Broadly neutralizing antibody responses in a large longitudinal sub-Saharan HIV primary infection cohort

Author Summary Understanding how HIV-1-broadly neutralizing antibodies (bnAbs) develop during natural infection is essential to the design of an efficient HIV vaccine. We studied kinetics and correlates of neutralization breadth in a large sub-Saharan African longitudinal cohort of 439 participants with primary HIV-1 infection. Broadly nAb responses developed in 15% of individuals, on average three years after infection. Broad neutralization was associated with high viral load, low CD4+ T cell counts, virus subtype C infection and HLA*A3(-) genotype. A correlation with high overall plasma IgG levels and anti-Env binding titers was also found. Specificity mapping of the bnAb responses showed that glycan-dependent epitopes, in particular the N332 region, were most commonly targeted, in contrast to other bnAb epitopes, suggesting that the HIV Env N332-glycan epitope region may be a favorable target for vaccine design

Correlation between clinical parameters and development of broadly neutralizing antibody responses.

<p>(A) Bivariate and multivariable GLM correlation analyses between the listed variables, and the best neutralization score for the M48+ subset of Protocol C participants. Number of participants in each subgroup (N) is indicated. Estimated coefficients (EstCoef), p-values, q-values, odd ratios (ExpEst) upper (U95) and lower (L95) values of the 95% confidence interval are indicated. P-values are color coded as follows: 0.01< p-value < 0.05, in green; 0.001< p-value < 0.01, in yellow; 2E-16 < p-value <0.001, in red. Q-values below 0.1 are indicated in bold. (B) Kaplan Meier curves recording the time for Protocol C neutralizers (best neutralization score ≥ 0.5, N = 157) within the indicated subgroups to reach a neutralization score ≥ 0.5. Log-Rank test p-values are indicated. DC: Discordant couple, OHS: Other Heterosexual transmission, HSM: Women to Men Heterosexual transmission, HSW: Men to Women Heterosexual transmission, MSM: Men who have Sex with Men.</p

Evolution of broadly neutralizing antibody responses in plasma from Protocol C participants.

<p>(A-C) Plasma from HIV-1 infected participants collected at various time points post infection were assessed for neutralizing activity on a predictive 6v-panel [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005369#ppat.1005369.ref016" target="_blank">16</a>]. Neutralization score on the 6v-panel was calculated as indicated in Material and Methods (A) Best neutralization score across all time points tested for Protocol C participants. (B) Fraction of Protocol C individuals with the indicated plasma neutralization score at the indicated visits. Neutralization score is color-coded as indicated in (A). (C) Detailed evolution of neutralization score over time (months) for individual Protocol C best neutralizers (N = 46), organized by time to reach neutralization score ≥ 1 in months post infection (MPI). NT: Not Tested. ART: Participants was on Anti-Retroviral Therapy at this visit, OFF: Participant was off-study at this visit.</p

Specificities mediating neutralization breadth and potency in the top 42 Protocol C neutralizers.

<p>(A) Samples are ranked by their neutralization score on the 37-virus panel (37vP) (S4 Fig in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005369#ppat.1005369.s001" target="_blank">S1 Text</a> and S2 Table in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005369#ppat.1005369.s001" target="_blank">S1 Text</a>). VC: Visit Code (months post infection). Symbols recapitulate the strength of the phenotypes tested using the different approaches detailed in this manuscript (S7-S11 Figures in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005369#ppat.1005369.s001" target="_blank">S1 Text</a>) to determine the Env epitope region targeted by the plasma broadly neutralizing activity: gp120 absorption of bnAb activity, effect of b6 competition in gp120 absorption experiments, RSC3 binding and neutralization competition, HIV-2 chimera neutralization, viruses produced in presence of kifunensine or bearing mutations. Absent (-), very weak (+/-), weak (+), moderate (++), strong (+++), phenotype was attributed based on i) the median fold or average percent decrease in ID50 and ii) the fraction of viruses which neutralization ID50 was decreased <2 fold, <10 <50 fold or <20%, <40%, <60%, <80%. Blank = not tested, NB: not binding. A dominant specificity was attributed for each sample based on results from all these experiments. UD: Undefined. (B) Overall distribution of dominant nAb specificities mediating plasma neutralization breadth in the top 42 Protocol C neutralizers as detailed in (A).</p

Correlation between total and antigen-specific IgG responses and development of broadly neutralizing antibody responses.

<p>Correlations were assessed by Spearman analyses: p-values and r-values are indicated; (ns) not significant. Linear, semi-Log or Log-log regressions are also shown as dotted lines. Neutralization score corresponds to a participant’s best neutralization score on the 6-virus panel across all tested time points. (A,C) IgG binding activity to recombinant MN gp41 (Subtype B), BG505 gp120 (subtype A) and IAVIC22 gp120 (Subtype B) was assessed, by ELISA, in plasma samples of Protocol C participants (N = 61) from the M48+ subset, at visits matching development of bnAb responses (M24-72, mean = 36.6 mpi). (B) Avidity index for IAVIC22-gp120 IgG titers were calculated from high salt (1.5M or 3M NaSCN) ELISA experiments. (C) Total IgG titers were assessed by ELISA. (D) Total IgG titers in pre-infection (N = 27), ~4mpi (N = 56, M00, mean = 4.0 mpi) and ~36mpi (N = 61) M24-72) samples. (E) Total IgG titers in ~36mpi samples (M24-72). (F) ELISA binding ID50 and neutralization score from (A) were standardized to a reference concentration of 20mg/mL of total plasma IgG.</p