Four potential broad-spectrum neutralizing epitopes in the spike protein of SARS-CoV-2 predicted by bioinformatics

ABSTRACT

Introduction: To date, seven human coronaviruses (HCoVs) have been discovered. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a newly emerged HCoV, which can induce fatal pneumonia infection. Coronavirus is a single-stranded RNA virus that is susceptible to mutation, making it difficult to develop vaccines. Broad-spectrum vaccines based on conserved neutralizing epitopes can not only prevent epidemic strains, but also has broad-spectrum antiviral property. In this study, bioinformatics was used to predict broad-spectrum neutralizing epitopes of HCoVs. Methods: The spike (S) protein amino acid sequence of SARS-CoV-2 Wuhan-Hu-1 strain was used as a template for epitope prediction. The linear B cell neutralization epitopes were primarily predicted by four online prediction servers, including ABCpred2006, BepiPred2.0, COBEpro and SVMTriP. The peptide fragments were selected according to their common prediction results, and were further screened using the server VaxiJen2.0. The conservation of high-score candidate epitopes was analyzed by Clustal X2 software, and the spatial position of candidate epitopes in S protein were analyzed by the PyMOL software. Results: According to the analysis above, four potential broad-spectrum linear B cell neutralizing epitopes were screened, which include the epitopes P6 (aa496-501) and P14 (aa1163-1168) conserved between SARS-CoV-2 and SARS-CoV;P15 (aa1196-1201) conserved among SARS-CoV-2, SARS-CoV and MERS-CoV;P12 (aa811-816) conserved among SARS-CoV-2, SARS-CoV and HCoVOC43. Conclusions: Four potential broad-spectrum linear B cell neutralizing epitopes in the S protein of SARS-CoV-2 were predicted, which lay a foundation for the development of HCoVs broad-spectrum vaccines.