RAPID: Probing SARS-CoV-2 evolution and vulnerabilities through its mutation and fitness landscape

在与病毒的斗争中，一个主要的挑战是它们巨大的遗传多样性，这是由庞大的种群规模和高突变率造成的。然而，对于SARS-CoV-2来说，这些变异出现的频率以及特定突变对病毒适应性的影响在很大程度上是未知的。该奖项支持的研究人员将测量来自世界各地的三种SARS-CoV- 2分离株的突变率和适应性景观。这项工作对于准确模拟SARS-CoV-2的未来进化至关重要，并可能有助于在分子水平上识别病毒的脆弱性。这些研究的结果也将被本科生和研究人员用于高级基因组分析的培训。这些研究的结果和数据将发表在同行评议的期刊上，在科学会议和公共STEM参与活动中展示，并通过博客文章和大众媒体在线分享。该奖项支持的研究将在Vero E6细胞中连续传代几轮后测量病毒种群的变异频率。所有可能变异频率的全基因组测量将使用环测序来测量突变率和适应性景观病毒。在连续传代过程中，变异频率的变化将用于推导每个变异的相对适应度。了解病毒的突变率（和谱）对于模拟其未来的进化至关重要，包括预计出现抗性变异的速度。通过测量基因组中数千个突变的适应度，研究人员希望确定对病毒复制周期至关重要的残基和蛋白质结构域，并缩小蛋白质结构域和残基的范围，以靶向治疗。在这些位点中，那些没有其他突变可以挽救病毒适应性的位点将会引起特别的兴趣。南加州大学的这项RAPID奖是由生物基础设施部利用《冠状病毒援助、救济和经济安全法案》的资金颁发的。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

A major challenge in the fight against viruses is their enormous amount of genetic diversity resulting from large population sizes combined with high mutation rates. However, the frequency at which such variants appear and the consequences of specific mutations on viral fitness are largely unknown for SARS-CoV-2. Researchers supported by this award will measure the mutation rate and fitness landscape of three SARS-CoV- 2 isolates from around the world. The work could be essential for accurately modeling the future evolution of SARS-CoV-2 and may help identify the virus’ vulnerabilities at the molecular level. Results from these studies will also be leveraged by undergraduate students and researchers for training in advanced genomic analyses. The findings and data from these studies will be published in peer-reviewed journals, presented at scientific meetings and in public STEM engagement activities, and shared on-line through blog posts and the popular press.Research supported by this award will measure variant frequencies in viral populations following several rounds of serial passaging in Vero E6 cells. Genome-wide measurements of all possible variants frequencies will be accomplished using the circle-sequencing to measure mutation rates and fitness landscape virus. Changes in variant frequencies over the course of serial passages will be used to derive the relative fitness of each variant. Knowing the mutation rate (and spectrum) of the virus is paramount to modeling its future evolution, including the rate at which resistant variants are expected to arise. By measuring the fitness of thousands of mutations across the genome, the researchers hope to identify residues and protein domains that are critical to the virus replication cycle and narrow the range of protein domains and residues to target with therapeutics. Among these sites, those for which no other mutation can rescue the viral fitness will be of particular interest. This RAPID award to University of Southern California is made by the Division of Biological Infrastructure using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.