Paired TCRαβ analysis of virus-specific CD8+ T cells exposes diversity in a previously defined 'narrow' repertoire

T-cell receptor (TCR) usage has an important role in determining the outcome of CD8(+) cytotoxic T-lymphocyte responses to viruses and other pathogens. However, the characterization of TCR usage from which such conclusions are drawn is based on exclusive analysis of either the TCR alpha chain or, more commonly, the TCR beta chain. Here, we have used a multiplexed reverse transcription-PCR protocol to analyse the CDR3 regions of both TCR alpha and beta chains from single naive or immune epitope-specific cells to provide a comprehensive picture of epitope-specific TCR usage and selection into the immune response. Analysis of TCR repertoires specific for three influenza-derived epitopes ((DNP366)-N-b, D(b)PA(224) and D(b)PB1-F2(62)) showed preferential usage of particular TCR alpha beta proteins in the immune repertoire relative to the naive repertoire, in some cases, resulting in a complete shift in TRBV preference or CDR3 length, and restricted repertoire diversity. The NP366-specific TCR alpha beta repertoire, previously defined as clonally restricted based on TCR beta analysis, was similarly diverse as the PA(224)-and PB1-F2(62)-specific repertoires. Intriguingly, preferred TCR characteristics (variable gene usage, CDR3 length and junctional gene usage) appeared to be able to confer specificity either independently or in concert with one another, depending on the epitope specificity. These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR chain does not accurately depict the nature of the antigen-specific TCR alpha beta repertoire.