SARS-CoV-2 has a high transmission rate and shows frequent mutations, thus making vaccine development an arduous task. However, researchers around the globe are working hard to find a solution e.g. synthetic vaccine. Here, we have performed genome-wide analysis of 566 Indian SARS-CoV-2 genomes to extract the potential conserved regions for identifying peptide based synthetic vaccines, viz. epitopes with high immunogenicity and antigenicity. In this regard, different multiple sequence alignment techniques are used to align the SARS-CoV-2 genomes separately. Subsequently, consensus conserved regions are identified after finding the conserved regions from each aligned result of alignment techniques. Further, the consensus conserved regions are refined considering that their lengths are greater than or equal to 60nt and their corresponding proteins are devoid of any stop codons. Subsequently, their specificity as query coverage are verified using Nucleotide BLAST. Finally, with these consensus conserved regions, T-cell and B-cell epitopes are identified based on their immunogenic and antigenic scores which are then used to rank the conserved regions. As a result, we have ranked 23 consensus conserved regions that are associated with different proteins. This ranking also resulted in 34 MHC-I and 37 MHC-II restricted T-cell epitopes with 16 and 19 unique HLA alleles and 29 B-cell epitopes. After ranking, the consensus conserved region from NSP3 gene is obtained that is highly immunogenic and antigenic. In order to judge the relevance of the identified epitopes, the physico-chemical properties and binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles.

SARS-CoV-2传播率高，突变频繁，疫苗研制任务艰巨。然而，全球的研究人员正在努力寻找解决方案，例如合成疫苗。在这里，我们对 566 个印度 SARS-CoV-2 基因组进行了全基因组分析，以提取潜在的保守区域，用于鉴定基于肽的合成疫苗，即。具有高免疫原性和抗原性的表位。在这方面，使用不同的多序列比对技术分别比对 SARS-CoV-2 基因组。随后，在从比对技术的每个比对结果中找到保守区域后，确定共有保守区域。进一步，考虑到它们的长度大于或等于 60nt，并且它们相应的蛋白质没有任何终止密码子，对共有保守区域进行了细化。随后，使用 Nucleotide BLAST 验证了它们作为查询覆盖率的特异性。最后，利用这些共有的保守区域，T 细胞和 B 细胞表位可根据其免疫原性和抗原性评分进行鉴定，然后用于对保守区域进行排序。因此，我们对与不同蛋白质相关的 23 个共有保守区域进行了排名。该排名还产生了 34 个 MHC-I 和 37 个 MHC-II 限制性 T 细胞表位，以及 16 个和 19 个独特的 HLA 等位基因和 29 个 B 细胞表位。排序后，获得来自 NSP3 基因的共有保守区域，该区域具有高度免疫原性和抗原性。