Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An <i>In Silico</i> Approach Applied to Emerging Infectious Diseases

Middle East respiratory syndrome coronavirus (MERS-CoV) with pandemic potential is a major worldwide threat to public health. However, vaccine development for this pathogen lags behind as immunity associated with protection is currently largely unknown. In this study, an immunoinformatics-driven genome-wide screening strategy of vaccine targets was performed to thoroughly screen the vital and effective dominant immunogens against MERS-CoV. Conservancy and population coverage analysis of the epitopes were done by the Immune Epitope Database. The results showed that the nucleocapsid (N) protein of MERS-CoV might be a better protective immunogen with high conservancy and potential eliciting both neutralizing antibodies and T-cell responses compared with spike (S) protein. Further, the B-cell, helper T-cell and cytotoxic T lymphocyte (CTL) epitopes were screened and mapped to the N protein. A total of 15 linear and 10 conformal B-cell epitopes that may induce protective neutralizing antibodies were obtained. Additionally, a total of 71 peptides with 9-mer core sequence were identified as helper T-cell epitopes, and 34 peptides were identified as CTL epitopes. Based on the maximum HLA binding alleles, top 10 helper T-cell epitopes and CTL epitopes that may elicit protective cellular immune responses against MERS-CoV were selected as MERS vaccine candidates. Population coverage analysis showed that the putative helper T-cell epitopes and CTL epitopes could cover the vast majority of the population in 15 geographic regions considered where vaccine would be employed. The B- and T-cell stimulation potentials of the screened epitopes is to be further validated for their efficient use as vaccines against MERS-CoV. Collectively, this study provides novel vaccine target candidates and may prompt further development of vaccines against MERS-CoV and other emerging infectious diseases.具有大流行潜能的中东呼吸综合征冠状病毒（MERS-CoV）是全球公共卫生领域的重大威胁。然而，由于目前对该病原体相关保护性免疫机制的认知仍十分有限，针对其的疫苗研发进展相对滞后。本研究采用免疫信息学驱动的全基因组疫苗靶点筛选策略，对针对MERS-CoV的关键且有效的优势免疫原进行了系统性筛选。研究借助免疫表位数据库（Immune Epitope Database）完成了表位的保守性与人群覆盖度分析。结果显示，与刺突蛋白（spike, S）相比，MERS-CoV的核衣壳蛋白（nucleocapsid, N）具有更高的保守性，且可诱导中和抗体与T细胞应答，或是更具潜力的保护性免疫原。随后，本研究对B细胞、辅助性T细胞（helper T-cell）以及细胞毒性T淋巴细胞（cytotoxic T lymphocyte, CTL）表位进行了筛选，并将其定位至N蛋白序列。最终共获得15条可诱导保护性中和抗体的线性B细胞表位与10条构象型B细胞表位。此外，本研究共鉴定出71条含9聚体核心序列的辅助性T细胞表位，以及34条CTL表位。基于最高人类白细胞抗原（Human Leukocyte Antigen, HLA）结合等位基因评分，本研究筛选出排名前10的辅助性T细胞表位与CTL表位，这些表位可诱导针对MERS-CoV的保护性细胞免疫应答，可作为MERS疫苗候选靶点。人群覆盖度分析结果显示，所预测的辅助性T细胞表位与CTL表位，可覆盖拟开展疫苗接种的15个地理区域内的绝大多数人群。后续还需对筛选出的表位的B细胞与T细胞刺激活性进行验证，以推动其作为MERS-CoV疫苗的高效应用。综上，本研究为MERS-CoV疫苗研发提供了全新的候选靶点，有望推动针对MERS-CoV及其他新发传染病的疫苗开发进程。