Evolution of the domain encoding the V1/V2 variable region of the simian immunodeficiency virus sm (SIVsm) envelope (env) gene was analyzed in relation to route of virus challenge, virus load, and neutralizing antibody (NAb) titers during primary infection of rhesus macaques with the pathogenic SIVsmE660 isolate. In this model system animals are initially infected with multiple viruses as evidenced by the presence of multiple V1/V2 genotypic variants that could be resolved by using a heteroduplex tracking assay (HTA). Overlapping subsets of the multiple variants were established in each animal. There was no selection for the establishment of specific variants in comparing intravenous-and intrarectal-challenged macaques at week 2 postinfection, suggesting that no genotypic selection occurred at the mucosal surface. There was an initial period of significant stability of the V1/V2 variants. Macaques challenged intravenously displayed subsequent V1/V2 diversification significantly earlier than macaques challenged intrarectally and well past the initial resolution of viremia. The time when SIVsmE660-specific NAbs reached a threshold titer of 100 was significantly correlated with the timing of V1/V2 diversification, even though antibodies to the Env protein could be detected much earlier. The time when NAbs reached a titer of 400 was significantly correlated with virus load late in infection. These results show that the route of infection affects the timing of V1/V2 diversification and that this diversification is correlated with the maturation of a specific NAb response. However, prior immunization capable of priming an anamnestic Env antibody response did not accelerate V1/V2 diversification. This result suggests that diversification of the SIV env V1/V2 region is the result of a type-specific antibody response.Both the human immunodeficiency virus type 1 (HIV-1) and the simian immune virus (SIV) envelope (Env) proteins contain variable regions (12, 34). The V1/V2 variable regions are a multifunctional domain on Env that undergoes a conformational change upon CD4 binding (46,56), modulates exposure of the coreceptor binding site on Env (55), can contribute to cell tropism and cytopathicity (20,42), and contains epitopes for antiviral antibodies (22,31,49). The V1/V2 region, along with the other variable regions, represents regions of the viral genome that express remarkable capacity to evolve in response to changing selective pressures within the host.Systemic and mucosal infection represent two major routes of HIV-1 entry into human hosts. Several studies have examined viral evolution in relation to route of infection (29,48,50,51). These results suggested that mucosal barriers act as selective filters for HIV-1 genotypes.The development of host neutralizing antibodies (NAbs) as part of the humoral response against HIV-1 and SIV most often occurs after the resolution of peak plasma viremia (43,45). The variable regions on the HIV-1 and SIV Env proteins can serve as linear and conformational epitopes for NAbs (1,9,...