The neutralization breadth of HIV-1 develops incrementally over four years and is associated with CD4+ T cell decline and high viral load during acute infection

Abstract

An understanding of how broadly neutralizing activity develops in HIV-1-infected individuals is needed to guide vaccine design and immunization strategies. Here we used a large panel of 44 HIV-1 envelope variants (subtypes A, B, and C) to evaluate the presence of broadly neutralizing antibodies in serum samples obtained 3 years after seroconversion from 40 women enrolled in the CAPRISA 002 acute infection cohort. Seven of 40 participants had serum antibodies that neutralized more than 40% of viruses tested and were considered to have neutralization breadth. Among the samples with breadth, CAP257 serum neutralized 82% (36/44 variants) of the panel, while CAP256 serum neutralized 77% (33/43 variants) of the panel. Analysis of longitudinal samples showed that breadth developed gradually starting from year 2, with the number of viruses neutralized as well as the antibody titer increasing over time. Interestingly, neutralization breadth peaked at 4 years postinfection, with no increase thereafter. The extent of cross-neutralizing activity correlated with CD4(+) T cell decline, viral load, and CD4(+) T cell count at 6 months postinfection but not at later time points, suggesting that early events set the stage for the development of breadth. However, in a multivariate analysis, CD4 decline was the major driver of this association, as viral load was not an independent predictor of breadth. Mapping of the epitopes targeted by cross-neutralizing antibodies revealed that in one individual these antibodies recognized the membrane-proximal external region (MPER), while in two other individuals, cross-neutralizing activity was adsorbed by monomeric gp120 and targeted epitopes that involved the N-linked glycan at position 332 in the C3 region. Serum antibodies from the other four participants targeted quaternary epitopes, at least 2 of which were PG9/16-like and depended on the N160 and/or L165 residue in the V2 region. These data indicate that fewer than 20% of HIV-1 subtype C-infected individuals develop antibodies with cross-neutralizing activity after 3 years of infection and that these antibodies target different regions of the HIV-1 envelope, including as yet uncharacterized epitopes.

Fig. 1.

Heterologous neutralizing activities in sera from the CAPRISA cohort at 3 years postinfection. The neutralization titer is shown as the reciprocal of the serum dilution required to inhibit 50% of infection for each virus-sample combination. Titers below detection, i.e., those of <1:45, have been omitted. The highest titers are shown in dark red and the lowest in light yellow, following the depicted legend. Autologous neutralization titers are highlighted in gray and were not included in the calculations of percentages of viruses neutralized. Participants were ranked based on cross-neutralizing activity. The pseudoviruses tested were from four panels: CAPRISA subtype C (15), reference subtype C (24), reference subtype B (23), and reference subtype A (5). Viruses are ranked from left to right within each panel based on the number of sera to which they were sensitive. The reference viruses ConC and Du151.12 are depicted separately on the left. Clinical progression is indicated for each participant (*, slow progressors; †, rapid progressors).

Fig. 2.

Factors correlated with the development of cross-neutralizing antibodies. The percentage of viruses neutralized by each serum was correlated with the 6-month (set point), 12-month, and 36-month (contemporaneous) viral loads (VL) (A, B, and C) and CD4⁺ T cell counts (D, E, and F). Neutralization breadth was also correlated using the viral load AUC from 6 to 36 months postinfection (G), the preinfection CD4⁺ T cell count (H), and the decline in CD4⁺ T cell count between preinfection and 6 months postinfection (I). Each correlation was analyzed using a Spearman nonparametric test. The number of pairs (N) and P value for each correlation are shown. Statistically significant P values are marked with asterisks.

Fig. 3.

Kaplan-Meier analysis of time from seroconversion until ARV initiation for CAPRISA participants with and without neutralization breadth. Study participants with similar viral loads were segregated based on their cross-neutralizing activity at 3 years postinfection, into BCN (group 1) (Fig. 1) and no BCN (groups 2 and 3) groups. A Cox proportional hazard analysis was used to compare the two groups based on time of infection until the first CD4⁺ T cell count below 200 cells/μl or therapy initiation.

Fig. 4.

Kinetics of development of heterologous neutralization in individuals with breadth. Sequential serum samples from 0 to 3 years of infection (10 to 19 samples) from all 7 participants with breadth were tested against all the viruses previously shown to be sensitive to the 3-year plasma samples. The ID₅₀ titers versus weeks postinfection (p.i.) are represented for each virus, with the autologous viruses shown in solid black, subtype C viruses in red, subtype B viruses in blue, and subtype A viruses in green. The time points when detectable heterologous activity emerged are indicated using dashed vertical lines, with the number of additional viruses neutralized displayed above. The viral loads over time are shown as dashed black curves.

Fig. 4.

Kinetics of development of heterologous neutralization in individuals with breadth. Sequential serum samples from 0 to 3 years of infection (10 to 19 samples) from all 7 participants with breadth were tested against all the viruses previously shown to be sensitive to the 3-year plasma samples. The ID₅₀ titers versus weeks postinfection (p.i.) are represented for each virus, with the autologous viruses shown in solid black, subtype C viruses in red, subtype B viruses in blue, and subtype A viruses in green. The time points when detectable heterologous activity emerged are indicated using dashed vertical lines, with the number of additional viruses neutralized displayed above. The viral loads over time are shown as dashed black curves.

Fig. 5.

Development of cross-neutralizing antibodies over 5 years of infection. The sera obtained at 1, 2, 3, 4, and 5 years of infection were tested for neutralization against a panel of 12 viruses of subtypes A, B, and C (4 of each subtype). The percentage of viruses neutralized was calculated for each sample. (A) Percentages of individuals capable of neutralizing more than 80%, 40 to 80%, 1 to 40%, and none of the 12 viruses at 5 different time points. (B and C) Percentages of viruses neutralized over time for the 15 and 12 participants that reached 4 and 5 years postinfection, respectively.

Fig. 6.

Adsorption of neutralizing antibodies using recombinant envelope proteins. Plasmas obtained at 3 years postinfection were adsorbed using recombinant ConC monomeric gp120- or trimeric gp145-coated beads. Blank beads were used as a negative control. (A) Depleted plasmas were tested for binding to ConC gp120 or ConC gp145 by ELISA. The percentage of antibody depleted was calculated using the following equation: [1 − (midpoint titer of plasma treated with gp120-coated beads/midpoint titer of plasma treated with blank beads)] × 100. (B) Plasmas adsorbed with ConC gp120 were tested for neutralizing activity against various envelope-pseudotyped viruses. The percent depletion was calculated as follows: [1 − (ID₅₀ of plasma treated with gp120-coated beads/ID₅₀ of plasma treated with blank beads)] × 100. Data represent the means for two separate neutralization experiments. (C) Plasmas adsorbed with ConC gp145 were tested for neutralizing activity against ConC and analyzed as described for gp120.

Fig. 7.

Epitope mapping of CAP177 and CAP255 anti-gp120 neutralizing antibodies. (A) The 3-year plasmas of these two participants were adsorbed using gp120 mutated in the CD4 binding site (D368R) or coreceptor binding site (I420R) and gp120 with the V1V2 and V3 loops deleted (core gp120). Wild-type gp120-coated beads and blank beads were used as positive and negative controls, respectively. Depleted plasmas were tested for neutralization of ConC. (B) CAP177 plasma was adsorbed with V1V2- or V3-deleted gp120 prior to testing of ConC neutralization. (C) Both plasmas were tested for neutralization against wild-type ConC and three mutants in the core DMR epitope. Data represent the means for two separate neutralization experiments.