Abstract
All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.
Highlights
Coronavirus disease 2019 (COVID-19) is a highly transmissible acute respiratory disease caused by a novel strain of coronavirus called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Using well-established prediction tools, we identified potential B- and T-cell epitopes in the structural proteins (S, E, M, and N) of SARS-CoV-2 (Fig 1a)
A heat map was generated using R software that showed the distribution of antigenic B-cell epitopes across the length of SARS-CoV-2 structural proteins (Fig 1b and 1c)
Summary
Coronavirus disease 2019 (COVID-19) is a highly transmissible acute respiratory disease caused by a novel strain of coronavirus called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genome of SARS-CoV-2 encodes both structural and nonstructural proteins (NSPs). There is a -1 frameshift between ORF1a and ORF1b leading to the production of two polypeptides (pp1a and pp1ab). These polyproteins are post-translationally processed by virusencoded chymotrypsin-like protease (3CLpro) or main protease (Mpro) and by one or two papain-like proteases into 16 NSPs. The structural proteins include spike glycoprotein (S), envelope protein (E), membrane protein (M), and nucleocapsid protein (N). The S proteins of SARS-CoV-2 and SARS-CoV are phylogenetically closely related with an amino acid sequence identity of approximately 77% [1] while utilizing the same cellular receptor angiotensin-converting enzyme 2 (ACE2) for entry into cells [3]
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