SARS-CoV-2 Omicron variant spike-specific unique cluster of differentiation cells

A recent article posted to the bioRxiv* preprint server presented a safe and efficient multi-epitope severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine construct against SARS-CoV-2 variants, including Omicron.

Background

The new SARS-CoV-2 variant, Omicron (B.1.1.529/BA.1), was swiftly proclaimed a variant of concern (VOC) after being discovered in South Africa in late 2021. This was due to its potential to rapidly infect numerous people throughout the world. Omicron has about 37 mutations in its spike (S) protein which are responsible for its high transmissibility and immune evasion capacity relative to the previous global dominant SARS-CoV-2 Delta VOC.

Furthermore, the recent emergence and rapid transmission of the Omicron BA.2 sublineage might mark a novel threat to public health. The existing coronavirus disease 2019 (COVID-19) vaccines have only limited efficacy against the SARS-CoV-2 Omicron VOC. As a result, there is an urgent need for effective booster vaccinations against Omicron to stop the spread of SARS-CoV-2.

About the study

In the present study, the investigators utilized the SARS-CoV-2 S protein mutant strains to identify the interferon-γ (IFNγ)-inducing cluster of differentiation 4+ (CD4+) and immunogenic CD8+ T cell epitopes to devise a multi-epitope COVID-19 vaccine effective against the circulating viral variants, including Omicron.

The authors selected CD4+ and CD8+ T cell epitopes with robust binding affinity for both major histocompatibility complex II (MHC II) and MHC I molecules using the Immune Epitope Database (IEDB). The authors tried to fully maximize the quality and efficiency of the vaccine candidate by incorporating additional clinical checkpoint determinants like instability, immunogenicity, population coverage, allergenicity, toxicity, and antigenicity.

After predicting CD8+ and CD4+ T cell epitopes, the researchers discovered the top nine-10 amino acid (aa) long immunogenic CD8 epitopes within IFNγ-producing 15 aa long CD4 epitopes that might be exploited to trigger a robust and long-term immunity against Omicron. PCOptim, a previously established software program by the authors, was used to further verify the CD8 epitopes.

The three-dimensional (3D) structures of the top CD8 epitopes were subsequently modeled with corresponding human leukocyte antigen (HLA) alleles to interrogate the binding contact between peptide-MHC-T cell receptor (TCR) and peptide-MHC complexes. The researchers estimated the binding affinity of the currently discovered CD8 epitopes to murine MHC alleles for evaluating the immunogenicity and efficacy of COVID-19 vaccine candidates in preclinical trials.

Results

The study results illustrated 11 Omicron-specific CD4+ and eight CD8+ T cell epitopes comprising a global population coverage of 97.46% and 76.16%, respectively. The authors depicted identical epitopes, such as D614G, G142D, and T478K, among the Omicron and the co-circulating Delta (B.1.617.2) VOC.

Of the 25 shared CD8+ T cell epitopes among the SARS-CoV-2 Omicron BA.1, Alpha, Beta, Gamma, Delta, Cluster 5 mink, and United States (US) variants, the scientists discovered 12 epitopes that might be utilized to establish a multi-epitope SARS-CoV-2 vaccine simultaneously targeting different viral variants. The remaining 13 epitopes did not demonstrate any Omicron-specific epitopes. 

Among the 25 BA.1-specific immunogenic CD8+ T cell epitopes, eight epitopes were non-toxic, antigenic, and non-allergenic, despite being unstable in vivo. The authors also found three BA.2-specific immunogenic CD8+ T cell epitopes, which were non-toxic, stable, non-allergic, and antigenic. The researchers discovered the shared CD8+ T cell epitope, KSHRRARSV, targeting mutations vital to the virulence of SARS-CoV-2 between the Omicron BA.2 and BA.1 lineages at the furin cleavage site.

Seven shared CD4+ T cell epitopes among the Omicron BA.1, Alpha, Beta, Gamma, Delta, Cluster 5 mink, and US variants were found. Further, 11 CD4+ T cell epitopes specific to BA.1 that were stable in vivo were discovered. Eight shared CD4+ T cell epitopes between the two Omicron sublineages were found. In addition, the Omicron BA.2 sublineage shared CD4+ and CD8+ T cell epitopes with the SARS-CoV-2 Alpha, Beta, Gamma, Delta, Cluster 5 mink, and US variants.

Three spike CD4+ T cell epitopes, namely SVLYNLAPFFTFKCY, VLYNLAPFFTFKCYG, and KSHRRARSVASQSII, were found to be in overlap with the top CD8+ T cell epitopes. These CD4+ T cell epitopes were non-toxic, non-allergenic, IFNγ inducing, and antigenic. Furthermore, the KSHRRARSVASQSII CD4+ T cell epitope overlapped with the KSHRRARSV CD8+ T cell epitope, which was common to the BA.2 and BA.1 sublineages.

Murine MHC restriction revealed seven shared S CD8+ T cell epitopes between the analyzed SARS-CoV-2 variants, four BA.1-specific S CD8+ T cell epitopes, and a BA.2-specific TPINLGRDL CD8+ T cell epitope.

While the 12 shared CD8 peptides between the Omicron VOC and other SARS-CoV-2 variants triggered immunity spanning over 84% of the global population, the BA.1-specific eight CD8 peptides covered 76.16%. The seven identical CD4+ T cell epitopes between Omicron and other circulating variants, like Delta, spanned over 96.65% of people around the globe. Notably, the 11 highest-quality BA.1-specific CD4 peptides covered 97.46% of the global population, whereas 92.66% of the people worldwide have been covered by the three overlapping CD4 peptides.

Among the eight optimized distinct CD8+ T cell epitopes with 98.55% population coverage, two were found in the BA.2-specific S CD8 epitope, and one in the top shared S CD8 epitopes between Omicron and other SARS-CoV-2s. HLA-B*08:01, HLA-B*07:02, HLA-A*31:01, HLA-B*51:01, and HLA-A*33:01 were among the HLA alleles found in the optimized dataset but not in the clinically significant dataset. These alleles could justify the disparity in population coverage between the optimized epitope dataset and datasets produced after passing epitopes via many clinical checkpoints.

3D visualization revealed that the analyzed YNLAPFFTF and KSHRRARSV epitopes were both significant MHC I binders. The KSHRRARSV-HLA-A*30:01 and YNLAPFFTF-HLA-A*24:02 were energy minimized and lowered overall potential energy between the MHC molecule and the epitope. Finally, the modeling of the YNLAPFFTF-HLAA*24:02 complex with the HLA-A24 unique structure C1-28 TCR offered a better understanding of the TCR contact with the peptide MHC (pMHC) complex.

Conclusions

The study findings revealed that CD4+ and CD8+ T cell epitopes were specific for the SARS-CoV-2 Omicron BA.2 and BA.1 lineages from the viral S protein mutants. The scientists also discovered shared epitopes between the SARS-COV-2 BA.1 and other circulating VOCs, such as B.1.617.2. The CD8 epitopes were verified by employing a previously established software tool by the authors named PCOptim. The discovered epitopes selectively targeted the S proteins mutations in the fusion sites and receptor-binding domains (RBDs). This might eradicate SARS-CoV-2 infections and establish long-standing immune responses relative to the short-lived mRNA vaccines, maximizing the efficiency of the vaccine candidate against the present COVID-19 pandemic and possible future viral variants.

To summarize, the present multi-epitope COVID-19 vaccine candidate designed against the SARS-CoV-2 S protein using immunoinformatic approaches might be a potential novel, efficient, and safe method to control infections by Omicron or any other viral variant in the future.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.