Department of Electrical Engeneering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil.
Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA.
Sci Rep. 2022 Oct 6;12(1):16731. doi: 10.1038/s41598-022-21207-2.
COVID-19 caused, as of September, 1rst, 2022, 599,825,400 confirmed cases, including 6,469,458 deaths. Currently used vaccines reduced severity and mortality but not virus transmission or reinfection by different strains. They are based on the Spike protein of the Wuhan reference virus, which although highly antigenic suffered many mutations in SARS-CoV-2 variants, escaping vaccine-generated immune responses. Multiepitope vaccines based on 100% conserved epitopes of multiple proteins of all SARS-CoV-2 variants, rather than a single highly mutating antigen, could offer more long-lasting protection. In this study, a multiepitope multivariant vaccine was designed using immunoinformatics and in silico approaches. It is composed of highly promiscuous and strong HLA binding CD4 and CD8 T cell epitopes of the S, M, N, E, ORF1ab, ORF 6 and ORF8 proteins. Based on the analysis of one genome per WHO clade, the epitopes were 100% conserved among the Wuhan-Hu1, Alpha, Beta, Gamma, Delta, Omicron, Mµ, Zeta, Lambda and R1 variants. An extended epitope-conservancy analysis performed using GISAID metadata of 3,630,666 SARS-CoV-2 genomes of these variants and the additional genomes of the Epsilon, Lota, Theta, Eta, Kappa and GH490 R clades, confirmed the high conservancy of the epitopes. All but one of the CD4 peptides showed a level of conservation greater than 97% among all genomes. All but one of the CD8 epitopes showed a level of conservation greater than 96% among all genomes, with the vast majority greater than 99%. A multiepitope and multivariant recombinant vaccine was designed and it was stable, mildly hydrophobic and non-toxic. The vaccine has good molecular docking with TLR4 and promoted, without adjuvant, strong B and Th1 memory immune responses and secretion of high levels of IL-2, IFN-γ, lower levels of IL-12, TGF-β and IL-10, and no IL-6. Experimental in vivo studies should validate the vaccine's further use as preventive tool with cross-protective properties.
截至 2022 年 9 月 1 日，COVID-19 已造成 59982.54 万确诊病例，包括 646.9458 万死亡病例。目前使用的疫苗降低了严重程度和死亡率，但不能降低不同毒株的病毒传播或再感染率。它们基于武汉参考病毒的刺突蛋白，尽管具有高度抗原性，但在 SARS-CoV-2 变体中发生了许多突变，逃避了疫苗产生的免疫反应。基于所有 SARS-CoV-2 变体的多种蛋白质的 100%保守表位而不是单一高度突变抗原的多表位疫苗，可以提供更持久的保护。在这项研究中，使用免疫信息学和计算机模拟方法设计了一种多表位多变体疫苗。它由 S、M、N、E、ORF1ab、ORF6 和 ORF8 蛋白的高度混杂和强 HLA 结合的 CD4 和 CD8 T 细胞表位组成。基于对每个世界卫生组织（WHO）进化枝的一个基因组的分析，这些表位在武汉-Hu1、Alpha、Beta、Gamma、Delta、Omicron、Mµ、Zeta、Lambda 和 R1 变体中 100%保守。使用 GISAID 元数据对这些变体的 3630666 个 SARS-CoV-2 基因组和 Epsilon、Lota、Theta、Eta、Kappa 和 GH490 R 进化枝的其他基因组进行扩展的表位保守性分析，证实了表位的高度保守性。所有 CD4 肽中有一个以上的肽显示出在所有基因组中大于 97%的保守水平。所有 CD8 表位中有一个以上的肽显示出在所有基因组中大于 96%的保守水平，其中绝大多数大于 99%。设计了一种多表位和多变体重组疫苗，该疫苗稳定、轻度疏水性且无毒。疫苗与 TLR4 具有良好的分子对接作用，并在没有佐剂的情况下促进了强烈的 B 和 Th1 记忆免疫反应以及高水平的 IL-2、IFN-γ 的分泌，同时降低了 IL-12、TGF-β 和 IL-10 的水平，而没有 IL-6。实验体内研究应验证该疫苗作为具有交叉保护特性的预防工具的进一步用途。
