CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation

Summary 

This study presents in-depth combinatorial ex-vivo profiling of CD8+ T cell specificity phenotype in SARS-CoV-2 convalescent individuals. In convalescent, SARS-CoV-2 T cell recognizes a broad range of epitopes against the SARS-CoV-2 proteome. The most prominent phenotypes of SARS-CoV-2 specific CD8+ T cells were stem-cell memory (SCM) and transitional memory (TM2), which agrees with previous studies (Sekine et al. and Fan et al.). However, high prevalence CD8+ T cell SARS-CoV-2 specificities had a distinct phenotype to low prevalence SARS-CoV-2 specificities; being enriched for TEMRA, EM, TM2 cells and SCM and CM cells, respectively. Cross-sectional data of the recovery period revealed an increase in the number of epitope responses detected over time. Lastly, evaluation of SARS-CoV-2-specific CD8+ T cell response was time-dependent during early recovery phase and was associated with decrease in inflammation and sustainment of antibody neutralizing activity. 

Research Highlights   

1. While CD8+ T cell responses to epitopes from the spike protein and ORF3a were the most common, CD8+ T cells recognising nucleocapsid epitopes were most frequent. The highest number of epitopes were presented by HLA-A*01:01 and HLA-A*02:01 and the lowest by HLA-B*07:02. Of the peptide responses detected, 52/132 have not been previously described. 

2. CD8+ T cells for which positive epitope specificity was detected in a high prevalence of the study population were detected at higher frequencies than CD8+ T cells which had less prevalent epitope specificities. While needing further investigation, this could suggest greater T cell expansion and persistence to certain dominant epitopes. 

3. Higher frequency SARS-CoV-2 specific CD8+ T cells, (as per point 2.) were negatively correlated with expression of early differentiated markers and positively correlated with late differentiation markers, indicating that the most prevalent epitope responses in the study population are demarcated by effective T cell differentiation. 

4. SARS-CoV-2 specific CD8+ T cells were less frequent than EBV and CMV specific CD8+ T cells but comparably frequent to Flu specific T cells. The SARS-CoV-2 T cells also had a distinct phenotype to these other virus specific CD8+ T cells. 

5. Neutralising antibody titers were negatively correlated with an early differentiation phenotype, effective humoral (antibody) and cellular (mature/ differentiated) responses occur complementary to each other. 

Impact for COVID-19 research:  

Detection of novel SARS-CoV-2 epitopes, including those from less commonly investigated non-structural antigens, could inform vaccine development. The differentiated and memory phenotypes of epitope specific T cells, which were associated with higher prevalence and frequency in the convalescent individuals, could be an important indicator of the efficacy of a T cell response to SARS-CoV-2 which leads to recovery, and merits further investigation in different disease severity recovery cohorts.   

Methodologies: 

• Study Type: ex vivo analysis of convalescent PBMC (CD8+ T cells), antibodies and plasma (cytokines). This is a particular strength in comparison to peptide pool stimulation studies.  

• Key Techniques: Mass cytometry combined analysis of CD8+ T cell SARS-CoV-2 epitope specificity and phenotype, neutralizing antibody titer analysis, sandwich immunoassay of cytokines and chemokines from plasma. In silico correlation analysis of these experimental parameters.  

Limitations: 

• Limitations noted by the authors include sample size (n= 30, divided into 3 groups of 10 individuals, based on IgG titers; high, medium and low, and only n=4 healthy controls sampled prior to the pandemic), HLA-I population coverage (6 HLA-I alleles representing 73% of the US population) and population representativeness; the sampling was geographically restricted (Washington and Baltimore, USA) and consisted of 80% (24/30) Caucasian participants. 

• The authors also note that while the study sample incorporated a (cross sectional) range of post-disease resolution timepoints, longitudinal data enable stronger conclusions to be made.  The minimum duration post-symptom resolution of 28 also does not capture the earliest recovery stages; other studies have reported distinct stages of T cell recovery 10-20 days after symptom onset (Mann et al., Rodriguez et al.) 

• Since the study population included few individuals who had been hospitalized, this does not allow the comparison of the T cell phenotype and breadth of epitope responses in severe vs. milder COVID-19. Therefore, it is not known if the breadth of epitope response could be a determinant of better T cell control of SARS-CoV-2 infection. Additionally, since T cells were analysed only from peripheral blood, key epitope responses and phenotypes at the site of infection were not determined. 

• Minimal evidence reported for clinical data and comorbidities of individuals. Therefore, it is not clear if any-existing conditions could contribute to the findings.