测序进行监测。使用 这一方法，我们将对种群遗传结构的后果进行系统的评估 病毒进化动力学。这种控制良好和系统的方法将允许识别过程 这阻碍了单个宿主内部和之间的选择，提供了对塑造力量的迫切需要的洞察 IAV进化从哪里开始。

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.