Immunoinformatics methods could be used to explore antigens of viruses, prediction of their epitopes and evaluation of its immunogenicity. Therefore, the development of effective drugs and vaccines against the control of emerging diseases is a priority of research and immunoinformatic is currently considered as a new method to find an effective way to control diseases. However, there is no specific and approved drug for SARS-COV-2 infection, and the treatment approach is more supportive, and the use of these therapies is said to reduce the resulting mortality rate. In case of emergency, Remdesivir is used against SARS-COV-2 or recovered patients’ plasma is used as a side-effect-free treatment. Although ritonavir and lopinavir are used as protease-inhibiting drugs for the treatment of SARS-COV-2, it has been reported in a clinical trial that its usefulness for the treatment of SARS-COV-2 is questionable. In addition, N protein is an early diagnostic marker for SARS-COV because it can be detected in clinical specimens one day after the onset of symptoms and it is stable due to very small mutations. N protein in its entirety is highly immunogenic and antigenic. Nucleoprotein (N) is a phosphoprotein and nucleocapsid protein that binds to genomic RNA and M protein and is the main stimulus of the host immune system during viral infection. S protein as a major antigenic component is an important target for vaccine development. DNA structures encoding the S protein have also produced virus-neutralizing antibodies. For SARS-COV, full-length and the active immunization part of S protein, S protein peptides and chimeric versions of S protein have been identified. S1 is responsible for binding to the cellular receptor, and S2 contains fusion peptide. Surface glycoprotein (S) is responsible for binding to the cellular receptor, which has two basic components (S1) and globular (S2). Each of these proteins is not only involved in the structure of the virus but also in various aspects, involved in virus replication. Most coronaviruses require structural protein to produce a complete viral particle. The structural proteins of SARS-CoV-2 include nucleoprotein (N), membrane (M), surface glycoprotein (S) and envelop protein (E). SARS-CoV-2, like other coronaviruses, encodes several structural proteins. Coronaviruses can infect humans and other vertebrates and cause infections in the respiratory system, gastrointestinal tract and central nervous system of humans, livestock, birds, bats and mice and many other wild animals. Their genome size is about 26–32 kilobases. SARS-CoV-2 belongs to the beta-coronavirus genus with an envelope with a single-stranded RNA genome, positive sense, and has a diameter of about 80–120 nm. Coronaviruses have four genera: alpha, beta, delta and gamma virus. Coronavirus 2019 (COVID-19), caused by SARS-CoV-2, was first reported in a number of patients with pneumonia of unknown etiology in Hubei Province, China, and subsequently in many parts of the world. Since the advent of SARS-CoV in 2002 and its spread to 32 countries, the world has experienced the outbreak of MERS-CoV and now nCoV 2019. We believe that the proposed multi-epitope vaccine can effectively evoke an immune response toward SARS-CoV-2. Therefore, 543-amino-acid-long multi-epitope vaccine formation was invented through linking 9 cytotoxic CTL, 5 HTL and 14 B cell epitopes with appropriate adjuvants and connectors that can control the SARS coronavirus 2 infection and could be more assessed in medical scientific researches. ResultsĮpitopes which were used in our survey were based on non-allergenic, non-toxic and antigenic. coli K12, the vaccine construct was cloned into pET28a (+) vector. Finally, after optimizing the codon to increase expression in E. The vaccine construct was ligated to MHCI. The three-dimensional structure of the structure was predicted and optimized, and its quality was evaluated. Then, in order to increase the safety of Hbd-3 and Hbd-2 as adjuvants, they were connected to the N and C terminals of the vaccine construct, respectively, with a linker. B cell, CTL and HTL were determined based on antigenicity, allergenicity and toxicity that were non-allergenic, non-toxic, and antigenic and were selected for the design of a multi-epitope vaccine structure. As the new pandemic created by COVID-19 virus created the need of rapid acquisition of a suitable vaccine against SARS-CoV-2 to develop Immunity and to reduce the mortality, the aim of this study was to identify SARS-CoV-2 S protein and N antigenic epitopes by using immunoinformatic methods to design a vaccine against SARS-CoV-2, for which S and N protein-dependent epitopes are predicted.
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