SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design

• Published in: Genomics (San Diego, Calif.) Calif.), 2020-11, Vol.112 (6), p.5044-5054
• Main Authors: Kushwaha, Sandeep Kumar, Kesarwani, Veerbhan, Choudhury, Samraggi, Gandhi, Sonu, Sharma, Shailesh
• Format: Article
• Language: English
• Subjects: B-Lymphocytes - immunology; Computational Biology; COVID-19; COVID-19 - genetics; COVID-19 - immunology; COVID-19 Vaccines; Epitopes; Epitopes, T-Lymphocyte - genetics; Epitopes, T-Lymphocyte - immunology; Gene Expression Profiling; Genes, MHC Class I; Genes, MHC Class II; Humans; Immunity, Innate - genetics; Immunodominant Epitopes - chemistry; Immunodominant Epitopes - genetics; Immunodominant Epitopes - metabolism; Molecular Docking Simulation; Original; Peptide; SAR-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - immunology; T- and B-cell; Vaccine
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.09.019

Genomics-led researches are engaged in tracing virus expression pattern, and induced immune responses in human to develop effective vaccine against COVID-19. In this study, targeted expression profiling and differential gene expression analysis of major histocompatibility complexes and innate immune system genes were performed through SARS-CoV-2 infected RNA-seq data of human cell line, and virus transcriptome was generated for T-and B-cell epitope prediction. Docking studies of epitopes with MHC and B-cell receptors were performed to identify potential T-and B-cell epitopes. Transcriptome analysis revealed the specific multiple allele expressions in cell line, genes for elicited induce immune response, and virus gene expression. Proposed T- and B-cell epitopes have high potential to elicit equivalent immune responses caused by SARS-CoV-2 infection which can be useful to provide links between elicited immune response and virus gene expression. This study will facilitate in vitro and in vivo vaccine related research studies in disease control. •SARS-CoV-2 transcriptome construction from RNA-seq data of infected human cell-lines.•T- and B-cell epitopes from SARS-CoV-2 transcriptome•Gene expression profiling of MHC alleles and innate immune system genes