Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates

Spike (S) protein has been recognized as a promising molecular target for diagnostic, vaccines and antiviral drugs development for COVID-19. In this study, we analyzed the most predominant mutations in the S protein of Brazilian isolates and predicted the effect of these amino acid alterations to protein conformation. A total of 25,924 sequences were obtained from GISAID for five regions of Brazilian territory (Midwest, North, Northeast, South, and Southeast), according to exclusion criteria. Most of the SARS-CoV-2 isolates belongs to the G clade and showed a large occurrence of D614G, N501Y and L18F substitutions. Prediction effects of these amino acid substitutions on the structure dynamics of the spike protein indicated a positive ΔΔG values and negative ΔΔS_Vib in most cases which is associated to structural stabilization and flexibility reduction of the S protein. Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates. These mutations have been described to increase RBD affinity to ACE-2 host and abolishment of RBD affinity to potent neutralizing ant-RBD. The increase in rates of infection and reinfection requires continuous genomic surveillance studies in order to characterize emerging mutations and monitor vaccine efficacy, and thus consideration structural data and dynamics in the observed phenotypes. Communicated by Ramaswamy H. Sarma

刺突（S）蛋白（Spike (S) protein）已被认定为新型冠状病毒肺炎（COVID-19）诊断、疫苗及抗病毒药物研发的极具潜力的分子靶点。本研究针对巴西分离株的刺突蛋白中最主要的突变位点展开分析，并预测了这些氨基酸变异对蛋白质构象的影响。按照排除标准，我们从全球流感数据共享倡议（Global Initiative on Sharing All Influenza Data, GISAID）获取了巴西境内中西部、北部、东北部、南部及东南部五个区域的共计25924条病毒序列。多数严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）分离株属于G进化分支，且频繁出现D614G、N501Y及L18F氨基酸替换。针对上述氨基酸替换对刺突蛋白结构动力学的影响进行预测后发现，多数情况下其ΔΔG值为正、ΔΔS_Vib为负，这与刺突蛋白的结构稳定性提升及柔性降低密切相关。E484K、N501Y及K417N突变属于Alpha、Beta、Gamma、Delta等多种新型冠状病毒关切变异株（Variant of Concern, VOC），且在巴西分离株中检出率较高。已有研究表明，此类突变可增强刺突蛋白受体结合域（Receptor Binding Domain, RBD）与宿主血管紧张素转换酶2（Angiotensin-Converting Enzyme 2, ACE2）的结合亲和力，并可削弱其与强效中和性抗RBD抗体的结合能力。感染及再感染率的上升，使得持续开展基因组监测研究成为必要，以对新发突变进行鉴定并监测疫苗保护效果，因此需将结构数据及动力学特征纳入对观测表型的分析考量。本文由Ramaswamy H. Sarma转交。