Ex vivodetection of SARS-CoV-2-specific CD8+ T cells: rapid induction, prolonged contraction, and formation of functional memory

Abstract

CD8+ T cells are critical for the elimination and long-lasting protection of many viral infections, but their role in the current SARS-CoV-2 pandemic is unclear. Emerging data indicates that SARS-CoV-2-specific CD8+ T cells are detectable in the majority of individuals recovering from SARS-CoV-2 infection. However, optimal virus-specific epitopes, the role of pre-existing heterologous immunity as well as their kinetics and differentiation program during disease control have not been defined in detail. Here, we show that both pre-existing and newly induced SARS-CoV-2-specific CD8+ T-cell responses are potentially important determinants of immune protection in mild SARS-CoV-2 infection. In particular, our results can be summarized as follows: First, immunodominant SARS-CoV-2-specific CD8+ T-cell epitopes are targeted in the majority of individuals with convalescent SARS-CoV-2 infection. Second, MHC class I tetramer analyses revealed the emergence of phenotypically diverse and functionally competent pre-existing and newly induced SARS-CoV-2-specific memory CD8+ T cells that showed similar characteristics compared to influenza-specific CD8+ T cells. Third, SARS-CoV-2-specific CD8+ T-cell responses are more robustly detectable than antibodies against the SARS-CoV-2-spike protein. This was confirmed in a longitudinal analysis of acute-resolving infection that demonstrated rapid induction of the SARS-CoV-2-specific CD8+ T cells within a week followed by a prolonged contraction phase that outlasted the waning humoral immune response indicating that CD8+ T-cell responses might serve as a more precise correlate of antiviral immunity than antibody measurements after convalescence. Collectively, these data provide new insights into the fine specificity, heterogeneity, and dynamics of SARS-CoV-2-specific memory CD8+ T cells, potentially informing the rational development of a protective vaccine against SARS-CoV-2.

Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics

“…Presented SARS-CoV-2 peptides are immunogenic Several studies have reported T cell reactivity toward the SARS-CoV-2 HLA-predicted peptides (Grifoni et al, 2020;Nelde et al, 2020;Sekine et al, 2020;Woldemeskel et al, 2020;Zhang et al, 2020). We compiled a map of all the available data of experimentally validated reactive SARS-CoV-2 peptides (Le Bert et al, 2020;Minervina et al, 2020;Nelde et al, 2020;Poran et al, 2020;Schulien et al, 2020;Shomuradova et al, 2020;Snyder et al, 2020;Tarke et al, 2020;Woldemeskel et al, 2020;Wong et al, 2020) and searched it to see if it includes any of our identified peptides (Figure 4). Indeed, seven of our peptides were previously found to be immunogenic in blood samples of COVID-19 patients.…”

Cross-Reactive Immune Responses toward the Common Cold Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Mini-Review and a Murine Study

“…As was the case for antibodies, reports of virus-specific T cell frequencies have varied between studies based on host group and assay. Both CD8+ and CD4+ T cell cross-reactive populations have been identified, and for each population, cross-reactive peptide epitopes have been described [73][74][75][76][77][78]80,81]. T cells may exhibit a variety of effector functions toward SARS-CoV-2 or common cold HCoVs including the secretion of cytokines/chemokines, the killing of SARS-CoV-2 infected cells (cytotoxic T lymphocyte, CTL), the provision of help by cognate interactions with B cells (T helper [TH] or T follicular helper [TFH]), and/or the targeted down-regulation of an immune response (Regulatory T cell, Treg).…”

T Cells Targeting SARS-CoV-2: By Infection, Vaccination, and Against Future Variants

“…To determine cellular recruitment efficiency and memory profiles, SARS-CoV-2-specific CD8 + T cell epitopes (peptides + MHC) have been identified using both peptide stimulations and peptide-MHC class I tetramer binding (23)(24)(25)(26)(27)(28)61). Identification of SARS-CoV-2 CD8 + T cell specificities restricted by prevalent human HLAs, including HLA-A * 01:01, HLA-A * 02:01, HLA-A * 03:01, HLA-A * 11:01, HLA-A * 24:02, HLA-B * 07:02, HLA-B * 27:05, HLA-B35:01, HLA-B * 40:01, and HLA-B * 44:03 allowed us to understand the magnitude and phenotype of SARS-CoV-2-specific CD8 + T cells directly ex vivo or after in vitro stimulation.…”

“…The characterization of functional antiviral cytokine and activated T cells elicited by SARS-CoV-2 infection by in vitro stimulation has used either HLA optimized peptide "megapools" (18,19), selected expected crossreactive peptides (20), comprehensive peptidome with the omission of ORF1 (21), or whole peptidome functional pools (22). Antigen-specific responses once a peptide epitope has been identified (23) can also be quantified by pMHC binding using tetramers or multimers which is useful for downstream cellular characterization (23)(24)(25)(26)(27)(28). Furthermore, antigen-specific responses have also been identified by mapping of HLA presented peptides during in vitro infection to reveal cryptic T cell epitopes within proteins that are boosted by recent infection in patients with COVID-19 (17), which can be ORF independent, and therefore cryptic epitopes can be generated during infection (19).…”