Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV

Abstract

A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a nonhuman primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two-amino-acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of human immunodeficiency virus (HIV)-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine-elicited or naturally elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.

Figure 1. Protection against SIV challenge

a, The fraction infected animals in each arm following each of 12 challenges is shown. Five animals in the mac239 Env arm and one animal in the mosaic Env arm remained uninfected after 12 challenges. b, For each arm, the geometric mean plasma viral load (RNA copies/ml) for infected animals is shown. Each animal is synchronized to its peak VL. Inset: expanded scale for the acute phase. c, The peak and set point plasma viral load distributions for all infected animals. d, The infection rate is the fraction of infections out of the total number of exposures; vaccine efficacy was calculated as described in the methods.

Figure 2. Analysis of transmitted/founder (T/F) viruses

a, The distribution of unique T/F viruses in the first virus-positive plasma sample is shown for all 80 animals. b, The average number of T/F viruses per exposure event was calculated. Here, vaccine efficacy (V_E) is computed as the reduction in the number of T/F viruses (ns: p > 0.05). c, For each position in Env, the p value is shown for a permutation test comparing the fraction of viruses with the consensus amino acid in the Env T/F vs the control and Gag T/F. p values at positions 23, 45, and 47 remain significant after correction for multiple comparisons. d–f, Based on the sequence at positions 45 and 47, T/F viruses were divided into “TR” (45T+47R) and “A/K” (45A or 47K) viruses. d, Proportion of A/K viruses in the E660 challenge stock was measured by deep sequencing or by SGA, and among T/F in the immunization arms by SGA. A Fisher’s exact test was performed to determine the significance of the difference in A/K viruses compared to the Control+Gag arms (ns: p > 0.05). e,f, Cumulative infection probabilities by TR or A/K viruses was done using a non-parametric estimate for competing risks; the V_E and p-values are computed using likelihoods from a modified Hudgens and Gilbert leaky vaccine model. Tick marks indicate censoring of animals solely infected by the other virus type (challenges 1–12), or remaining uninfected after 12 challenges.

Figure 3. Sequences accounting for neutralization resistance

a,b, Neutralization curves of CP3C, a sensitive clone from E660 (a), and of CR54, a resistant clone from E660 (b), using dilutions of sera from five Env-immunized animals (selected to show the range of potency). Black arrows indicate which dilutions were tested in duplicate; curves represent non-linear least squares regressions of a four-parameter binding model. Nearly 100% of CP3C virions, but only 40–50% of CR54 virions, can be neutralized by immune sera. Red dashed lines show how IC_HM is derived for animal 08D161. c,d, Neutralization curves of 9 viral variants using sera from one animal (c) or CD4-Ig (d). The parent virus into which mutations were made is listed, along with the amino acids at positions 23, 45, 47, and 70. e, All variants were assayed using serial dilutions of sera from all 40 Env-immunized animals. Shown is the maximum fraction of each virus that was neutralized (determined by regression analysis). Blue letters indicate amino acid substitutions compared to the parent virus. The numbers above the graphic indicate the mean resistant fraction for each virus.

Figure 4. Immunological correlates of risk

a,b, Week 52 plasma IgG against the CP3C envelope is graphed against time to infection (uninfected animals were assigned a value of 13). No significant correlation was found when all infection events were considered (a); however, by excluding infected solely with A/K viruses, a strong predictive relationship is seen (b). The line is from a linear regression; statistics are based on Spearman correlation. c, Week 52 plasma IgG against the mac239 V1V2 is significantly associated with protection against TR viruses, and also against all viruses (Extended Fig 7B). d, Kaplan Meier (KM) analysis was performed by dividing the 40 Env-immunized animals in two equal groups based on the anti-CP3C IgG responses (median = 570). Animals remaining uninfected or infected solely with A/K viruses were censored as shown by vertical lines. e, KM analysis comparing Env-immunized animals with higher vs. lower week 32 serum activity against the CD4 binding site of envelope. f, KM analysis comparing Env-immunized animals with higher vs. lower week 52 against virus pseudotyped with a CP3C Env containing a T45A mutation (“VARN”), a sequence shared by E543. g, The mean response (upper) and proportion of responders (lower) against each linear peptide is shown for animals grouped by time to infection: 1–3 challenges (red) vs 4 or more challenges (blue). Green boxes highlight regions potentially associated with protection identified by a Fisher’s exact test; overlapping peptide numbers are in green, with sequences given in Supplementary Table 5. h, Average binding to the linear C3 peptides 119 and 120 correlates strongly with time to infection. i, KM analysis comparing Env-immunized animals with a positive response to C3 peptides to those with a negative response. j, KM analyses comparing all animals in the control and Gag arms (black), all Env-immunized animals having a CP3C IgG response <570 and a negative C3 peptides response (grey), and animals in either Env arm having either antibody response.

Figure 5. Vaccine-mediated selection at V1V2

a, The binding of plasma from all 40 Env-immunized animals to linear 15mer peptides spanning the V1V2 region of either E543 (top) or mac239 (bottom) was measured; bars represent the average binding for the 20 mosaic- (orange) or the 20 mac239- (green) immunized animals. Arrows indicate an area of V1V2 showing vaccine-specific responses, encompassing amino acids 154–170. b, Sieving analysis was done as in Fig 2b, but after excluding neutralization-resistant A/K viruses. The only significant association with immunization arm was at position 162. c, Representation of 162N (vs 162S) as determined by SGA for TR viruses in the swarm or in T/F. Note that all immunogens encode 162N, so selection is likely mediated against a neighboring epitope; this epitope is found only in (one of) the mosaic immunogens, and occurs in linkage disequilibrium with 162N in the E660 swarm.

Figure 6. C1 Sequences and HIV Env Neutralization

a, Neutralization profiles of 51 different HIV-1 strains by the V1V2 antibodies PG9 and PG16 were determined. Example curves of PG16 on six viruses are shown. As for SIV A/K viruses, a variable fraction of each clonal virus is completely neutralization resistant; the remainder is highly sensitive. b, The influence of variants at each position in envelope on the fraction of neutralization resistant virus is shown as a p value from a Fisher’s test; shown is the C1 region. c, The most significant association for all positions in Env was amino acid 47. The distribution of the fraction of neutralization resistant virus is shown for the two variants, 47K and 47R. d, Alignment of SIV and HIV Env proteins in the middle of the C1 region highlighting the positions of the neutralization signatures.