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.

为了最终与正在出现的COVID-19大流行作斗争，需要开发一种有效且安全的疫苗，以应对由SARS-CoV-2冠状病毒引起的这种高度传染性疾病。我们的文献和临床试验调查表明，已经对整个病毒以及刺突（S）蛋白，核衣壳（N）蛋白和膜（M）蛋白进行了抗SARS和MERS疫苗开发的测试。但是，这些候选疫苗可能缺乏完全保护的诱导，并存在安全隐患。然后，我们应用了Vaxign和新开发的基于机器学习的Vaxign-ML反向疫苗学工具来预测COVID-19候选疫苗。我们的Vaxign分析发现，SARS-CoV-2 N蛋白序列与SARS-CoV和MERS-CoV保守，但与其他四种引起轻度症状的人冠状病毒却不一样。通过研究SARS-CoV-2的整个蛋白质组，预测包括S蛋白和5个非结构蛋白（nsp3、3CL-pro和nsp8-10）在内的6种蛋白质是粘附素，这对病毒至关重要坚持和宿主入侵。Vaxign-ML还预测了S，nsp3和nsp8蛋白会诱导高保护性抗原性。除了常用的S蛋白外，nsp3蛋白还没有在任何冠状病毒疫苗研究中进行过测试，因此被选择作进一步研究。发现nsp3在SARS-CoV-2，SARS-CoV和MERS-CoV中比在15种感染人类和其他动物的冠状病毒中更保守。还预测该蛋白质包含混杂的MHC-1和MHC-II T细胞表位，并且发现预测的线性B细胞表位位于该蛋白质的表面上。我们预测的疫苗目标具有开发有效和安全的COVID-19疫苗的潜力。我们还建议，含有结构蛋白（Sp）和非结构蛋白（Nsp）的“ Sp / Nsp鸡尾酒疫苗”将刺激有效的互补免疫应答。