In chronically HIV infected individuals, a number of functional B cell abnormalities have been described. However, the immediate changes that occur in the B cell compartment following viral exposure and how they affect the long-term course of infection are not well understood. We report the longitudinal analysis of B cell repertoires during early infection in untreated and treated individuals receiving highly active antiretroviral therapy (HAART). Analysis was based on IgG heavy chain gene utilization and CDR3 length measurement and relationship with CD4/CD8 counts, viral load, and total serum IgG, and anti-HIV antibodies levels. Repertoires were assessed at baseline and at weeks 2, 4, 12, 24, and 72 after initiation of therapy. The findings indicate a stable peripheral B cell repertoire during the first 72 weeks following infection, particularly in the HAART treated patients. A modest association between B cell repertoire integrity and viremia levels as well as treatment was detected. Genes and Immunity (2005) The factors underlying the transition from the asymptomatic state in primary HIV infection to pathogenic immune dysregulation and AIDS have not been entirely elucidated. A role for humoral immunity in this process is supported by the common development of hypergammaglobulinemia in chronically infected individuals, associated with B cell hyperactivation, clonal expansions and deletions, and deficient costimulatory function. [1][2][3][4][5][6] It is unclear, however, if these abnormalities are the result of viremia and a direct effect of virus on B lymphocytes or, alternatively, mediated by long-term infectioninduced changes in T-cell subsets and cytokine production. To assess the early effect of HIV infection on the integrity of the peripheral B cell repertoires, we analyzed the B cellreceptor diversity in a longitudinal cohort of 10 affected individuals who had been treated with HAART immediately after diagnosis and 10 infected individuals who chose not to be treated. The results were compared with observations from uninfected controls. Analysis was based on IgG heavy chain gene utilization and CDR3 length measurement (spectratyping), 7 and relationship with CD4/CD8 counts, viral load, and serologic responses. Individuals with acute or recent HIV-1 infection were eligible for this study if the initial evaluation indicated that they met one or more of the criteria for recent HIV-1 infection: (1) detectable HIV-1 RNA in blood plasma and a negative or indeterminate Western blot assay for anti-HIV-1 antibodies; (2) a positive enzyme-linked immunosorbent assay (ELISA) with Western blot confirmation within 12 months of a documented negative HIV-1 antibody test; or (3) a sensitive/less sensitive (S/LS) dual ELISA testing optical density ratio of less than 0.75 8,9 with a history compatible with recent HIV infection. 10 The dual enzyme immunoassay (EIA) testing strategy using a standard high sensitivity EIA and an LS EIA takes advantage of the progressive development of HIV antibody response during the initial p...