Protection against a mixed SHIV challenge by a broadly neutralizing antibody cocktail

Abstract

HIV-1 sequence diversity presents a major challenge for the clinical development of broadly neutralizing antibodies (bNAbs) for both therapy and prevention. Sequence variation in critical bNAb epitopes has been observed in most HIV-1-infected individuals and can lead to viral escape after bNAb monotherapy in humans. We show that viral sequence diversity can limit both the therapeutic and prophylactic efficacy of bNAbs in rhesus monkeys. We first demonstrate that monotherapy with the V3 glycan-dependent antibody 10-1074, but not PGT121, results in rapid selection of preexisting viral variants containing N332/S334 escape mutations and loss of therapeutic efficacy in simian-HIV (SHIV)-SF162P3-infected rhesus monkeys. We then show that the V3 glycan-dependent antibody PGT121 alone and the V2 glycan-dependent antibody PGDM1400 alone both fail to protect against a mixed challenge with SHIV-SF162P3 and SHIV-325c. In contrast, the combination of both bNAbs provides 100% protection against this mixed SHIV challenge. These data reveal that single bNAbs efficiently select resistant viruses from a diverse challenge swarm to establish infection, demonstrating the importance of bNAb cocktails for HIV-1 prevention.

Figure 1. SHIV-SF162P3 escape from 10-1074 in rhesus monkeys

(A) Log plasma viral RNA copies/ml in chronically SHIV-SF162P3-infected rhesus monkeys following infusion with a single dose of 10 mg/kg 10-1074 or PGT121 on day 0. Detection limit is 50 copies/ml.

Figure 2. Analysis of SHIV env sequences in 10-1074 treated animals

Viral sequences by single genome amplification (SGA) of plasma viruses before and after 10-1074 administration. Highlighted in red are amino acid residues that were detected at day 14 and 42.

Figure 3. Frequencies of amino acids at critical PGT121 and 10-1074 contact sites in the SHIV-SF162P3 challenge stock

(A) “O” indicates an Asn that is part of a potential N-linked glycosylation site (PNGS) (positions 295, 301, 332). The critical N332 and S334 residues are circled in red. (B) PGT121 and 10-1074 neutralization potency of SHIV-SF162P3 (wild-type) and SHIV-SF162P3 containing an N332A mutation.

Figure 4. Complementarity of neutralization profiles of PGDM1400 and PGT121 against HIV-1

(A) IC80 titers for PGDM1400, PGT121, and the combination of PGT121+PGDM1400 against a panel of 118 multiclade viruses. IC80 titers are shown as a heatmap with viruses represented in rows. Dark red indicates more potent neutralization and light yellow indicates less potent neutralization. Blue indicates IC80 neutralization titers >50 μg/ml. The IC80 titers in the combination reflect the concentration of each bNAb. (B) IC80 breadth-potency plots for PGDM1400, PGT121, and the combination of PGT121+PGDM1400. (C) IC80 titers for PGDM1400, PGT121, and the combination of PGT121+PGDM1400 for pseudoviruses from clades A, B, C, and CRF01. Bold horizontal lines represent medians, thin horizontal lines are are 25th and 75th percentiles. The percent of viruses with IC80 titers >50 μg/ml are shown on the top of each panel. P values reflect Fisher’s exact tests.

Figure 5. Protective efficacy of the combination of PGT121+PGDM1400 against a mixed SHIV challenge in rhesus monkeys

5 animals per group received either an i.v. single dose of PGDM1400, PGT121, the combination of PGT121+PGDM1400, or saline (Sham) before being rectally challenged with a high dose of both SHIV-SF162P3 and SHIV-325c. Log plasma viral RNA copies/ml following mixed challenge with SHIV-SF162P3 and SHIV-325C. Red line indicates median values. Detection limit is 50 copies/ml.

Figure 6. Analysis of SHIV env sequences in breakthrough infections

Maximum likelihood tree depicting SHIV env sequences by single genome amplification (SGA) of plasma viruses at weeks 2-6 following challenge. Highlighted in green are the sequences of the challenge stock SHIVs.

Figure 7. Intrapatient variation in key contact signatures for PGDM1400 and PGT121

LOGO plots of viral sequence diversity in the key PGDM1400 and PGT121 contact sites (Figs. S6-S8) in 10 HIV-1-infected individuals for whom >150 full-length env sequences were available in the Los Alamos Sequence Database. The subject ID is indicated above each plot. The x-axis indicates the amino-acid position based on HxB2 numbering. The y-axis indicates the probability of an amino-acid at this location. “O” indicates an Asn that is part of a potential N-linked glycosylation site (PNGS). Blue reflects sensitivity signatures, red reflects resistance signatures, and black reflects no statistically significant associated with antibody sensitivity.