Integrating measurements of immune escape and in vitro replication with computational models to understand and predict the antigenic evolution of seasonal A/H3N2 influenza viruses

项目摘要 季节性流感病毒疫苗大多数年份必须重新配制，主要是由于免疫逃逸引起的 通过表面血凝素（HA）蛋白的突变。HA的遗传变异只是偶尔引起 抗原表型的改变和随后的免疫逃逸。对于长时间的菌株， 遗传差异保持在单个抗原簇中。2013年，我们（Koel等人）1发现氨基酸 在人类A/H3 N2病毒中，负责抗原簇转换的替换仅发生在7个关键位点， HA受体结合位点（RBS）周围的位置，并且10个A/H3 N2簇中有7个 转变仅由单个氨基酸取代引起。此外，在其他组织中的主要抗原变化 人类流感病毒的（亚）型以及其他物种中的流感病毒，也主要是由于单氨基 在相同的七个关键HA位点以及附近，在HA RBS的外围上的酸取代。这一发现 提出了一个直接的，以前不明显的问题：如果仅仅一个氨基酸的变化通常需要 逃避免疫，流感病毒的抗原进化为何如此缓慢？甲型H3 N2人类季节性流感 病毒保持在抗原簇中的平均时间为3.1年，偶尔长达8年。这 尤其令人困惑的是，作为一种RNA病毒，流感病毒的分子进化速度很快。一 对簇转换置换固定延迟的可能解释是抗原性变化引起了 健身成本逃避突变与RBS的接近为这种成本提供了一种机制：病毒需要 接近RBS的变化，因为靶向RBS的抗体需要逃逸，但该区域的变化也 影响受体结合功能。使菌株抗原性提高的置换只能是竞争性的 当足够的群体免疫力已经建立到当代流行的变体，这样， 从逃避免疫（“外在”健身增益）超过潜在的健身损失与 受体结合位点的伴随变形（“内在”适应性丧失）。我们称之为“适应性 交换”假说。要了解流感的进化动力学， 抗原性变化在这个提议中，我们开始测试适应性交换假设，以了解 病毒内在适应性的变化和影响，并确定内在适应性的相对重要性， 新突变的随机效应在病毒群体中变得固定，并整合经验 这些影响的测量到一个概率框架，用于预测季节性流感的抗原演变， 流感病毒。

PROJECT SUMMARY Seasonal influenza virus vaccines have to be reformulated most years primarily due to immune escape caused by mutations in the surface hemagglutinin (HA) protein. The genetic variation in HA only occasionally causes change in antigenic phenotype and consequent immune escape. For extended periods of time strains with genetic differences remain in a single antigenic cluster. In 2013 we (Koel et al.)1 found that the amino acid substitutions responsible for antigenic cluster transitions in human A/H3N2 viruses occurred at only seven key positions on the periphery of the HA receptor binding site (RBS), and that seven out of ten A/H3N2 cluster transitions were caused by just single amino acid substitutions. Furthermore, major antigenic change in other (sub)types of human influenza, as well as influenza viruses in other species, is also primarily due to single amino acid substitutions at the same seven key HA sites, and nearby, on the periphery of the HA RBS. This discovery raises an immediate, and not previously obvious question: If just one amino acid change is typically required to escape immunity, why is the antigenic evolution of influenza viruses so slow? Human seasonal influenza A/H3N2 viruses remain in an antigenic cluster for an average of 3.1 years, and occasionally as long as eight years. This is especially perplexing given that, as an RNA virus, influenza viruses have a fast rate of molecular evolution. A possible explanation for the delay in fixation of cluster transition substitutions is that antigenic change incurs a fitness cost. The proximity of escape mutations to the RBS offers a mechanism for this cost: the virus needs to change close to the RBS as antibodies targeting the RBS need to be escaped, but change in this area also affects receptor-binding function. Substitutions which advance a strain antigenically may only be competitive when sufficient population immunity has built to contemporary circulating variants, such that the gain in fitness from escaping immunity (the “extrinsic” fitness gain) outweighs the potential fitness loss associated with the concomitant distortion of the receptor binding site (the “intrinsic” fitness loss). We refer to this as the “fitness exchange” hypothesis. To understand the evolutionary dynamics of influenza requires understanding what paces antigenic change. In this proposal we set out to test the fitness exchange hypothesis, to gain understanding of the variation and impact of viral intrinsic fitness, and to determine the relative importance of intrinsic fitness and stochastic effects in novel mutations becoming fixed in viral populations, and to integrate empirical measurements of these effects into a probabilistic framework for predicting the antigenic evolution of seasonal influenza viruses.