Abstract
This study maps spike-specific CD4⁺ T cells in paired blood and draining lymph nodes three and six months after BNT162b2 mRNA vaccination. Using single-cell transcriptomics and antigen annotation, including a deep learning–based reverse epitope mapping approach (Trex), the authors characterize more than a thousand spike-specific cells. Lymph node T follicular helper (Tfh) cells show heterogeneous transcriptional states, including germinal center–like and IL-10–producing Tfh subsets. Comparison with individuals recovering from SARS-CoV-2 infection reveals distinct circulating CD4⁺ T cell profiles after vaccination versus natural infection. The work provides an atlas of spike-specific CD4⁺ T cell phenotypes across tissues and time, clarifying how mRNA vaccination imprints CD4⁺ T cell immunity.