Macaques vaccinated with simian immunodeficiency virus SIVmac239Delta nef delay acquisition and control replication after repeated low-dose heterologous SIV challenge

Abstract

An effective human immunodeficiency virus (HIV) vaccine will likely need to reduce mucosal transmission and, if infection occurs, control virus replication. To determine whether our best simian immunodeficiency virus (SIV) vaccine can achieve these lofty goals, we vaccinated eight Indian rhesus macaques with SIVmac239Delta nef and challenged them intrarectally (i.r.) with repeated low doses of the pathogenic heterologous swarm isolate SIVsmE660. We detected a significant reduction in acquisition of SIVsmE660 in comparison to that for naïve controls (log rank test; P = 0.023). After 10 mucosal challenges, we detected replication of the challenge strain in only five of the eight vaccinated animals. In contrast, seven of the eight control animals became infected with SIVsmE660 after these 10 challenges. Additionally, the SIVsmE660-infected vaccinated animals controlled peak acute virus replication significantly better than did the naïve controls (Mann-Whitney U test; P = 0.038). Four of the five SIVsmE660 vaccinees rapidly brought virus replication under control by week 4 postinfection. Unfortunately, two of these four vaccinated animals lost control of virus replication during the chronic phase of infection. Bulk sequence analysis of the circulating viruses in these animals indicated that recombination had occurred between the vaccine and challenge strains and likely contributed to the increased virus replication in these animals. Overall, our results suggest that a well-designed HIV vaccine might both reduce the rate of acquisition and control viral replication.

FIG. 1.

Vaccine-induced cellular immune responses. Cellular immune responses against pools of peptides, detected using whole PBMC (A) or PBMC depleted of CD8⁺ cells (B) in IFN-γ ELISPOT assays during the vaccine phase of the study. For each animal, the black boxes indicate positive responses against specific pools.

FIG. 2.

Weak in vitro neutralization of SIVmac239 by vaccine-induced antibodies. (A) Percent neutralization of SIVmac239, after a single round of replication in a luciferase reporter assay using a SIVmac239-pseudotyped virus, by sera from SIVmac239Δnef-vaccinated animals (blue) or naïve controls (red) collected on the day of first challenge with SIVsmE660. (B) Representative data for CD4 IgG2, which was used as a positive control for each assay. Percent neutralization is presented as the reduction of luciferase activity at the end of the assay in comparison to that for cells infected with the pseudotyped virus alone. Negative values represent an enhancement of infection.

FIG. 3.

Kaplan-Meier rate of infection after repeated low-dose inoculations with SIVsmE660. The percentage of animals vaccinated with SIVmac239Δnef or control animals remaining uninfected after each of the 10 inoculations with SIVsmE660 is shown. The statistical significance of the difference between SIVmac239Δnef-vaccinated and control animals was determined by the log rank test.

FIG. 4.

Peak acute plasma virus concentrations after infection with SIVsmE660. A scatter plot comparison of the peak plasma virus replication occurring at any point during the first 3 weeks of infection with SIVsmE660 is shown for the SIVmac239Δnef-vaccinated macaques and their controls. The line represents the geometric mean for each group. The differences between the vaccinated and control animals are statistically significant (Mann-Whitney U test).

FIG. 5.

Plasma virus levels after detectable SIVsmE660 replication. (A) vRNA copies per ml of plasma for the individual vaccinated (blue) and control (red) animals in the weeks following the first detection of SIVsmE660. The week prior to detectable virus replication is labeled week 0. (B) Geometric means of vRNA copy Eq/ml for the vaccinated (blue) and control (red) groups during the first 20 weeks after detectable SIVsmE660 replication. The differences between the geometric means of the plasma virus concentrations of the vaccinees and controls were significant at weeks 2 and 3 (Mann-Whitney U test). †, animal rh2270 was euthanized at day 17 p.i. due to an underlying medical condition not directly related to SIV infection.

FIG. 6.

Expansion of anamnestic cellular immune responses after detectable infection with SIVsmE660. The sum of SFC in IFN-γ ELISPOT assays using 15-mer peptides identified as inducing positive responses during the vaccine phase of the study is shown for each animal (see Table S1 in the supplemental material). Whole PBMC were used in the assays, but peptides stimulating CD8⁺ T cells are represented by black boxes and peptides stimulating CD4⁺ T cells are represented by white boxes. The responses are plotted with the plasma virus concentrations during the first 4 weeks after detectable SIVsmE660 infection. Week 0 is the week prior to detectable SIVsmE660 infection.