Vaccinomics Approach for Multi-Epitope Vaccine Design against Group A Rotavirus Using VP4 and VP7 Proteins

Abstract

Rotavirus A is the most common cause of Acute Gastroenteritis globally among children <5 years of age. Due to a segmented genome, there is a high frequency of genetic reassortment and interspecies transmission which has resulted in the emergence of novel genotypes. There are concerns that monovalent (Rotarix: GlaxoSmithKline Biologicals, Rixensart, Belgium) and pentavalent (RotaTeq: MERCK & Co., Inc., Kenilworth, NJ, USA) vaccines may be less effective against non-vaccine strains, which clearly shows the demand for the design of a vaccine that is equally effective against all circulating genotypes. In the present study, a multivalent vaccine was designed from VP4 and VP7 proteins of RVA. Epitopes were screened for antigenicity, allergenicity, homology with humans and anti-inflammatory properties. The vaccine contains four B-cell, three CTL and three HTL epitopes joined via linkers and an N-terminal RGD motif adjuvant. The 3D structure was predicted and refined preceding its docking with integrin. Immune simulation displayed promising results both in Asia and worldwide. In the MD simulation, the RMSD value varied from 0.2 to 1.6 nm while the minimum integrin amino acid fluctuation (0.05-0.1 nm) was observed with its respective ligand. Codon optimization was performed with an adenovirus vector in a mammalian expression system. The population coverage analysis showed 99.0% and 98.47% in South Asia and worldwide, respectively. These computational findings show potential against all RVA genotypes; however, in-vitro/in-vivo screening is essential to devise a meticulous conclusion.

Keywords: acute gastroenteritis; in silico; multivalent; rotavirus; vaccinology; viruses.

Figure 1

Schematic representation of the strategy followed for the in silico vaccine design against RV.

Figure 2

The sequence of the vaccine construct. (Green: Adjuvant, Yellow: Linker for attaching adjuvant to CTL; Cyan: Cytotoxic T-cell epitopes; Magenta: Helper T-cell epitopes; Red: B cell. Uncolored residues include AAY linker between CTL epitopes, KK linker between HTL epitopes, and GGGGS linker joining the B cell epitopes.

Figure 3

(a) Epitopes displaying a range of affinities to different human leukocyte antigen (HLA) Class I alleles. Red, purple and pink show strong, intermediate and weak, respectively. (b) Shows the affinity of screened epitopes with HLA Class II alleles. Pink shows the weakest while red indicates the highest binding score.

Figure 4

Percent class combined coverage of vaccine construct in (a) South Asia population and (b) worldwide population.

Figure 5

(a) The secondary structure of the vaccine. (b) 3D structure of the vaccine construct (from N (Purple) to C (Red) terminus) predicted by trRosetta) (c). Docked model of the vaccine construct (red) with an integrin receptor (cyan) visualized using BIOVIA, Dassault Systèmes, Discovery studio, 2021. (d) ERRAT scores of vaccine peptide. (e) Ramachandran plot of the vaccine peptide. A total of 93.5% residues in the favored region, 5.9% in the allowed region and only one residue in the disallowed region.

Figure 6

Immune simulation result of the vaccine construct showing clear immune system activity against the vaccine. Simulation of B cells (a,b), T cells (c–f), Dendritic cells (g), antibodies (h), and various cytokines (i). IFN: Interferon, IgM/G: Immunoglobulin M/G, IL: Interleukins, TNF: Tumor necrosis factor, TGF: Transforming growth factor, TC cells: Cytotoxic T cells, TH cells: T-helper cells. Y2: Scale of Memory Cells, B Mem: Memory B cells, TH Mem: Memory T-helper cells.

Figure 6

Immune simulation result of the vaccine construct showing clear immune system activity against the vaccine. Simulation of B cells (a,b), T cells (c–f), Dendritic cells (g), antibodies (h), and various cytokines (i). IFN: Interferon, IgM/G: Immunoglobulin M/G, IL: Interleukins, TNF: Tumor necrosis factor, TGF: Transforming growth factor, TC cells: Cytotoxic T cells, TH cells: T-helper cells. Y2: Scale of Memory Cells, B Mem: Memory B cells, TH Mem: Memory T-helper cells.