In silico identification of vaccine targets for 2019-nCoV (Data tables)

<strong>Background</strong> The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. <strong>Methods</strong> The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. <strong>Results</strong> We report <em>in silico</em> identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a <em>de novo</em> search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. <strong>Conclusions</strong> Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.**研究背景** 本研究针对新近发现的2019新型冠状病毒（2019-nCoV），该病毒已对全球公共卫生构成严重威胁。根据2020年2月18日发布的最新报告，该病毒在全球范围内已造成超过72000人感染，其中中国境内死亡病例逾1016例。 **研究方法** 本研究将2019新型冠状病毒的蛋白质组与经人工注释整理的病毒免疫原性肽段数据库进行序列比对，并通过免疫原性预测模型及NetMHCpan 4.0工具，对检测到的肽段的免疫原性及其与人类白细胞抗原（Human Leukocyte Antigen, HLA）等位基因的结合潜能进行预测。 **研究结果** 本研究通过计算机模拟（in silico）手段，鉴定得到一系列可作为2019新型冠状病毒（2019-nCoV）疫苗开发潜在靶点的免疫原性肽段并形成全面列表。具体包括：其一，我们发现28条与严重急性呼吸综合征冠状病毒（Severe Acute Respiratory Syndrome Coronavirus, SARS-CoV）序列完全一致的2019-nCoV肽段，此前已有研究通过T细胞实验证实此类肽段具备免疫原性；其二，我们鉴定得到48条与免疫表位数据库（Immune Epitope Database, IEDB）中收录的免疫原性肽段高度同源的2019-nCoV肽段；最后，我们通过位置权重矩阵及新近开发的免疫原性算法iPred，对2019-nCoV的9聚体肽段开展从头（de novo）搜索，筛选同时满足以下两个条件的肽段：①可与中国及欧洲人群常见人类白细胞抗原（HLA）等位基因结合，②具备T细胞受体（T Cell Receptor, TCR）识别潜能，最终共得到63条高免疫原性潜能的肽段。 **研究结论** 鉴于当前开发2019-nCoV疫苗与治疗手段的时间与资源均较为有限，本研究筛选得到的候选肽段可作为实验验证的目标候选列表，从而加速相关研发管线的推进进程。