We have developed a method which provides a global and detailed view of T-cell receptor (TCR) repertoires and of their changes in vivo. This new technique of TCR B chain population analysis, based on the extensive nucleotide sequence variation between VDJ junction regions, was used to obtain a very high resolution picture of TCR repertoires in vivo. Using this molecular tool, cellular responses will be measured following vaccination with attenuated SIVmac delta nef, primary infection with pathogenic SIVmac 51 and subsequent disease progression, and effective anti HIV-1 therapy. To obtain a direct in vivo measure of the strength (frequency) and diversity(number) of CD8+ cell expansions associated with effective vaccinations, the TCR repertoire changes induced by SIVmac Delta nef will be compared to both protected and unprotected animals challenged with SIVmac251. To determine whether greater CD8+ cell TCR repertoire changes are associated with more efficient control of viremia, the extent of B chain repertoire changes following primary infection with SIVmac251 will be compared in rapid and slow disease progressors. The effect of long term HIV-1 infection on the polyclonality of CD4+ cell TCR repertoires will also be measured at various stage of disease progression. Whether increases in CD4+ cells resulting from effective anti-viral treatment are associated with the re- appearance of a more polyclonal CD4+ cell repertoire will be determined using samples from individuals undergoing combination therapy. To investigate the in vivo significance of CTL precursor frequencies determined in vitro, the CDJ junction sequences from HIV-1 specific CTL clones will be used to determine their transcript frequency in vivo. The combination of a new molecular tool of T-cell population analysis and well characterized sets of PBMC samples will allow us to study in greater detains T-cell population changes associated with SIV and HIV-1 infection.
