Simultaneous detection and characterization of antigen-specific B cells and CD4+ and CD8+ T cell responses upon natural infection and vaccination

Abstract An important lesson learned from the COVID-19 pandemic is the need for a more comprehensive assessment of the immune status upon a natural infection and vaccination. In addition to measuring antibody titers, monitoring the status of antigen-specific B and T cell must be taken into consideration to gain a more complete understanding of the elicited immune response and its durability. The objective of this study was to develop an immune monitoring assay based on the Dextramer® technology for simultaneous monitoring of antigen-specific B and T cells (CD4 and CD8). The assay can be applied in combination with flow cytometry and in single cell RNA-seq analysis. The assay builds on Dextramer® reagents displaying full-length spike protein (specific B cell assessment) or MHC-peptide complexes displaying virus peptides (detecting specific CD8 or CD4 T cells). The assay was evaluated by longitudinal assessment of immunity in individuals vaccinated against SARS-CoV-2 by combining the assay with flow cytometry (n=5) and the Chromium 10× RNA-seq platform (n=2). The latter allows an in-depth view of the immune status by simultaneous investigation of the transcriptome, surface proteins and receptor sequences of antigen-specific cells. Our results show that by using the virus-specific Dextramer® assay we could monitor changes in SARS-CoV-2-specific B- and T-cell responses before and after primary vaccination and booster doses using flow cytometry and single cell RNA-seq analysis. These results show that the Dextramer® assay can aid in understanding the elicitation and persistence of antigen-specific responses. Moreover, the assay can easily be tailored to any antigen-specificity by replacing the ligands coupled to the Dextramer® reagents.