Sequential Turnover of Human Immunodeficiency Virus Type 1envthroughout the Course of Infection

Abstract

We examined the rates of variant population turnover of the V1-V2 and V4-V5 hypervariable domains of the human immunodeficiency virus type 1 (HIV-1) gp120 molecule in longitudinal plasma samples from 14 men with chronic HIV-1 infection using heteroduplex tracking assays (HTA). Six men had high rates of CD4 ؉ T-cell loss, and eight men had low rates of CD4 ؉ T-cell loss over 2.5 to 8 years of infection. We found that V1-V2 and V4-V5 env populations changed dramatically over time in all 14 subjects; the changes in these regions were significantly correlated with each another over time. The subjects with rapid CD4 loss had significantly less change in their env populations than the subjects with slow CD4 loss. The two subjects with rapid CD4 loss and sustained low CD4 counts (<150/l for at least 2 years) showed stabilization of their V1-V2 and V4-V5 populations as reflected by low levels of total change in HTA pattern and low HTA indices (a novel measure of the emergence of new bands and band distribution); this stabilization was not observed in other subjects. The stabilization of env variant populations at low CD4 counts following periods of rapid viral evolution suggests that selective pressure on env, likely from new immune responses, is minimal when CD4 counts drop dramatically and remain low for extended periods of time.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)(33)(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, an...

Independent Evolution of Human Immunodeficiency Virus Type 1 env V1/V2 and V4/V5 Hypervariable Regions during Chronic Infection

“…In the present study we characterized V4/V5 env genetic populations over time in 24 chronically infected subjects by using a V4/V5-specific HTA (11,21). We then compared V4/V5 population changes to those previously observed in V1/V2 from the same subjects to assess the degree of independence or linkage of V1/V2 and V4/V5 sequence evolution.…”

“…These sequences code for highly accessible and often heavily glycosylated regions in the Env glycoprotein, and sequence evolution in these regions within infected individuals is thought to play an important role in virus evasion from neutralizing antibody (7,8,19,23). Longitudinal analysis of env genetic populations in infected individuals can reveal key features of neutralizing antibody or other selective pressures driving env sequence evolution (1,4,9,15,21,22), although few studies of chronically infected subjects have monitored viral genetic changes over short time intervals (Ͻ3 months).We previously characterized blood plasma V1/V2 genetic populations at 2 to 4 week intervals over an approximately 6-to 9-month period in a cohort of 21 subjects in late chronic infection by using a DNA heteroduplex tracking assay (HTA) (12), which resolves mixtures of coexisting viral genotypes as a series of distinct bands on a polyacrylamide gel (5, 6, 16). Most subjects had complex V1/V2 genetic populations, with major population changes occurring in about two-thirds of the subjects over the course of study, suggesting continual evolution of selective pressures targeting the Env V1/V2 loops.…”

“…These sequences code for highly accessible and often heavily glycosylated regions in the Env glycoprotein, and sequence evolution in these regions within infected individuals is thought to play an important role in virus evasion from neutralizing antibody (7,8,19,23). Longitudinal analysis of env genetic populations in infected individuals can reveal key features of neutralizing antibody or other selective pressures driving env sequence evolution (1,4,9,15,21,22), although few studies of chronically infected subjects have monitored viral genetic changes over short time intervals (Ͻ3 months).…”

“…Viral RNA was extracted from blood plasma samples, reverse transcribed, and PCR amplified with V4/V5-targeted primers using conditions previously described (11, 21). The DNA amplicons were then characterized by HTA using a V4/V5 probe based on the HIV-1 NL4-3 clone, and the migration and relative abundance of heteroduplex bands were analyzed and quantified by phosphorimaging (11,21).…”

Polymorphism characteristics of HIV-1 gp120 and 5 hypervariable regions

“…The V1/ V2 domains can act as targets for neutralizing antibodies, and variability in these regions may contribute to immune escape from neutralization (16)(17)(18). V4 and V5 participate in CD4 binding and contribute to autologous neutralization (19,20). The functional interactions between the V1-V5 hypervariable regions especially facilitate viral escape from the host immune responses (5).…”