Data_Sheet_1_COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning.PDF

To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that the whole virus, as well as the spike (S) protein, nucleocapsid (N) protein, and membrane (M) protein, have been tested for vaccine development against SARS and MERS. However, these vaccine candidates might lack the induction of complete protection and have safety concerns. We then applied the Vaxign and the newly developed machine learning-based Vaxign-ML reverse vaccinology tools to predict COVID-19 vaccine candidates. Our Vaxign analysis found that the SARS-CoV-2 N protein sequence is conserved with SARS-CoV and MERS-CoV but not from the other four human coronaviruses causing mild symptoms. By investigating the entire proteome of SARS-CoV-2, six proteins, including the S protein and five non-structural proteins (nsp3, 3CL-pro, and nsp8-10), were predicted to be adhesins, which are crucial to the viral adhering and host invasion. The S, nsp3, and nsp8 proteins were also predicted by Vaxign-ML to induce high protective antigenicity. Besides the commonly used S protein, the nsp3 protein has not been tested in any coronavirus vaccine studies and was selected for further investigation. The nsp3 was found to be more conserved among SARS-CoV-2, SARS-CoV, and MERS-CoV than among 15 coronaviruses infecting human and other animals. The protein was also predicted to contain promiscuous MHC-I and MHC-II T-cell epitopes, and the predicted linear B-cell epitopes were found to be localized on the surface of the protein. Our predicted vaccine targets have the potential for effective and safe COVID-19 vaccine development. We also propose that an “Sp/Nsp cocktail vaccine” containing a structural protein(s) (Sp) and a non-structural protein(s) (Nsp) would stimulate effective complementary immune responses.

为最终应对新型冠状病毒肺炎（COVID-19）疫情大流行，亟需开发针对由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引发的这一高传染性疾病的安全有效疫苗。我们通过文献调研与临床试验梳理发现，全病毒制剂以及刺突（S）蛋白、核衣壳（N）蛋白、膜（M）蛋白均已在针对重症急性呼吸综合征（SARS）和中东呼吸综合征（MERS）的疫苗研发中得到测试。但此类候选疫苗可能无法诱导完全免疫保护，且存在安全隐患。随后我们应用了Vaxign以及新开发的基于机器学习的反向疫苗学工具Vaxign-ML，对新型冠状病毒候选疫苗进行预测分析。Vaxign分析结果显示，SARS-CoV-2的N蛋白序列与SARS-CoV及MERS-CoV的N蛋白序列保守性较高，但与另外4种引发轻症的人类冠状病毒的N蛋白序列保守性较低。通过对SARS-CoV-2的全蛋白质组进行系统分析，我们预测出6种蛋白可作为黏附素——这类蛋白对病毒黏附宿主细胞并入侵宿主至关重要，其中包括S蛋白以及5种非结构蛋白（nsp3、3CL-pro、nsp8至nsp10）。经Vaxign-ML预测，S、nsp3及nsp8蛋白可诱导较高水平的保护性抗原性。除当前常用的S蛋白外，nsp3蛋白此前未在任何冠状病毒疫苗研究中得到测试，因此我们将其选为进一步研究对象。相较于感染人类及其他动物的15种冠状病毒，nsp3蛋白在SARS-CoV-2、SARS-CoV与MERS-CoV之间的序列保守性更强。同时该蛋白被预测含有多特异性的主要组织相容性复合体I型（MHC-I）与主要组织相容性复合体II型（MHC-II）T细胞表位，且预测得到的线性B细胞表位定位于该蛋白的表面区域。我们预测的疫苗靶点有望助力开发安全有效的新型冠状病毒疫苗。此外我们还提出“结构蛋白/非结构蛋白（Sp/Nsp）联合疫苗”策略，即包含一种或多种结构蛋白（Sp）与非结构蛋白（Nsp），该策略可诱导有效的互补免疫应答。