Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2

被引:25
作者
Lon, Jerome Rumdon [1 ]
Bai, Yunmeng [1 ]
Zhong, Bingxu [1 ]
Cai, Fuqiang [1 ]
Du, Hongli [1 ]
机构
[1] South China Univ Technol, Sch Biol & Biol Engn, Guangzhou 510006, Peoples R China
基金
国家重点研发计划;
关键词
SARS-CoV-2; Epitopes; Bioinformatics; Evolution; SEQUENCE;
D O I
10.1186/s12985-020-01437-4
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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 SARS-CoV-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.
引用
收藏
页数:9
相关论文
共 38 条
[1]   ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules [J].
Ashkenazy, Haim ;
Abadi, Shiran ;
Martz, Eric ;
Chay, Ofer ;
Mayrose, Itay ;
Pupko, Tal ;
Ben-Tal, Nir .
NUCLEIC ACIDS RESEARCH, 2016, 44 (W1) :W344-W350
[2]   Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends [J].
Bai, Yunmeng ;
Jiang, Dawei ;
Lon, Jerome R. ;
Chen, Xiaoshi ;
Hu, Meiling ;
Lin, Shudai ;
Chen, Zixi ;
Wang, Xiaoning ;
Meng, Yuhuan ;
Du, Hongli .
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 2020, 100 :164-173
[3]   Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV [J].
Baruah, Vargab ;
Bose, Sujoy .
JOURNAL OF MEDICAL VIROLOGY, 2020, 92 (05) :495-500
[4]   Sequence and structure-based prediction of eukaryotic protein phosphorylation sites [J].
Blom, N ;
Gammeltoft, S ;
Brunak, S .
JOURNAL OF MOLECULAR BIOLOGY, 1999, 294 (05) :1351-1362
[5]   RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy [J].
Burley, Stephen K. ;
Berman, Helen M. ;
Bhikadiya, Charmi ;
Bi, Chunxiao ;
Chen, Li ;
Di Costanzo, Luigi ;
Christie, Cole ;
Dalenberg, Ken ;
Duarte, Jose M. ;
Dutta, Shuchismita ;
Feng, Zukang ;
Ghosh, Sutapa ;
Goodsell, David S. ;
Green, Rachel K. ;
Guranovic, Vladimir ;
Guzenko, Dmytro ;
Hudson, Brian P. ;
Kalro, Tara ;
Liang, Yuhe ;
Lowe, Robert ;
Namkoong, Harry ;
Peisach, Ezra ;
Periskova, Irina ;
Prlic, Andreas ;
Randle, Chris ;
Rose, Alexander ;
Rose, Peter ;
Sala, Raul ;
Sekharan, Monica ;
Shao, Chenghua ;
Tan, Lihua ;
Tao, Yi-Ping ;
Valasatava, Yana ;
Voigt, Maria ;
Westbrook, John ;
Woo, Jesse ;
Yang, Huanwang ;
Young, Jasmine ;
Zhuravleva, Marina ;
Zardecki, Christine .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D464-D474
[6]   The Evolutionary Pattern of Glycosylation Sites in Influenza Virus (H5N1) Hemagglutinin and Neuraminidase [J].
Chen, Wentian ;
Zhong, Yaogang ;
Qin, Yannan ;
Sun, Shisheng ;
Li, Zheng .
PLOS ONE, 2012, 7 (11)
[7]   WebLogo: A sequence logo generator [J].
Crooks, GE ;
Hon, G ;
Chandonia, JM ;
Brenner, SE .
GENOME RESEARCH, 2004, 14 (06) :1188-1190
[8]   Immuno-informatics: Mining genomes for vaccine components [J].
De Groot, AS ;
Sbai, H ;
Aubin, CS ;
McMurry, J ;
Martin, W .
IMMUNOLOGY AND CELL BIOLOGY, 2002, 80 (03) :255-269
[9]  
El-Manzalawy Yasser, 2010, Immunome Res, V6 Suppl 2, pS2, DOI 10.1186/1745-7580-6-S2-S2
[10]   INDUCTION OF HEPATITIS-A VIRUS-NEUTRALIZING ANTIBODY BY A VIRUS-SPECIFIC SYNTHETIC PEPTIDE [J].
EMINI, EA ;
HUGHES, JV ;
PERLOW, DS ;
BOGER, J .
JOURNAL OF VIROLOGY, 1985, 55 (03) :836-839