Longitudinal tracking of T-cell repertoire reveals long-lasting CD4⁺ yellow fever specific clone cluster

Infection is inconceivable without T cells. T cells not only eliminate virus-infected cells and participate in the formation of immunological memory, but also indirectly modulate the humoral response through the selection and maintenance of specific B cells. The T-cell receptor (TCR) recognizes processed antigen presented on the surface of cells in the MHC of one of two classes. Thus, the formed TCR repertoire reflects the history of encountered antigens through the prism of the specific organism with a particular set of MHC. To investigate changes in the TCR repertoire in response to acute viral infection, we utilized a yellow fever vaccination model. The yellow fever vaccine has been a benchmark for both safety and efficacy for over half a century. The vaccine is based on a live attenuated virus, allowing the study of the immune response under conditions closely to the viral infection. The yellow fever-specific T-cell response to immunodominant peptides presented on HLA-A02 is well studied, but experiments with HLA-A02-negative donors are still lacking. The aim of this study was to examine the dynamics of changes in the T-cell repertoire structure that occur in response to yellow fever vaccination in a donor without the HLA-A02 allele. We found that the overall T-cell response dynamics were similar to that in HLA-A02-positive donors: vaccination led to rapid expansion of yellow fever-reactive clones by day 14. Despite the absence of a known immunodominant epitope for HLA I alleles in this donor, the immune response also shifted towards CD8⁺ T cells, with increasing of the CD8⁺ clones fraction by day 53. The amino acid sequences of CDR3 TCRb yellow fever specific clones formed a stable cluster by CD4⁺ T cells, further confirming the presence of novel immunogenic epitopes.