CD8+ T-Cell Epitope Variations Suggest a Potential Antigen HLA-A2 Binding Deficiency for Spike Protein of SARS-CoV-2

Abstract

We identified SARS-CoV-2 specific antigen epitopes by HLA-A2 binding affinity analysis and characterized their ability to activate T cells. As the pandemic continues, variations in SARS-CoV-2 virus strains have been found in many countries. In this study, we directly assess the immune response to SARS-CoV-2 epitope variants. We first predicted potential HLA-A*02:01-restricted CD8+ T-cell epitopes of SARS-CoV-2. Using the T2 cell model, HLA-A*02:01-restricted T-cell epitopes were screened for their binding affinity and ability to activate T cells. Subsequently, we examined the identified epitope variations and analyzed their impact on immune response. Here, we identified specific HLA-A2-restricted T-cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides were confirmed to bind with HLA-A*02:01 and potentially be presented by antigen-presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. These epitopes could activate and generate epitope-specific T cells in vitro, and those activated T cells showed cytolytic activity toward target cells. Meanwhile, n-Sp1 epitope variant 5L>F significantly decreased the proportion of specific T-cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A*02:01 and decreased proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SARS-CoV-2. Our data indicate that the variation of a dominant epitope will cause the deficiency of HLA-A*02:01 binding and T-cell activation, which subsequently requires the formation of a new CD8+ T-cell immune response in COVID-19 patients.

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules

“…Thus, we predicted the complete absence of T-cell immunity evasion at the level of the whole virus. This agrees with the recent findings by Xiao and Qiu with co-authors: while several peptides lost binding ability to HLA-A*02 because of mutations, overall levels of T-cell immunity were not strongly decreased ( Qiu et al, 2021 ; Xiao et al, 2022 ). When the analysis was limited to the Spike protein, remarkably higher number of alleles was identified: eight alleles showed enhanced ability of Omicron/Delta peptide presentation, while four remaining alleles showed significant decrease in the number of tight binders.…”

CD8+ T-cell immune escape by SARS-CoV-2 variants of concern

“…Thus, hypothetical new CD8 + T-cell epitopes would be loaded onto corresponding HLA-I molecules and trigger new and specific T-cell activation for a completedelayed-VOC clearance. Studies by Qiu et al (75) and Elisa Guo and Hailong Guo (74) demonstrated the possibility of new CD8 + T-cell epitopes from mutated epitopes of SARS-CoV-2, with the ability to increase T-cell activation marker CD69 and CD137 and induce low titer CD8 + T-cell response specific to the mutants, but then, no more specific to the WT SARS-CoV-2. Future studies need to assess the possibility of new epitopes from SARS-CoV-2 VOC infections and their effectiveness in the clearance of SARS-CoV-2 VOCs.…”

“…However, this-early-immunity effectiveness might be mainly attributed to memory CD4 + T-cells and, to a lesser extent, to memory B-cells and antibodies, but probably not to memory CD8 + T-cells. This is because, as described in Section 4, mutated epitopes carried by VOCs may no longer be recognized by preexisting CD8 + T-cell immunity, as mutations in SARS-CoV-2 negatively affect mainly CD8 + T-cell epitopes that are more vulnerable (62,75), but not CD4 + T-cell epitopes for which the same preexisting SARS-CoV-2 immune response still retains efficacy against mutants and may appropriately reduce VOC infection-associated severity (72). Consequently, we suggested that the clearance of VOC infections later on without intensive care admission could be possibly attributed to the development of new CD8 + T-cell epitopes specific to variants, together with the conserved preexisting CD4 + T-cell, which aligns with the global pattern of the COVID-19 pandemic [surges in new cases followed by prevalence declines months later (https:// covid19.who.int/)].…”

“…They may lead to indescribable fatalities due to more virulent mutants, as reported by Elisa Guo and Hailong Guo ( 74 ). They found that “CD8 + T-cell epitope mutants of SARS-CoV-2 proteins lead to persistently variable SARS-CoV-2 infections with different susceptibility and severity” ( 74 , 75 ). Indeed, several other studies demonstrated with solid evidence that, despite the preexisting SARS-CoV-2–specific cellular immunity in COVID-19 recovered patients, the viral replication rate after reinfection with SARS-CoV-2, but specifically SARS-CoV-2 VOCs, is increased in these patients ( 76 ).…”

“…Indeed, CD8 + T-cell HLA-I epitopes are shorter (8 to 10 residues) than CD4 + T-cell HLA-II epitopes (12 to 16 residues). A single mutation in one of the CD8 + T-cell HLA epitopes is enough and sufficient to impair and compromise recognition of epitopes by HLA, thus inhibiting activation, functionality, and cytotoxic activity of CD8 + T-cells, which considerably and specifically inhibits the destruction of infected host cells ( 62 , 75 ) and generally affects the overall T-cell response efficacy. Understandably, subversion of CD8 + T-cell response affects the potency of the whole T-cell response because, in the context of the SARS-CoV-2 threat, the viral replication mechanism is exclusively intracellular, and the main involved T-cell response is led by CD8 + CTLs, due to efficient presentation of endogenously produced antigens on MHC-I molecules.…”