Functional and antigenic evolution of SARS-related coronaviruses

项目总结 与SARS相关的冠状病毒(也称为肉毒杆菌病毒)在蝙蝠宿主中传播，但有两名人类 过去20年的溢出效应--2002年的SARS-CoV-1和2019年的SARS-CoV-2--在全球范围内造成了 毁灭性的疫情爆发。从以前未知的蝙蝠血统中出现的SARS-CoV-2突显了 迫切需要追踪病毒特性的进化起源，这些特性使人类能够溢出和发展 治疗试剂，可以广泛地抑制不同的、可能未抽样的肉瘤病毒谱系的感染。 人畜共患病部分依赖于病毒与ACE2受体相互作用的进化。 病毒刺激物受体结合域介导的人和潜在中间宿主细胞表面 (RBD)。RBD也是治疗控制SARS-CoV-2和其他病毒的关键组成部分 肉瘤病毒，因为它是最有效的中和抗体的目标，包括临床上的那些抗体 在发育和多克隆人血清中。尽管我和其他人已经开始调查 SARS-CoV-2自身重要生化表型的突变，包括与ACE2受体的结合 和抗病毒抗体，这些研究在理解更广泛的人类免疫缺陷病毒进化方面的作用有限。 在序列和功能上表现出相当大的差异。 为了表征肉瘤病毒的功能和抗原进化，我建议将高通量蛋白质 将实验与计算进化分析、功能病毒学和生物化学相结合： 1.我将描述所有已知的肉瘤病毒rbd的ACE2结合特异性及其进化 先驱物。我推测，包括人类ACE2同源基因在内，结合ACE2的能力更强 在进化上和地理上都比以前认识到的更广泛。 2.我将系统地描述不同的RBD突变如何影响ACE2结合表型。我 假设人血管紧张素转换酶2结合在肉瘤病毒谱系中是一个很容易进化的特征，而它不是 之前曾被考虑过。我还假设，肉瘤病毒谱系之间的分歧改变了基因 随着进化时间的推移，ACE2结合的生化决定因素。 3.我将确定对广泛的泛肉瘤病毒抗体结合敏感的RBD表位。通过 确定跨RBD表位的广度和其他抗体属性之间的关系，我强调 在设计下一代泛肉瘤病毒疫苗和抗体疗法时要针对的关键特征。 鉴定肉瘤病毒关键特征的进化和生化基础增强病毒 监测和治疗发展，为未来的肉瘤病毒溢出做准备，甚至预防。这个 在这项工作中开发的新的实验专业知识、更广泛的培训和指导以及研究系统将 使我能够实现我的目标，领导一个学术实验室研究宿主-病毒界面上的蛋白质进化。

PROJECT SUMMARY SARS-related coronaviruses (also known as sarbecoviruses) circulate in bat reservoirs, but two human spillovers in the past 20 years—SARS-CoV-1 in 2002 and SARS-CoV-2 in 2019—have caused globally devastating outbreaks. The emergence of SARS-CoV-2 from a previously unknown bat lineage highlights the pressing need to trace the evolutionary origins of viral properties that enable human spillover and develop therapeutic reagents that can broadly inhibit infection by diverse, potentially unsampled sarbecovirus lineages. Sarbecovirus zoonosis depends in part on the evolution of viruses to interact with ACE2 receptors on the surface of human and potential intermediate hosts’ cells, mediated by the viral spike receptor-binding domain (RBD). The RBD is also a key component to therapeutic control of SARS-CoV-2 and presumably other sarbecoviruses, as it is the target of the most potently neutralizing antibodies, including those in clinical development and in polyclonal human sera. Although I and others have begun surveying the impacts of mutations within SARS-CoV-2 itself on important biochemical phenotypes including binding to ACE2 receptor and antiviral antibodies, these studies have only limited utility in understanding the broader evolution of sarbecovirus RBDs, which exhibit considerable divergence in sequence and function. To characterize sarbecovirus functional and antigenic evolution, I propose to combine high-throughput protein binding experiments with computational evolutionary analyses, functional virology, and biochemistry: 1. I will profile the ACE2-binding specificities of all known sarbecovirus RBDs and their evolutionary precursors. I hypothesize that the ability to bind ACE2, including the human ACE2 ortholog, is more evolutionarily and geographically widespread than previously appreciated. 2. I will systematically characterize how diverse RBD mutations affect ACE2-binding phenotypes. I hypothesize that human ACE2 binding is an easily evolvable trait in sarbecovirus lineages where it has not been previously considered. I also hypothesize that divergence among sarbecovirus lineages shifts the genetic and biochemical determinants of ACE2 binding over evolutionary time. 3. I will identify RBD epitopes that are susceptible to broad pan-sarbecovirus antibody binding. By determining the relationship between breadth and other antibody properties across RBD epitopes, I highlight key features to target in the design of next-generation pan-sarbecovirus vaccines and antibody therapeutics. Identification of the evolutionary and biochemical basis for key sarbecovirus features enhances viral surveillance and therapeutic development, preparing for or even preventing future sarbecovirus spillovers. The new experimental expertise, broader training and mentorship, and research systems developed in this work will enable me to achieve my goal of leading an academic lab studying protein evolution at the host-virus interface.