Design of a Multiepitope-Based Peptide Vaccine against the E Protein of Human COVID-19: An Immunoinformatics Approach

Abstract

Background: A new endemic disease has spread across Wuhan City, China, in December 2019. Within few weeks, the World Health Organization (WHO) announced a novel coronavirus designated as coronavirus disease 2019 (COVID-19). In late January 2020, WHO declared the outbreak of a "public-health emergency of international concern" due to the rapid and increasing spread of the disease worldwide. Currently, there is no vaccine or approved treatment for this emerging infection; thus, the objective of this study is to design a multiepitope peptide vaccine against COVID-19 using an immunoinformatics approach.

Method: Several techniques facilitating the combination of the immunoinformatics approach and comparative genomic approach were used in order to determine the potential peptides for designing the T-cell epitope-based peptide vaccine using the envelope protein of 2019-nCoV as a target.

Results: Extensive mutations, insertion, and deletion were discovered with comparative sequencing in the COVID-19 strain. Additionally, ten peptides binding to MHC class I and MHC class II were found to be promising candidates for vaccine design with adequate world population coverage of 88.5% and 99.99%, respectively.

Conclusion: The T-cell epitope-based peptide vaccine was designed for COVID-19 using the envelope protein as an immunogenic target. Nevertheless, the proposed vaccine rapidly needs to be validated clinically in order to ensure its safety and immunogenic profile to help stop this epidemic before it leads to devastating global outbreaks.

Figure 1

Descriptive workflow for the epitope-based peptide vaccine prediction.

Figure 2

Artemis analysis of the envelope protein displaying 3 windows. The upper window represents the HCoV-HKU1 reference sequence, and its genes are highlighted in blue starting from orflab gene and ending with N gene. The middle window describes the similarities and the difference between the two genomes. Red lines indicate a match between genes from the two genomes; blue lines indicate inversion which represents the same sequences in the two genomes, but they are organized in the opposite direction. The lower window represents COVID-19 and its genes starting from orflab gene and ending with N gene.

Figure 3

Sequence alignment of the envelope protein of COVID-19 using BioEdit software (total conservation through the 4 strains: 2 from China and 2 from the USA).

Figure 4

Maximum likelihood phylogenetic tree which describes the evolutionary relationship between the seven strains of coronavirus.

Figure 5

Schematic diagrams (a) and (b) showing world population coverage of the envelope protein of COVID-19 binding to the MHC class I and MHC class II molecules, respectively.

Figure 6

3D structures visualized by UCSF Chimera: (a) and (b) show the most promising peptides in the envelope protein of COVID-19 (yellow colored) binding to MHC class I and MHC class II, respectively, while (c), (d), and (e) show the molecular docking of the YVYSRVKNL, LAILTALRL, and SLVKPSFYV peptides of coronavirus docked in HLA-A∗02:01, respectively.