Human immunodeficiency virus type 1 (HIV-1) infection of an individual generates a population of related but distinct cocirculating viral variants (15). This high level of genetic diversity allows HIV-1 to adapt quickly to multiple selective pressures, including neutralizing antibodies, cytotoxic T lymphocytes, and antiretroviral drugs (17, 21, 32-34, 42). The highest level of diversity within the HIV genome is found in the env gene. The five hypervariable domains, named V1 through V5, form loops on the outside of the gp120 molecule (22). The V3 loop is involved in binding a chemokine receptor for viral entry after gp120 binds the CD4 receptor (40, 43). Changes in the V3 domain determine in part whether HIV utilizes CCR5 (R5 variants) or CXCR4 (X4 variants) chemokine coreceptors (6). The V1-V2 loop is thought to interact with the V3 loop within the gp120 trimer on the virion surface (5, 23). The V4 and V5 domains are on a different face of gp120 than V1-V2 and V3 are (22) and are not directly involved in receptor binding. The V1-V2 and V4-V5 regions of gp120 are highly variable in sequence and length within an infected individual and between infected individuals (19, 37, 41). The domains are heavily glycosylated, and changes in the location and number of N- and O-linked glycosylation sites in the V1-V2 and V4-V5 regions are associated with escape from neutralization (reviewed in reference 29). Removal of some of the glycosylation sites from the V1 and V2 regions results in increased immunogenicity of the domains (31) and has been shown in one study to redirect the immune response toward V3 rather than V1-V2 (7). Sequence changes observed in V1-V2 and V3 to V5, including insertions, deletions, and point mutations, have been linked to escape from neutralizing antibodies. The accumulation of nonsynonymous substitutions was associated with escape in two separate studies (11, 12), while changes in the glycosylation sites of gp120 have been described in terms of an evolving glycan shield that leads to escape from neutralizing antibodies in a third study (42). It has also been shown that mutations in env lead to escape from neutralizing antibodies through conformational masking of epitopes (21). Mutations in env have also been shown to affect cytotoxic T-lymphocyte (CTL) epitopes (11, 17), indicating that both neutralizing antibodies and CTL apply selective pressure on HIV-1 in vivo. High levels of env sequence diversity have been linked with both slower disease progression and more-effective immune responses against the virus, both in simian immunodeficiency virus and HIV (3, 8, 14, 16, 26), thereby implying a link between strong immune selection and slower disease progression. Heteroduplex assays are powerful methods for displaying the number and variety of variants within a viral population (reviewed in reference 4) without the potential selection bias inherent to sequence-based analyses. Heteroduplex mobility assays reveal the diversity within a sample through the visualization of heteroduplexes formed between different variants within the sample, while heteroduplex tracking assays (HTA) use a radiolabeled probe to display differences between the probe and the sample. We have previously used HTA to examine the diversity and changes in V1-V2 in monthly samples from subjects with low CD4 counts (18). In 12 of 21 of these subjects, at least one V1-V2 variant population was gained or lost over 5 to 9 months. Sequence analysis of the V1-V2 regions for several of the subjects revealed point mutations, recombination events, and deletions as the main mechanisms of sequence change. Delwart et al. analyzed the V3 to V5 variant populations in semiannual samples from subjects with different rates of progression, showing that subjects with faster CD4+ T-cell decline had slower diversification of the region from V3 to V5 and that progression of disease was correlated with reduced diversity (8). These latter results support the idea that the level of sequence diversity directly correlates with immune selection. In the present study, we have used HTA analysis to examine the V1-V2 and V4-V5 regions of HIV-1 env in semiannual plasma samples from subjects in the San Francisco Men's Health Study. Subjects with different rates of progression, as defined by rate of CD4 cell loss, were compared for rates of change in the env viral population using a newly developed HTA index algorithm that highlights periods of increasing env diversity.