1  Introduction
The outbreak of COVID-19 in the Hubei region of the Chinese city of Wuhan [37] has resulted in a difficult situation for the global populace and for the World Health Organization (WHO). On 30 Jan 2020, WHO declared an emergency regarding COVID-19 spread, prevention, and control [28,29]. As of 20 March 2020, there are over 240,000 cases and over 10,000 confirmed deaths, affecting 181 countries [9]. Present updates indicate that there are over 1 million confirmed cases and over 100,000 deaths worldwide [39] (information is obtained from https://www.worldometers.info/coronavirus/). The coronavirus is an RNA type virus with positive sense strand feature and is associated with the Coronaviridae family under order Nidovirales, and is found to be dispersed among Primate order, members of class Mammalia, and specifically in humans [31]. Severe acute respiratory syndrome coronavirus (SARS-CoV) [11,21,22] and Middle East respiratory disorder coronavirus (MERS-CoV) [7,40], classified as β-coronaviruses, are found to be related to the novel SARS-COV-2. Until now, there has been no efficacious therapy to regulate its spread [24]. Investigating its spread across continents and the vulnerability, there is an urgent need to craft vaccines for reinforcing immune defense against the SARS-COV-2 virus. One of the strategies to combat it is the development of vaccines that can initiate an adaptive immune response in humans. Here an attempt has been made to design an epitope based vaccine directed at SARS-COV-2, by analyzing the proteome of the virus by using Immuno-informatics tools. In this study, we deployed the use of various bioinformatics servers and Immuno-informatics tools for identifying and recognizing the T-cell epitopes from the intensive study of available protein sequences and structures that are related to SARS-COV-2. These epitope stretches can interact with MHC Class I and Class II HLA alleles; further validation of epitopes was analyzed by Ramachandran Plot analysis, Antigenicity parameters evaluation, Toxicity analysis, Population coverage, Molecular dynamics, and ProtParam analysis [19]. This approach is an excellent method in modern vaccine design, as it provides a lead over classical trial and error methods of wet labs [23]. We tried to identify T-cell epitopes that can elicit a robust immune response in the global human population and act as potential vaccine candidates. However, the ability of these epitopes to act as a vaccine candidate needs to be analyzed in Molecular biology lab studies. Our investigation can open new dimensions in crafting peptide-based vaccine regimens for Novel SARS-COV2. The greatest decline in virus expansion was noted following ORF3a removal. ORF7a encodes a 122-amino-acid type I transmembrane protein and structural studies disclose a packed seven-stranded β sandwich comparable in fold and topology to members of the immunoglobulin super family. SARS-CoV is an enveloped, positive-stranded RNA virus with a genome of around 29,700 bases. The genome incorporates at least 14 open reading frames (ORFs) that encode 28 proteins in three distinct classes: two large polyproteins P1a and P1ab that are cleaved into 16 non-structural proteins (nsp1–nsp16) during viral RNA synthesis; four structural proteins (S, E, M and N) that are necessary for viral entrance and gathering; and eight accessory proteins that are assumed to be dispensable for viral replication, but may facilitate viral assembly and take part in virulence and pathogenesis (Fig. 1 ).
Fig. 1 Genome organization and viral proteins of SARS-CoV [44].
In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab.