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.