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

将免疫逃逸和体外复制的测量与计算模型相结合，以了解和预测季节性 A/H3N2 流感病毒的抗原进化

• 批准号: 10349839
• 负责人: Derek James Smith
• 金额: $ 51.78万
• 依托单位: UNIVERSITY OF CAMBRIDGE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-07 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10349839
• 关键词: Affect; Amino Acid Substitution; Amino Acids; Antibodies; Area; Binding Sites; Biological Assay; Codon Nucleotides; Computer Models; Data; Development; Disease; Evolution; Future; Genetic; Genetic Variation; Goals; Growth; Hemagglutinin; Human; Immune; Immunity; In Vitro; Influenza; Influenza A Virus, H3N2 Subtype; Influenza A virus; Investigation; Laboratories; Maps; Measurement; Measures; Methods; Modeling; Modernization; Molecular; Molecular Evolution; Mutation; Nature; Pattern; Phenotype; Plant Roots; Population; Positioning Attribute; Process; Proteins; RNA Viruses; Recommendation; Resolution; Resources; Risk; Seasons; Serology; Site; Statistical Models; Surface; Testing; Time; Use Effectiveness; Vaccination; Vaccines; Variant; Viral; Virus; Virus Replication; Work; computerized tools; cost; data streams; fitness; fitness test; improved; influenza virus vaccine; influenzavirus; mutant; neutralizing antibody; novel; receptor binding; response; sample fixation; seasonal influenza; transmission process; vaccine candidate; vaccine effectiveness

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.

项目总结 季节性流感病毒疫苗大多数年份都必须重新配制，主要是因为引起免疫逃逸 通过表面血凝素(HA)蛋白的突变。HA的遗传变异只是偶尔会导致 抗原表型的改变和随后的免疫逃逸。对于较长时间的紧张状态 遗传差异仍然存在于单一的抗原簇中。2013年，我们(Koel等人)1发现氨基酸 导致人类A/H3N1病毒抗原簇转换的替换仅发生在7个关键字上 位于HA受体结合位点(RBS)外围的位置，以及十分之七的A/H3N2簇 转变仅仅是由单一的氨基酸替换引起的。此外，其他病毒的主要抗原变化 (亚)人类流感类型以及其他物种的流感病毒也主要是由单一氨基酸引起的 在相同的七个HA关键部位及其附近的HA RBS外围的酸替换。这一发现 提出了一个直接的、以前并不明显的问题：如果通常只需要改变一个氨基酸来 逃避免疫，为什么流感病毒的抗原性进化如此缓慢？人类季节性甲型流感/H3N1流感 病毒在抗原簇中的平均保留时间为3.1年，有时长达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。一个 对簇转移替换固定延迟的可能解释是，抗原变化引起 健身费用。RBS附近的逃逸突变为这一成本提供了一种机制：病毒需要 当针对RBS的抗体需要逃逸时，靠近RBS的变化，但这一区域的变化也 影响受体结合功能。在抗原性上推进菌株的替换可能只是竞争性的 当对当代循环变异建立了足够的种群免疫力时，适应度的增加 逃避免疫力(“外在的”健康收益)超过了潜在的健康损失。 伴随而来的受体结合部位的扭曲(“固有的”适合性丧失)。我们把这称为“健身” “交换”假说。要了解流感的进化动态，需要了解它的步调。 抗原性改变。在这项建议中，我们开始检验健康交换假说，以了解 病毒内在适合度的变化和影响，并确定内在适合度和病毒内在适合度的相对重要性 在病毒种群中固定的新突变中的随机效应，并整合经验 将这些影响的测量转化为预测季节性流感病毒抗原进化的概率框架 流感病毒。