ABSTRACT
Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2) is a newly discovered infectious coronavirus, which can cause Coronavirus Disease 2019 (COVID-19). The outbreak of the disease has caused severe impact both at home and abroad. Compared with the other three structural proteins encoded by SARS-CoV-2, Nucleocapsid phosphoprotein (Np) is more conservative and plays an important role in pathogen diagnosis, vaccine design, and treatment. This paper aims to predict the spatial structure of Np in Wuhan-Hu-1 strain and its B-cell epitope,and lay a foundation for the development of epitope vaccine and related monoclonal antibody of SARS-CoV-2. In this study, the Neighbor-joining method in MEGA5.05 was used to construct a phylogenetic tree based on the base sequence of Np of SARS-CoV-2 strain. The SARS-CoV-2 Wuhan-Hu-1 strain was used as the research object, and parameters such as hydrophilicity index, flexible region, surface possibility, and antigenic index were analyzed and predicted by the Protean module in the DNAStar software, combined with the spatial structure simulated by the Phyre2 online tool, so as to comprehensively predict the dominant B-cell epitopes of Np of Wuhan-Hu-1. Results show that the gene sequences of Np of SARS-CoV-2 isolated from different regions were highly similar (99.6%-100%). The amino acid sequence of Np in Wuhan-Hu-1 strain was 419 aa.The spatial structure of Np in Wuhan-Hu-1 strain was fairly regular. It contained only a small amount of α-helixes, while most of the structures were β-sheets, β-turns, and random coils. Results of multi-parameter comprehensive analysis showed that the possible antigenic epitope regions of B-cell were located in the amino acid regions of 52-9,9-5,3-9,6-5,9-4,0-6,4-6,7-7,3-9,7-3,9-5,3-9,7-3,9-5,9-401,and 403-411. The results of this study can provide theoretical information for the development of epitope vaccine, rapid diagnostic reagents, and monoclonal antibodies with respect to SARS-CoV-2, and offer new strategies for COVID-19 treatments. (English) [ FROM AUTHOR] 新型冠状病毒(Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2)是最新发现的一种可侵染人体的β属冠状病毒, 该病毒入侵机体可引发新型冠状病毒肺炎(Coronavirus Disease 2019, COVID-19), 该疫情的暴发在国内甚至国际上造成了严重影响。核衣壳蛋白(Nucleocapsid phosphoprotein, Np)相较于病毒编码的其它三种结构蛋白保守性更强, 在病原诊断, 疫苗设计和治疗等方面占据重要地位。预测Wuhan-Hu-1 Np的空间结构及其B细胞抗原表位, 为开发SARS-CoV-2的表位疫苗和相关单抗奠定基础。采用MEGA5.05中的Neighbor-joining法构建基于SARS-CoV-2 Np的碱基序列的系统发生树；以SARS-CoV-2 Wuhan-Hu-1株为研究对象, 其柔性区段, 亲水性指数, 抗原指数和蛋白质表面可能性等参数由DNAStar软件中的Protean模块进行分析预测, 结合Phyre2在线工具模拟的空间结构, 综合预测Wuhan-Hu-1 Np的B细胞优势抗原表位。结果发现:不同地区SARS-CoV-2 Np的碱基序列高度相似(99.6%-100%), Wuhan-Hu-1 Np氨基酸序列长419 aa, 其空间构型相对规则, 仅含少量α-螺旋而多见β-折叠, β-转角和无规则卷曲结构；多参数综合分析结果指示, 可能的B细胞抗原表位位于52~59, 69~75, 83~89, 106~115, 119~124, 130~136, 154~166, 217~227, 243~249, 267~273, 299~315, 333~339, 347~363, 379~385, 389~401, 403~411氨基酸区段。本研究旨在为开发SARS-CoV-2表位疫苗, 快速诊断试剂, 单克隆抗体等提供理论信息, 为医治COVID-19给予一些新策略. (Chinese) [ FROM AUTHOR] Copyright of Chinese Journal of Bioinformatics is the property of Bioinformatics and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)