Human immunodeficiency virus/simian immunodeficiency virus (SIV) diversification is a direct consequence of viral replication and occurs principally in secondary lymphoid organs where CD4؉ T cells are activated and proliferate. However, the evolution of viral quasispecies may also be driven by various nonexclusive mechanisms, including adaptation to specific immune responses and modification of viral fitness. Analysis of viral quasispecies in SIV-infected macaques subjected to repeated antigenic stimulations allowed us to demonstrate transient expansions of SIV populations that were highly dependent upon activation of antigen-specific T cells. T-cell clones expanded in response to a particular antigen were infected by a specific viral population and persisted for prolonged periods. Upon a second stimulation by encounter with the same antigen, these specific genomes were at the origin of a new burst of replication, leading to rapid but transient replacement of the viral quasispecies in blood. Finally, longitudinal analysis of SIV sequence variation during and between antigenic stimulations revealed that viral evolution is mostly constrained to periods of strong immunological activity.Genetic variation of the AIDS viruses (human immunodeficiency virus [HIV] and macaque simian immunodeficiency virus [SIVmac]), a direct consequence of the error-prone reverse transcription in the absence of proofreading activity, has been extensively described both in patients and in experimentally infected macaques (35,40,47,50). After an initial transmission bottleneck characterized by relative homogeneity of sequences in acute infection (14, 42), viral populations are constantly evolving during the course of disease development (8, 43). The relative importance of viral adaptation through increased viral fitness and resistance to host immune responses is still a matter of debate (2,15,18,28,30). However, spatial and temporal analyses of viral quasispecies demonstrated that viral evolution is not only related to adaptation but also results from stochastic events such as a antigen induced activation of viral transcription (3,5,6,9,10,20,41).The long-term persistence of HIV/SIV is principally attributed to the presence of latently infected CD4 ϩ T cells in which the virus is transcriptionally silent (22,27,39). HIV/SIV replication is essentially confined to the immunocompetent structures of secondary lymphoid organs such as the germinal centers of the lymph nodes and spleen or the intestinal Peyer's patches (31,32,48,49). In both HIV and SIV infection, antigenic stimulation has been shown to be the driving force of viral replication in vivo, a probable consequence of the NF-kB dependence of viral transcription (5,6,45,46,52). Latently infected CD4ϩ T cells involved in antigen-specific immune responses transport the proviruses into these immunocompetent structures, where they become transcriptionally active after T-cell activation (1). This "Trojan horse" mechanism is at the origin of local viral replication, characterized by discrete...