The structural characterization and antigenicity of the S protein of SARS-CoV

An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

Background

The pandemic situation of SARS-CoV-2 infection has sparked global concern due to the disease COVID-19 caused by it. Since the first cluster of confirmed cases in China in December 2019, the infection has been reported across the continents and inflicted upon a substantial number of populations.

Method

This study is focused on immunoinformatics analyses of the SARS-CoV-2 spike glycoprotein (S protein) which is key for the viral attachment to human host cells. Computational analyses were carried out for the prediction of B-cell and T-cell (MHC class I and II) epitopes of S protein and the analyses were extended further for the prediction of their immunogenic properties. The interaction and binding affinity of T-cell epitopes with HLA-B7 were also investigated by molecular docking.

Result

Three distinct epitopes for vaccine design were predicted from the sequence of S protein. The potential B-cell epitope was KNHTSPDVDLG possessing the highest antigenicity score of 1.4039 among other B-cell epitopes. T-cell epitope for human MHC class I was VVVLSFELL with an antigenicity score of 1.0909 and binding ability to 29 MHC-I alleles. The predicted T-cell epitope for human MHC class II molecule was VVIGIVNNT with a corresponding 1.3063 antigenicity score, less digesting enzymes, and 7 MHC-II alleles binding ability. All these three peptides were predicted to be highly antigenic, non-allergenic, and non-toxic. Analyses of the physiochemical properties of these predicted epitopes indicate their stable nature for plausible vaccine design. Furthermore, molecular docking investigation between the MHC class-I epitopes and human HLA-B7 reflects the stable interaction with high affinity among them.

Conclusion

The present study posits three potential epitopes of S protein of SARS-CoV-2 predicted by immunoinformatic methods based on their immunogenic properties and interactions with the host counterpart that can facilitate the development of vaccine against SARS-CoV-2. This study can act as the springboard for the future development of the COVID-19 vaccine.

Immunization of mice with a DNA vaccine based on severe acute respiratory syndrome coronavirus spike protein fragment 1

According to data in GenBank, a gene encoding SARS spike protein fragment 1 (S1) was synthesized. After recombination with an immunostimulatory sequence (ISS), the gene was cloned into the plasmid pIRES to produce pIRES-ISS-S1. On confirmation of the expression of S1 protein by indirect immunofluorescence assay (IFA), after the transfection of pIRES-ISS-S1 into BHK-21 cells, the DNA vaccine was repeatedly administrated to BALB/c mice. CD4+ and CD8+ spleen T lymphocytes were analyzed by flow cytometry (FCM) to evaluate T cell-mediated immune responses, the antigen-specific responses of T cells were evaluated by cytotoxic T lymphocyte (CTL) assay, and the level of IgG in antisera from immunized mice was determined by enzyme-linked immunosorbent assay. Results showed that the counts of spleen CD4+ and CD8+ T lymphocytes were increased, that the T cell-mediated immune responses showed antigen specificity, and that IgG was significantly induced with DNA vaccines pIRES-ISS-S1 and pIRES-S1 at titers of 1:320 and 1:160, respectively. These results are promising for the protective immunization of humans.

Molecular advances in severe acute respiratory syndrome-associated coronavirus (SARS-CoV)

The sudden outbreak of severe acute respiratory syndrome (SARS) in 2002 prompted the establishment of a global scientific network subsuming most of the traditional rivalries in the competitive field of virology. Within months of the SARS outbreak, collaborative work revealed the identity of the disastrous pathogen as SARS-associated coronavirus (SARS-CoV). However, although the rapid identification of the agent represented an important breakthrough, our understanding of the deadly virus remains limited. Detailed biological knowledge is crucial for the development of effective countermeasures, diagnostic tests, vaccines and antiviral drugs against the SARS-CoV. This article reviews the present state of molecular knowledge about SARS-CoV, from the aspects of comparative genomics, molecular biology of viral genes, evolution, and epidemiology, and describes the diagnostic tests and the anti-viral drugs derived so far based on the available molecular information.