Primary antigenic exposure defines COVID-19 vaccine-boosted SARS-CoV-2 spike-specific responses

The durability and phenotype of immune responses generated by vaccination or infection are critical determinants of long-term protection against viral pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whether primary antigenic exposure influences the magnitude and quality of vaccine-boosted antigen-specific immune responses remains incompletely understood. Spike-specific B and CD8+ T cell responses were characterized in individuals who received a prime-boost Comirnaty® vaccination and were stratified according to SARS-CoV-2 infection history as previously hospitalized, non-hospitalized, or infection-naïve. Antigen-specific immune responses were assessed using multiparameter flow cytometry and high-dimensional phenotypic analyses. Primary antigenic exposure shapes vaccine-boosted SARS-CoV-2 spike-specific immune responses, with the greatest expansion observed in previously hospitalized individuals. Phenotypic profiling reveals distinct differences in spike-specific B cells within this group. Previously hospitalized individuals exhibit higher proportions of unswitched (IgD+) and short-lived memory B cells following infection, which improve following vaccination. However, spike-specific B cells after vaccination display lower CD38 expression and sustained CD95 expression, suggesting altered responses following antigen re-exposure. Spike-specific CD8⁺ T cell frequencies are similarly enhanced following vaccination in previously infected individuals, with carriers of the HLA-A*03:01 allele demonstrating the greatest boosting. Although phenotypic analyses identify dominant clusters expressing T cell exhaustion-associated markers, these clusters are shared across antigen-specific CD8⁺ T cell populations and do not differ between groups, indicating heterogeneity within activated cells rather than dysfunctional exhaustion states. Primary antigenic exposure history shapes both the magnitude of vaccine-boosted SARS-CoV-2 spike-specific B and CD8⁺ T cell responses and the phenotypic landscape of spike-specific B cells. These findings highlight the importance of immune phenotype, beyond response magnitude alone, in defining long-term antiviral immunity. COVID-19 vaccines protect against severe disease, but vaccinated individuals have experienced the virus in different ways. Some have never been infected, while others had mild or severe illness following infection with SARS-CoV-2. It is not fully understood how this past exposure affects responses to vaccination. This study examined blood samples from people who received the Pfizer-BioNTech vaccine, comparing those who had been hospitalized with COVID-19, those with milder infection, and those never infected. The study measured two important immune cell types: B cells, which produce antibodies, and CD8+ T cells, which eliminate infected cells. Vaccination increased these immune cells in all groups, especially in previously hospitalized individuals. However, important differences in B cell characteristics were observed. These findings show that past infection shapes vaccine responses and may influence long-term protection. Underwood et al., characterise spike-specific B and CD8⁺ T cell responses following prime-boost vaccination in individuals with severe, mild, or no SARS-CoV-2 infection using high-dimensional immune profiling. Previous infection, particularly severe infection requiring hospitalisation, enhances vaccine-boosted B and CD8⁺ T cell responses and reshapes B cell phenotypes, while CD8⁺ T cells expressing exhaustion-associated markers appear to represent heterogeneous activated populations rather than clear dysfunctional exhaustion.