Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype.

IF 6.7 1区 医学 Q1 Immunology and Microbiology
Ruthiran Kugathasan, Ksenia Sukhova, Maya Moshe, Paul Kellam, Wendy Barclay
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引用次数: 1

Abstract

New variants of SARS-CoV-2 are continually emerging with mutations in spike associated with increased transmissibility and immune escape. Phenotypic maps can inform the prediction of concerning mutations from genomic surveillance, however most of these maps currently derive from studies using monomeric RBD, while spike is trimeric, and contains additional domains. These maps may fail to reflect interdomain interactions in the prediction of phenotypes. To try to improve on this, we developed a platform for deep mutational scanning using whole trimeric spike. We confirmed a previously reported epistatic effect within the RBD affecting ACE2 binding, that highlights the importance of updating the base spike sequence for future mutational scanning studies. Using post vaccine sera, we found that the immune response of vaccinated individuals was highly focused on one or two epitopes in the RBD and that single point mutations at these positions can account for most of the immune escape mediated by the Omicron BA.1 RBD. However, unexpectedly we found that the BA.1 RBD alone does not account for the high level of antigenic escape by BA.1 spike. We show that the BA.1 NTD amplifies the immune evasion of its associated RBD. BA.1 NTD reduces neutralistion by RBD directed monoclonal antibodies, and impacts ACE2 interaction. NTD variation is thus an important mechanism of immune evasion by SARS-CoV-2. Such effects are not seen when pre-stabilized spike proteins are used, suggesting the interdomain effects require protein mobility to express their phenotype.

利用全三聚体SARS-CoV-2刺突进行深度诱变扫描,强调了NTD-RBD相互作用在确定刺突表型中的重要性。
SARS-CoV-2的新变体不断出现,其突变与传播性和免疫逃逸增加有关。表型图谱可以通过基因组监测预测相关突变,然而目前这些图谱大多来自使用单体RBD的研究,而刺突是三聚体的,并且包含额外的结构域。这些图谱在预测表型时可能无法反映区域间的相互作用。为了改进这一点,我们开发了一个使用全三聚体尖峰进行深度突变扫描的平台。我们证实了先前报道的RBD内影响ACE2结合的上位性效应,这突出了更新碱基尖峰序列对未来突变扫描研究的重要性。使用疫苗后血清,我们发现接种个体的免疫应答高度集中在RBD中的一个或两个表位上,这些位置的单点突变可以解释Omicron BA.1 RBD介导的大部分免疫逃逸。然而,出乎意料的是,我们发现BA.1 RBD本身并不能解释BA.1尖峰的高水平抗原逃逸。我们发现BA.1 NTD放大了其相关RBD的免疫逃避。BA.1 NTD降低了RBD定向单克隆抗体的中和作用,并影响ACE2的相互作用。因此,NTD变异是SARS-CoV-2免疫逃避的重要机制。当使用预稳定的刺突蛋白时,没有看到这种效应,这表明结构域间效应需要蛋白质的流动性来表达其表型。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
PLoS Pathogens
PLoS Pathogens 生物-病毒学
CiteScore
11.40
自引率
3.00%
发文量
598
审稿时长
2 months
期刊介绍: Bacteria, fungi, parasites, prions and viruses cause a plethora of diseases that have important medical, agricultural, and economic consequences. Moreover, the study of microbes continues to provide novel insights into such fundamental processes as the molecular basis of cellular and organismal function.
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