Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

Abstract

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

Keywords: HIV diversity; Hamming distance; PAR score; epitope; sieve analysis.

Fig. 1.

Features discriminating prevention efficacy in HVTN 703/HPTN 081 (Africa trial). Treatment-adjusted Spearman rank correlations between pairs of the following five viral features of the predicted most resistant lineages isolated from the primary end point cases: predicted probability of IC80 > 1 µg/mL, predicted quantitative IC80 (µg/mL), VRC01 epitope distance from the subtype C VRC01-sensitive reference sequence, physicochemical-weighted Hamming distance from the VRC01-sensitive reference sequence, and IC80 measured by the TZM-bl target cell assay. The font sizes of the correlations are proportional to their magnitude. The scatter plots are superimposed with LOWESS curves and the histograms with probability density estimates.

Fig. 2.

Prevention efficacy (PE) of VRC01 treatment in the AMP trials by PAR score defined as the logit of the predicted probability that an isolated virus is resistant to neutralization by VRC01. The solid black curves show PE of both VRC01 dose groups pooled (A and B), the 30 mg/kg VRC01 group (C and D), and the 10 mg/kg VRC01 group (E and F) as a function of the predicted probability that the predicted most resistant lineage of the primary end point case in HVTN 704/HPTN 085 (Americas trial) (A, C, and E) or HVTN 703/HPTN 081 (Africa trial) (B, D, and F) has VRC01 80% inhibitory concentration (IC80) > 1 µg/mL. The dashed black curves represent 95% pointwise CIs. Horizontal box plots at the top of each panel show the distributions of the predicted probability of IC80 > 1 µg/mL PAR score for the predicted most resistant lineage, for primary end points in the designated VRC01 treatment group (open red triangles) or in the placebo group (open blue circles). “One-sided Sieve P” is a P-value from testing whether PE decreases with the predicted probability of IC80 > 1 µg/mL.

Fig. 3.

Prevention efficacy (PE) of both VRC01 dose groups pooled vs. placebo by simultaneously i) the predicted probability that the predicted most resistant lineage of the primary end point case in HVTN 704/HPTN 085 (Americas trial) (A) or HVTN 703/HPTN 081 (Africa trial) (B) has VRC01 80% inhibitory concentration (IC80) > 1 µg/mL and ii) the indicator of measured IC80 > 1 µg/mL. The two curves show variation in PE with the predicted probability of IC80 > 1 μg/mL for isolated viruses with measured IC80 ≤ 1 μg/mL (green) or >1 μg/mL (red). The green and red shaded areas represent 95% pointwise CIs. The horizontal box plots at the top of each panel show the distributions of the predicted probability of IC80 > 1 µg/mL for the predicted most resistant lineage in both VRC01 dose groups pooled and the placebo group, stratified by IC80 ≤ 1 µg/mL (green) vs. > 1 µg/mL (red).

Fig. 4.

VRC01 prevention efficacy associated with a N-linked glycosylation site motif. (A) Prevention efficacy by PNGS status at Env positions 230 to 232 of the predicted most resistant lineage in HVTN 704/HPTN 085 (Americas trial) (Top) or HVTN 703/HPTN 081 (Africa trial) (Lower). (B) Distribution of IC80 values of the most resistant synthesized variant among primary end points in the Americas trial, separated by PNGS status at positions 230 to 232 and treatment assignment. (C) Amino acid residue distributions among predicted most resistant lineages at amino acid position 230. Each vertical bar represents an analyzed primary end point.

Fig. 5.

Prevention efficacy (PE) by the physicochemical (PC)-weighted Hamming distance from the VRC01-sensitive reference sequence. The predicted most resistant lineage of observed sequences isolated from a primary end point case was matched to the reference sequence by subtype and trial region (see the text for details). Distance was calculated based on the 12 alignable positions and five PNGS position triplets predictive of neutralization resistance (A and B) or based on the 50 positions constituting the union of the VRC01 binding footprint and the CD4 binding site (C and D). The solid black curves show PE of both VRC01 dose groups pooled in HVTN 704/HPTN 085 (Americas trial) in panels (A) and (C) and in HVTN 703/HPTN 081 (Africa trial) in panels (B) and (D). The dashed black curves represent the 95% pointwise CIs. The horizontal box plots at the top of each panel show the distributions of the PC-weighted Hamming distance in the corresponding amino acid position set, for primary end points in both VRC01 dose groups pooled (open red triangles) or in the placebo group (open blue circles). “One-Sided Unadjusted Sieve P” is a P-value from testing whether PE decreases with the distance on the X axis.

Fig. 6.

Prevention efficacy (PE) by VRC01 epitope distance from the VRC01-sensitive subtype-specific reference sequence. The solid black curves show PE of both VRC01 dose groups pooled (A and B), the 30 mg/kg VRC01 group (C and D), and the 10 mg/kg VRC01 group in (E and F). The dashed black curves represent 95% pointwise CIs. Data from HVTN 704/HPTN 085 (Americas trial) are shown in panels (A), (C), and (E) and from HVTN 703/HPTN 081 (Africa trial) in panels (B), (D), and (F). The horizontal box plots at the top of each panel show the distributions of the epitope distance from the designated reference sequence, for primary end points in the designated VRC01 treatment group (open red triangles) or in the placebo group (open blue circles). “One-Sided Unadjusted Sieve P” is a P-value from testing whether PE decreases with the VRC01 epitope distance.