Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2
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RESEARCH
Prediction and evolution of B cell epitopes of surface protein in SARS‑CoV‑2 Jerome Rumdon Lon, Yunmeng Bai, Bingxu Zhong, Fuqiang Cai and Hongli Du*
Abstract Background: 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 SARSCoV-2 vaccine. Methods: 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. Results: 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. Conclusion: 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. Keyword: SARS-CoV-2, Epitopes, Bioinformatics, Evolution Introduction In late December 2019, a novel coronavirus was officially named as SARS-CoV-2 by the International Committee on Taxonomy of Viruses (ICTV) and identified as the pathogen causing outbreaks of SARS-like and MERS-like illness in Chinese city of Wuhan, which was a zoonotic disease. As of August 13, 2020, the outbreak of SARS-CoV-2 has been reported in many areas of the world, with more than 20,423,000 people infected [1]. *Correspondence: [email protected] School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
With an alarming epidemicity, the reproductive number of SARS-CoV-2 has been computed to around 3.28 [2]. According to the data in the National Genomics Data Center (NGDC, https://bigd.big.ac.cn/ncov/), 15,118 genomic variations of SARS-CoV-2 has been reported at 13:00(GMT + 8) on August 13, 2020, which has aroused widespread concern. The B cell epitope of viral surface protein can specifically bind to the host’s B cell antigen receptor and induce the body to produce pr
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