Abstract
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began in 2019 but it remains as a serious threat today. To reduce and prevent spread of the virus, multiple vaccines have been developed. Despite the efforts in developing vaccines, Omicron strain of the virus has recently been designated as a variant of concern (VOC) by the World Health Organization (WHO).
Objective: To develop a vaccine candidate against Omicron strain (B.1.1.529, BA.1) of the SARS-CoV-19.
Methods: We applied reverse vaccinology methods for BA.1 and BA.2 as the vaccine target and a control, respectively. First, we predicted MHC I, MHC II and B cell epitopes based on their viral genome sequences. Second, after estimation of antigenicity, allergenicity and toxicity, a vaccine construct was assembled and tested for physicochemical properties and solubility. Third, AlphaFold2, RaptorX and RoseTTAfold servers were used to predict secondary structures and 3D structures of the vaccine construct. Fourth, molecular docking analysis was performed to test binding of our construct with angiotensin converting enzyme 2 (ACE2). Lastly, we compared mutation profiles on the epitopes between BA.1, BA.2, and wild type to estimate the efficacy of the vaccine.
Results: We collected a total of 10 MHC I, 9 MHC II and 5 B cell epitopes for the final vaccine construct for Omicron strain. All epitopes were predicted to be antigenic, non-allergenic and non-toxic. The construct was estimated to have proper stability and solubility. The best modelled tertiary structures were selected for molecular docking analysis with ACE2 receptor.
Conclusions: These results suggest the potential efficacy of our newly developed vaccine construct as a novel vaccine candidate against Omicron strain of the coronavirus.
Keywords: In silico; Omicron; Reverse vaccinology; SARS-CoV-2; Vaccine design.
【저자키워드】 SARS-CoV-2, in silico, omicron, reverse vaccinology, Vaccine design., 【초록키워드】 Structure, Efficacy, ACE2, Vaccine, coronavirus, pandemic, Mutation, Vaccines, VoC, Vaccine design, angiotensin converting enzyme 2, variant, ACE2 receptor, Toxicity, severe acute respiratory syndrome Coronavirus, virus, angiotensin converting enzyme, Spread, Epitopes, stability, vaccine candidate, WHO, B.1.1.529, antigenicity, epitope, 3D structure, wild type, estimation, predict, binding, 3D Structures, angiotensin, secondary structure, B cell epitopes, B cell epitope, Physicochemical properties, Health Organization, secondary structures, World Health Organization, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, profile, enzyme, antigenic, non-allergenic, vaccine construct, effort, molecular docking analysis, second, solubility, viral genome sequences, allergenicity, MHC II, MHC I, Prevent, non-toxic, final vaccine construct, RaptorX, selected, tested, predicted, collected, develop, applied, was performed, were used, reduce, the vaccine, physicochemical property, 【제목키워드】 SARS-CoV-2 vaccine,