Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy

Abstract

Neutralizing antibodies (NAb) against autologous virus can reach high titers in human immunodeficiency virus type 1 (HIV-1)-infected patients with progressive disease. Less is known about the role of NAb in HIV-1-infected patients with viral loads of <50 copies/ml of plasma, including patients on effective highly active antiretroviral therapy (HAART) and elite suppressors, who control HIV-1 replication without antiretroviral therapy. In this study, we analyzed full-length env sequences from plasma viruses and proviruses in resting CD4(+) T cells of HAART-treated patients, elite suppressors, and untreated HIV-1-infected patients with progressive disease. For each patient group, we assessed plasma virus neutralization by autologous, contemporaneous plasma. The degree of env diversity, the number of N-linked glycosylation sites, and the lengths of variable loops were all lower in elite suppressors than in HAART-treated and untreated viremic patients. Both elite suppressors and HAART-treated patients had lower titers of NAb against HIV-1 lab strains than those of untreated viremic patients. Surprisingly, titers of NAb against autologous, contemporaneous plasma viruses were similarly low in chronic progressors, elite suppressors, and HAART-treated patients. In elite suppressors and HAART-treated patients, titers of NAb against autologous plasma viruses also did not differ significantly from titers against autologous proviruses from resting CD4(+) T cells. These results suggest that high-titer NAb are not required for maintenance of viral suppression in elite suppressors and that NAb do not select plasma virus variants in most HAART-treated patients. Both drug-mediated and natural suppression of HIV-1 replication to levels below 50 copies/ml may limit the stimulation and maintenance of effective NAb responses.

FIG. 1.

Intrapatient env gene diversity. Diversity was calculated for each patient's viral quasispecies as the average genetic distance between full-length env clones by the two-parameter (Kimura) method. Analysis was performed on plasma virus env genes from chronic progressors. Plasma virus env sequences were distinct from proviral sequences in both ES and HAART-treated individuals, so plasma virus env and proviral env were analyzed separately for these study groups. Diversity was calculated only for individuals from whom at least three independent env genes were amplified from plasma viruses or proviruses. Each diamond represents the diversity of env genes amplified from plasma viruses of one individual. Each circle represents the diversity of env genes amplified from proviruses in resting CD4⁺ T cells of one individual. Horizontal hash marks indicate the median diversity for each study group.

FIG. 2.

Predicted numbers of N-linked glycans and numbers of amino acids in the V1-V5 region of env from chronic progressors, ES, and HAART-treated patients. (A) Numbers of predicted N-linked glycans in V1-V5. Each diamond represents the mean number of predicted V1-V5 N-linked glycans for all env clones amplified from the plasma of one individual. Each circle represents the mean number of predicted V1-V5 N-linked glycans for all proviral env clones amplified from resting CD4⁺ T cells from one individual. Horizontal hash marks indicate the median N-linked glycan number for each study group. (B) Numbers of amino acids in the V1-V5 region of env. Each diamond represents the mean number of V1-V5 amino acids for all env clones amplified from the plasma of one individual. Each circle represents the mean number of V1-V5 amino acids for all proviral env clones amplified from resting CD4⁺ T cells from one individual. Horizontal hash marks indicate the median V1-V5 length for each study group.

FIG. 3.

Binding antibody titers against HIV-1. Each data point indicates the reciprocal of the plasma dilution at which ELISA binding of antibody to lysed HIV-1 virion proteins was one-half the maximum. Horizontal hash marks indicate the median titer for each patient group.

FIG. 4.

Neutralizing antibody titers against neutralization-sensitive HIV-1 subtype B lab strains. (A) Neutralizing antibody titers against pseudovirus with strain SF162 Env. The titer is the reciprocal of the plasma dilution at which infection was 50% of the level measured in wells with control plasma (IC₅₀). Each data point indicates the reciprocal IC₅₀ of an individual patient plasma against SF162 pseudovirus. Horizontal hash marks indicate the median reciprocal IC₅₀ for each study group. (B) Infectivities relative to control of pseudovirus with NL4-3 Env in the presence of serial dilutions of plasma from each study subject. The dashed line indicates a level of infection that is 50% of that seen in control wells with uninfected human plasma. Red lines indicate neutralization by plasmas from chronic progressors. Green lines indicate neutralization by plasmas from ES. Blue lines indicate neutralization by plasmas from HAART-treated patients.

FIG.5.

Autologous neutralization of pseudoviruses with env genes from plasma virus or provirus by serial dilutions of chronic progressor, elite suppressor, and HAART-treated patient plasmas. Dashed lines indicate a level of infection that is 50% of that seen in control wells with uninfected human plasma. (A) Infectivities relative to control of clonal pseudoviruses with plasma virus env from chronic progressors in the presence of serial dilutions of autologous, contemporaneous plasma. (B) Infectivities relative to control of pseudoviruses with env from ES in the presence of serial dilutions of autologous plasma. Pseudoviruses with plasma virus env were tested for neutralization by autologous, contemporaneous plasma (red lines) or autologous, noncontemporaneous plasma (orange lines). Proviral env pseudoviruses (blue lines) were tested for neutralization by autologous plasma. One env variant tested from ES6 (red line with blue points) was amplified independently from both plasma virus and provirus. (C) Infectivities relative to control of pseudoviruses with env from HAART-treated patients in the presence of serial dilutions of autologous plasma. Pseudoviruses with plasma virus env (red lines) were tested for neutralization by autologous, contemporaneous plasma. Proviral env pseudoviruses (blue lines) were tested for neutralization by autologous plasma.

FIG.5.

Autologous neutralization of pseudoviruses with env genes from plasma virus or provirus by serial dilutions of chronic progressor, elite suppressor, and HAART-treated patient plasmas. Dashed lines indicate a level of infection that is 50% of that seen in control wells with uninfected human plasma. (A) Infectivities relative to control of clonal pseudoviruses with plasma virus env from chronic progressors in the presence of serial dilutions of autologous, contemporaneous plasma. (B) Infectivities relative to control of pseudoviruses with env from ES in the presence of serial dilutions of autologous plasma. Pseudoviruses with plasma virus env were tested for neutralization by autologous, contemporaneous plasma (red lines) or autologous, noncontemporaneous plasma (orange lines). Proviral env pseudoviruses (blue lines) were tested for neutralization by autologous plasma. One env variant tested from ES6 (red line with blue points) was amplified independently from both plasma virus and provirus. (C) Infectivities relative to control of pseudoviruses with env from HAART-treated patients in the presence of serial dilutions of autologous plasma. Pseudoviruses with plasma virus env (red lines) were tested for neutralization by autologous, contemporaneous plasma. Proviral env pseudoviruses (blue lines) were tested for neutralization by autologous plasma.

FIG. 6.

Comparison between study groups of geometric mean reciprocal NAb titers against autologous virus. Each point represents the geometric mean reciprocal IC₅₀ titer in plasma from an individual patient against all autologous plasma virus or proviral env variants tested from that patient. Horizontal hash marks indicate the median of the reciprocal IC₅₀ values for each patient group. Mean reciprocal IC₅₀ titers against pseudoviruses with plasma virus env genes and pseudoviruses with proviral env genes from the same subject are linked by lines.