ABSTRACT
Background: The rapid development of SARS-CoV-2 mRNA vaccines has been a remarkable success of the COVID-19 pandemic, but vaccine-induced immunity is heterogeneous in immunocompromised populations. We sought to determine the immunogenicity of SARS-CoV-2 mRNA vaccines in a cohort of people with idiopathic CD4 lymphopenia (ICL). Method(s): 25-patients with ICL followed at the National Institutes of Health on a natural history protocol were evaluated between 2020-2022. Blood and serum was collected within 4-12 weeks after their second and/or third SARS-CoV-2 mRNA vaccine dose. Twenty-three matched healthy volunteers (HVs) provided blood samples at similar timepoints post-mRNA vaccination on a separate clinical protocol. Pre-vaccine blood samples were also used when available. Anti-spike and anti-receptor binding domain antibodies were measured. T-cell stimulation assays were performed to quantify SARS-CoV-2 specific T-cell responses. Comparisons were made with Wilcoxon test. Result(s): Twenty-participants with ICL had samples collected after their second mRNA vaccine and 7-individuals after the third dose. Median age at vaccination was 51-years (IQR: 44-62) and 12 were women (48%). Median CD4 T-cell count was 150 cells/muL (IQR: 85-188) at the time of vaccination, and 11-individuals (44%) had a baseline CD4 count <=100 cells/muL. HVs had a median age of 54-years (IQR: 43-60) with 13-women (56.5%). Anti-spike IgG antibody levels were significantly greater in HVs than those with ICL after 2-doses. Lower SARS-CoV-2 IgG antibody production was primarily observed in those with baseline CD4 T-cells <=100 cells/mul (Figure-1A). The decreased production in ICL remained after a third vaccine dose (Figure-1B). There was a significant correlation between anti-spike IgG and baseline CD4 count. Spike-specific CD4 T-cell responses in volunteers compared to those with ICL demonstrated similar levels of activation induced markers (CD154+CD69+) and cytokine production (IFNgamma+, TNFalpha+, IL2+) after two or three mRNA vaccine doses. Quantitatively the smallest responses were observed in those with lower baseline CD4 T-cells (Figure 1C-D). Minimal SARS-CoV-2 CD8 T-cell responses were detected in both groups. Conclusion(s): Patients with ICL and baseline CD4 T-cells >100 mount similar humoral and cellular immune responses to SARS-CoV-2 vaccination as healthy volunteers. Those with baseline CD4 T-cells <=100 have impaired vaccine- induced immunity and should be prioritized to additional boosters and continue other risk mitigation strategies. (Figure Presented).
ABSTRACT
Background: T cells play a critical role in the adaptive immune response to SARS-CoV-2 in both infection and vaccination. Identifying T cell epitopes and understanding how T cells recognize these epitopes can help inform future vaccine design and provide insight into T cell recognition of newly emerging variants. Here, we identified SARS-CoV-2 specific T cell epitopes, analyzed epitope-specific T cell repertoires, and characterized the potency and cross-reactivity of T cell clones across different common human coronaviruses (HCoVs). Method(s): SARS-CoV-2-specific T cell epitopes were determined by IFNgamma ELISpot using PBMC from convalescent individuals with mild/moderate disease (n=25 for Spike (S), Nucleocapsid (N) and Membrane (M)), and in vaccinated individuals (n=27 for S). Epitope-specific T cells were isolated based on activation markers following a 6-hour peptide stimulation, and scRNAseq was performed for TCR repertoire analysis. T cell lines were generated by expressing recombinant TCRs in Jurkat cells and activation was measured by CD69 upregulation. Result(s): We identified multiple immunodominant T cell epitopes across S, N and M proteins in convalescent individuals. In vaccinated individuals, we detected many of the same dominant S-specific epitopes at similar frequencies as compared to convalescent individuals. T cell responses to peptide S205 (amino acids 817-831) were observed in 56% and 59% of individuals following infection and vaccination, respectively, while 20% and 19% of individuals responded to S302 (a.a. 1205-1219) following infection and vaccination, respectively. For S205, a CD4+ T cell response, we confirmed 8 unique TCRs and determined the minimal epitope to be a 9mer (IEDLLFNKV). While TCR genes TRAV8-6*01 and TRBV30*01 were commonly utilized across the TCRs, we did identify TCRs with unique immunogenetic properties with different potencies of cross-reactivity to other HCoVs. For S302, a CD8+ T cell response, we identified two unique TCRs with different immunogenetic properties that recognized the same 9mer (YIKWPWYIW) and cross-reacted with different HCoV peptides (Figure 1). Conclusion(s): These data identify immunodominant T cell epitopes following SARS-CoV-2 infection and vaccination and provide a detailed analysis of epitope-specific TCR repertoires. The prospect of developing a vaccine that broadly protects against multiple human coronaviruses is bolstered by the identification of conserved immunodominant SARS-CoV-2 T cell epitopes that cross react with multiple other HCoVs.
ABSTRACT
Background: T cells have been shown to play a role in the immune response to SARS-CoV-2. Identification of T cell epitopes and a better understanding of the T cell repertoire will provide important insights into how T cells impact antiviral immunity. Here, we identified T cell epitopes within the Spike (S), Nucleocapsid (N) and Membrane (M) proteins from SARS-CoV-2 convalescent individuals and performed TCR sequencing on epitope-specific T cells. Methods: Epitope mapping was performed by IFNγ ELISpot on PBMC from SARS-CoV-2 convalescent patients with mild/moderate disease (n = 19 for S;n=15 for N and M), and minimum epitopes were determined using truncated peptides and ICS. TCR sequence analysis was performed on a subset of individuals (n=9 donors;2-3 epitopes/donor), with longitudinal samples for 7 donors (2-3 time points/donor;33 to 236 days post-symptom onset). T cells were stimulated with individual peptides for 6 hours and sorted based on the expression of activation markers (CD4+: CD69, CD40L;CD8+: CD69, CD107a, surface TNF). scRNAseq was performed on sorted cells for TCR repertoire and transcriptome analysis. Results: We identified several peptides recognized by multiple individuals, including S42 (amino acids 165-179;7/19 donors), S302 (a.a. 1205-1219;6/19 donors), N27 (a.a. 106-120;6/14 donors) and M45 (a.a. 177-191;10/14 donors). S42 elicited both CD4+ (n=5) and CD8+ (n=1) T cell responses, with one individual having both a CD4+ and CD8+ response. The minimum epitope for S42 was determined to be a 9mer (FEYVSQPFL) for both CD4+ and CD8+ cells. TCR sequencing of S42-specific T cells identified a dominant gene pairing for TCRα across multiple donors (TRAV35;TRAJ42) and for both CD4+ and CD8+ T cells (Figure 1). In general, epitope-specific CD4+ responses (S42, M45) were more clonally diverse than CD8+ responses (S42, S302, N27). For both CD4+ and CD8+ T cells, conserved TCR gene usage and gene pairings could be identified within multiple donors responding to the same epitope. Conclusion: These data suggest that in SARS-CoV-2 convalescent people, epitope-specific CD4+ and CD8+ T cells can differ in their clonal diversity and that related TCRs can be identified across multiple donors. S42-specific T cell studies are ongoing to determine their transcriptional profile and pMHC presentation. Ongoing longitudinal analysis will provide a better understanding of different epitope-specific TCR repertoires and T cell transcriptional profiles, and how they evolve after infection.
ABSTRACT
Background: The role that CD4+ and CD8+ T cells play in the protection from and disease severity of COVID-19 is not completely understood. A better understanding of T cell function and the epitopes that they target will be invaluable in the development of the next generation of vaccines and therapeutics. To better understand the role of T cells, we characterized the frequency, effector functions and phenotype of SARS-CoV-2-specific CD4+ and CD8+ T cells in a cohort of patients who recovered from COVID-19, and identified multiple peptides that contain T cell epitopes within the Spike protein (S), Nucleocapsid protein (N) and Membrane protein (M). Methods: The frequency and phenotype of SARS-CoV-2-specific T cells from convalescent patients with mild or moderate disease (n=27, 25 to 92 days post-symptom onset) were determined by polychromatic flow cytometry and intracellular cytokine staining (ICS). Cells were stimulated for 6 hours with peptide pools corresponding to S, N and M. Cytokine production, memory phenotype, chemokine receptor expression and PD-1 expression were analyzed. For a subset of individuals (n = 19 for S;n=14 for N and M), IFNg ELISpot assays and peptide matrices were utilized to identify peptides that contain T cell epitopes. Results: CD4+ T cell responses to S, N and/or M were detected in almost all donors by ICS and were predominantly a Th1-type response as determined by cytokine production (IFNg, IL-2 or TNF) and expression of CXCR3. A majority of the antigen-specific CD4+ cells were found in the effector memory compartment. Although less robust than the CD4+ T cell response, antigenspecific CD8+ T cells were detected in a majority of donors, were found within the effector memory compartments and displayed modest PD-1 upregulation. Multiple peptides that contain T cell epitopes were identified by IFNg ELISpot (Figure 1). Some of the most commonly identified peptides include S42 (amino acids 165-179;7/19 donors), S205 (a.a. 817-831;10/19 donors), N83 (a.a. 329-343;7/14 donors), M37 (a.a. 145-159;8/14 donors) and M45 (a.a. 177-191;10/14 donors). Conclusion: These data suggest that T cells that target S, N and M play an important role in the immune response to SARS-CoV-2 and should be considered in future vaccine development. Further studies such as transcriptomic analysis and the TCR usage in longitudinal samples will provide a better understanding of epitope-specific T cells and their longevity.