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. 2023;12(1):5.
doi: 10.1186/s43088-023-00341-4. Epub 2023 Jan 10.

Cross-variant proof predictive vaccine design based on SARS-CoV-2 spike protein using immunoinformatics approach

Lavanya Kumar Sahu  1 , Kiran Singh  1
Affiliations

Cross-variant proof predictive vaccine design based on SARS-CoV-2 spike protein using immunoinformatics approach

Lavanya Kumar Sahu et al. Beni Suef Univ J Basic Appl Sci. 2023.

Abstract

Background: Coronavirus Disease (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 virus is evolving continuously. The omicron variant of SARS-CoV-2 has the highest mutation in its spike protein, thus making the presently available vaccine ineffective or reducing its efficiency. Furthermore, the majority of the vaccines are constructed using a spike protein sequence from wild-type SARS-CoV-2. This raises the possibility of the virus evolving to the point where the vaccine's effectiveness is completely lost, even after booster doses. The study aims to develop a predictive vaccine as well as the epitopes for the updating of the vaccine sequences of currently available vaccines. In this study, following the immunoinformatics approach, predictive vaccine construction was done with the help of epitopes present on spike proteins of wild-type, delta, and omicron variants that encompass the majority of variants and possible new variants that arise from the combination of circulating variants.

Results: The vaccine that was constructed was stable and immunogenic. The vaccine was constructed with the help of 18 B-cell epitopes, 5 MHC class I epitopes, and 6 MHC class II epitopes. The epitope conservancy analysis suggests that the vaccine will work for the previously known variant of concern. The vaccine bound to TLR4, TLR2, B-cell receptor chains A and B, and ACE2 receptors with a z score of - 1.4, - 1.7, - 1.4, - 1.7, and - 1.4, respectively, with a cluster size of 121 highest for the ACE2 receptor and 46 lowest for B-cell receptor chain A. The C-ImmSim simulation results indicate that the vaccine is generating both humoral and cell-mediated responses at a sufficient level throughout the month upon injection of the vaccine as an antigen.

Conclusion: The study's findings indicate that the vaccine was both stable and immunogenic, providing a sufficient level of immunity. Following experimental validation, the vaccine can be used, and the epitopes can be employed for therapeutic purposes such as antibody synthesis.

Supplementary information: The online version contains supplementary material available at 10.1186/s43088-023-00341-4.

Keywords: And omicron; COVID-19; Delta; Immunoinformatics; Multi-epitope vaccine; SARS-CoV-2.

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Conflict of interest statement

Competing interestThe authors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
The sequential arrangements of epitopes to form vaccine construct
Fig. 2
Fig. 2
Confidence level of prediction of the secondary structure via PSIPRED
Fig. 3
Fig. 3
The modelled and refined structure of vaccine construct and validation via Ramachandran plot
Fig. 4
Fig. 4
Interaction of vaccine construct (blue) with immune receptors and HLAs
Fig. 5
Fig. 5
C-ImmSim simulation generated immune response after injection of vaccine construct as an antigen
See this image and copyright information in PMC

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