Discussion
SARS-CoV-2 vaccines inducing specific antibody production, meanwhile the specific antiviral T cell responses may present better protective effects for people. Therefore, exploring the vaccine-induced SARS-CoV-2-specific CD8+ T cell responses based on CD8+ T cell epitopes might be one of the important approaches. In this study, we identified four nonamer epitopes on SARS-CoV-2 restricted by HLA-E molecule, which could elicit epitope-specific CD8+ T cell responses in SARS-CoV-2 vaccinated population. Importantly, the HLA-E-restricted SARS-CoV-2 epitope-specific CD8+ T cells showed high frequencies in Ad5-nCoV vaccinated individuals. The frequencies of epitope-specific CD8+ T cells were decreased in the individuals receiving two doses of Ad5-nCoV vaccination than only one dose. These results may greatly advance the understanding of the cellular immune defense against SARS-CoV-2 infection, meanwhile contribute to more comprehensive evaluating the protective effects of vaccines for SARS-CoV-2 covering all the HLA-diverse populations.
The most ideal result after infection or vaccination is highly protective and lasting immunity, so as to establish a high level of immunity of the population. The large-scale inoculation of SARS-CoV-2 vaccine in population has greatly reduced the rates of infection and severity. T cell response plays a key role in vaccine mediated protection. It has been confirmed that vaccines that could induce SARS-CoV-2 specific T cell response could effectively control infection, avoid severe tissue damage, and significantly reduce hospitalization rate and mortality. In clinical trials of SARS-CoV-2 mRNA vaccine (BNT162b2; Modern VRC) or adenovirus vector vaccine (AdV5; ChAdOx), SARS-CoV-2 specific CD8+ T cells could secrete high level of IFN- γ, which was similar to the level of specific CD8+ T cell response in patients with COVID-19. The inoculation of SARS-CoV-2 mRNA vaccine or adenovirus vector vaccine could induce high frequency of CD8+ T cell response specific to S protein with CCR7-CD45RA+effect phenotype, meanwhile could induce persistent memory CD8+ T cells [3, 22-24]. Moreover, the strong SARS-CoV-2 specific T cell responses could be detected in naturally infected individuals after vaccination. Our results showed that the HLA-E restricted SARS-CoV-2 epitopes-specific CD8+ T cell responses could be detected in the subjects vaccinated with adenovirus vector vaccine Ad5-nCoV, further indicating that Ad5-nCoV inoculation could induce effective T cell responses in the population.
HLA-E has been proved to present epitope to interact with αβTCR on CD8+ T cells in several infectious diseases. Since HLA-E is a ubiquitous HLA allele locus in the population, HLA-E could be used as the first choice in more specific and effective peptide vaccine design and research. The current research mainly focuses on the mechanism of HLA-E mediated NK cell function in the process of SARS-CoV-2 infection. It has been found that SARS-CoV-2 could induce HLA-E expression on the surface of pulmonary epithelial cells, which could bind peptides derived from S protein and interact with CD94/NKG2A on NK cells [25]. The peptide derived from nsp13 of SARS-CoV-2 presented by HLA-E could not interact with NKG2A on NK cells, thus mediating the killing effects of NK cells to virus-infected target cells [26]. Therefore, it is necessary to identify HLA-E restricted epitope of SARS-CoV-2, which would provide information for people who suffered from COVID-19 disease or vaccinated with SARS-CoV-2 vaccine. Based on the general rule of epitope binding motifs, nonapeptides which could be presented by HLA-E molecule always showed mainly anchor residues methionine (M), isoleucine (I) or leucine (L) at position 2, and isoleucine (I) or leucine (L) at position 9. Therefore, the six SARS-CoV-2 nonapeptides we identified with residue M/I/L at position 2 and residue L at C-terminal were conformed the general rule of HLA-E-restricted peptides. Notably, our study found that two epitopes S7 and S19 on SARS-CoV-2 restricted by HLA-E could also be resented by HLA-A*02 reported in other studies [14]. Considering that 86% sequence was similar between HLA-E and HLA-A*02 molecules, and HLA-A*02 molecules may share binding peptides with HLA-E molecule. Therefore, this is a common phenomenon that HLA-E*01 and HLA-A*02 molecules always could present the same epitopes such as influenza M159-167, M158-166 and Epstein-Barr virus BZLF139-147 due to conserved deep pockets [27]. The co-presentation of antigen epitopes by both HLA-E*01 and HLA-A*02 seems to be more important in inducing CD8+ T cell response for HLA-E restriction epitopes.
It has been proved that receptor-binding domain (RBD) on S protein contains a variety of conformational epitopes that could induce high levels of antibody production [8], especially specific antibody with neutralizing activity. In addition, S protein also contains multiple dominant T cell epitopes, which could induce effective T cell immune response [28]. Therefore, S protein is the primary antigen used in development of SARS-CoV-2 vaccines. RBD region of S protein has become the core target for research of therapeutic neutralizing antibody and the mechanisms for specific T cell responses. HLA-E restricted specific CD8+ T cell epitopes identified in this study were all from S protein of SARS-CoV-2. Although these epitopes aa269-aa277, aa576-aa584, aa958-aa966 and aa1185-aa1193 were not locus within the RBD region (aa329-aa521), they are still important for the potential applications in future.
In fact, although SARS-CoV-2 non-structural protein (nsp) and open reading frames (ORFs) such as ORF3, nsp3, nsp4 and nsp12 showed low levels in SARS-CoV-2 infected cells, they also contain very important CD8+ T cell epitopes. For example, ORF9b derived epitopes could induce high-level virus specific CD8+ T cell responses in COVID-19 patients, confirming good immunogenicity of epitopes in vivo [29]. Therefore, identification of HLA-E restricted epitopes on nsp and ORFs of SARS-CoV-2 also make sense for research the effects of CD8+ T cells in further study.
In conclusion, HLA-E-restricted SARS-CoV-2 epitope-specific CD8+ T cell responses could be detected in Ad5-nCoV vaccinated population. Importantly, the levels of epitope specific CD8+ T cell responses could maintain for a long time after only one dose vaccination. The study may be a good supplement for evaluation of vaccination effects of Ad5-nCoV from the perspective of T cell responses. However, HLA-E-restricted CD8+ T cell responses induced in naturally infected individuals after vaccination still need to be investigated in the future.