Srivastava, Sukrit; Verma, Sonia; Kamthania, Mohit; Agarwal, Deepa; Saxena, Ajay Kumar; Kolbe, Michael; Singh, Sarman; Kotnis, Ashwin; Rathi, Brijesh; Nayar, Seema A; Shin, Ho-Joon; Vashisht, Kapil; Pandey, Kailash C
Journal of biomolecular structure & dynamics
2020Nov ; 6 ( 47 ) :1-20.
PMID : 33155524
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Srivastava, Sukrit -
Verma, Sonia -
Kamthania, Mohit -
Agarwal, Deepa -
Saxena, Ajay Kumar -
Kolbe, Michael -
Singh, Sarman -
Kotnis, Ashwin -
Rathi, Brijesh -
Nayar, Seema A -
Shin, Ho-Joon -
Vashisht, Kapil -
Pandey, Kailash C -
ABSTRACT
The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, 'overlapping-epitope-clusters-to-patches' method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as 'Ag-Patch or Ag-Patches', for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide. Communicated by Ramaswamy H. Sarma.
keyword
Ag-Patch (antigenic patch); COVID-19; Coronavirus; Multi-Epitope Vaccine; Multi-Patch Vaccine; Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2); Toll-Like Receptor (TLR); epitope; overlapping-epitope-clusters-to-patches; reverse epitomics
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