In order to obtain antibodies that recognize natural proteins, it is possible to predict the antigenic determinants of natural proteins, which are eventually embodied as polypeptides. The polypeptides can be coupled with corresponding vectors to stimulate the immune system to produce corresponding antibodies, which is also a simple and effective vaccine development method. The discovery of epitopes is helpful to the development of SARS-CoV-2 vaccine. The analyses were related to epitopes on 3 proteins, including spike (S), envelope (E) and membrane (M) proteins, which are located on the lipid envelope of the SARS-CoV-2. Based on the NCBI Reference Sequence: NC_045512.2, the conformational and linear B cell epitopes of the surface protein were predicted separately by various prediction methods. Furthermore, the conservation of the epitopes, the adaptability and other evolutionary characteristics were also analyzed, the sequences of the whole genome of SARS-CoV-2 were obtained from the GISAID. 7 epitopes were predicted, including 6 linear epitopes and 1 conformational epitope. One of the linear and one of the conformational consist of identical sequence, but represent different forms of epitopes. It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. The findings would facilitate the vaccine development, had the potential to be directly applied on the prevention in this disease, but also have the potential to prevent the possible threats caused by other types of coronavirus.

中文翻译：

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SARS-CoV-2表面蛋白B细胞表位的预测和进化


为了获得识别天然蛋白质的抗体，可以预测天然蛋白质的抗原决定簇，最终体现为多肽。多肽可以与相应的载体偶联，刺激免疫系统产生相应的抗体，这也是一种简单有效的疫苗研发方法。表位的发现有助于SARS-CoV-2疫苗的研发。分析与 3 种蛋白上的表位相关，包括刺突蛋白 (S)、包膜蛋白 (E) 和膜蛋白 (M)，这些蛋白位于 SARS-CoV-2 的脂质包膜上。基于NCBI参考序列：NC_045512.2，通过多种预测方法分别预测表面蛋白的构象和线性B细胞表位。此外，还分析了表位的保守性、适应性等进化特征，从GISAID获得了SARS-CoV-2的全基因组序列。预测了7个表位，其中6个线性表位和1个构象表位。一种线性表位和一种构象表位由相同的序列组成，但代表不同形式的表位。值得一提的是，所有6个鉴定的表位在近3500个SARS-CoV-2基因组中都是保守的，表明在氨基酸突变频率较高的情况下有助于获得稳定且长效的表位，值得进一步研究实验水平。这些发现将有助于疫苗的开发，有可能直接应用于预防这种疾病，而且也有可能预防其他类型的冠状病毒可能造成的威胁。