Macaques vaccinated with live-attenuated SIV control replication of heterologous virus

Abstract

An effective AIDS vaccine will need to protect against globally diverse isolates of HIV. To address this issue in macaques, we administered a live-attenuated simian immunodeficiency virus (SIV) vaccine and challenged with a highly pathogenic heterologous isolate. Vaccinees reduced viral replication by approximately 2 logs between weeks 2-32 (P < or = 0.049) postchallenge. Remarkably, vaccinees expressing MHC-I (MHC class I) alleles previously associated with viral control completely suppressed acute phase replication of the challenge virus, implicating CD8(+) T cells in this control. Furthermore, transient depletion of peripheral CD8(+) lymphocytes in four vaccinees during the chronic phase resulted in an increase in virus replication. In two of these animals, the recrudescent virus population contained only the vaccine strain and not the challenge virus. Alarmingly, however, we found evidence of recombinant viruses emerging in some of the vaccinated animals. This finding argues strongly against an attenuated virus vaccine as a solution to the AIDS epidemic. On a more positive note, our results suggest that MHC-I-restricted CD8(+) T cells contribute to the protection induced by the live-attenuated SIV vaccine and demonstrate that vaccine-induced CD8(+) T cell responses can control replication of heterologous challenge viruses.

Figure 1.

Plasma virus concentrations after SIVsmE660 challenge. (a) Plasma virus concentrations of the ten SIVmac239Δnef-vaccinated macaques and their ten MHC-I–matched naive controls. (b) Geometric means for the ten vaccinated and ten naive controls. (c) Plasma virus concentrations of the vaccinated and naive Mamu-B*08⁺ and -B*17⁺ macaques. (d) Geometric means for the vaccinated and naive Mamu-B*08⁺ and -B*17⁺ macaques. (e) Plasma virus concentrations of the vaccinated and naive Mamu-A*01⁺, -A*02⁺, and -A*11⁺ macaques. (f) Geometric means for the vaccinated and naive Mamu-A*01⁺, -A*02⁺, and -A*11⁺ macaques.

Figure 2.

No in vitro neutralization of SIVsmE660 by vaccine-induced antibodies. Percent neutralization of SIVsmE660 replication in rhesus macaque PBMC after 7 d in culture by plasma collected before challenge in SIVmac239Δnef vaccinees. The chimeric molecule CD4-IgG2 was used as a positive control for neutralization and plasma collected from an unvaccinated animal, 84070, before challenge was used as a negative control. Percent neutralization is presented as the reduction in the amount of virus at the end of the assay in comparison to cells infected with SIVsmE660 alone. Similar negative plasma neutralization results were observed in a TZM-bl cell neutralization assay (65). Error bars represent SEM of experiments done in triplicate.

Figure 3.

Expansion of virus-specific cells in SIVmac239Δnef-vaccinated macaques at 2 wk p.c. with SIVsmE660. Expansion in vaccinated macaques of the number of SFC above prechallenge levels in IFN-γ ELISPOT assays at 2 wk p.c. with SIVsmE660. To determine the expansion of SFC p.c., we subtracted the number of SFC per pool before challenge from the number of SFC detected p.c. The sum of the expanded cells per protein is displayed in the graph.

Figure 4.

Frequency of tetramer binding cells in the PBMC of SIVmac239Δnef-vaccinated macaques p.c. with SIVsmE660. (a) The frequency of MHC-I tetramer binding cells in the PBMC after challenge with SIVsmE660. Frequencies of tetramer positive cells are reported as the percentage of CD3⁺/CD8⁺/tetramer⁺ lymphocytes. The plasma virus concentrations for each animal are displayed with the red line and symbols. * distinguishes Nef_221-229YY9 from Nef_159-167YY9. (b) Comparison of amino acid sequences between SIVmac239-derived peptides and SIVsmE660. The SIVmac239 sequence is shown above SIVsmE660 sequence for comparison of the two viruses. Periods represent conserved amino acids, capital letters indicate amino acid substitutions, and lowercase letters represent mixed populations.

Figure 5.

Plasma virus concentrations and CD8⁺ T cell and NK cell counts after in vivo depletion of CD8⁺ cells. (a) Plasma virus concentrations of the four SIVmac239Δnef-vaccinated macaques were transiently depleted of their peripheral CD8⁺ cells. (b and c) The number of CD8⁺ T cells (CD3⁺/CD8⁺ lymphocytes; b) and the number of NK cells (CD3⁻/CD8⁺/CD16⁺; c) in the PBMC after in vivo CD8 depletion.

Figure 6.

Virus replication in Mamu-B*17⁺ macaques. Plasma virus concentrations in SIVmac239Δnef vaccinated (blue) and unvaccinated (red) Mamu-B*17⁺ macaques for 60 wk p.c.

Figure 7.

Recombination events between SIVmac239Δnef and SIVsmE660. During the chronic phase of infection or after in vivo CD8 depletion we used bulk sequencing to detect recombination between SIVmac239Δnef and SIVsmE660. Represented are the regions that most closely align to either SIVmac239Δnef (red) or SIVsmE660 (blue). Positioning of putative break points and size of either SIVmac239Δnef or SIVsmE660 regions are approximations based on sequencing data. Open boxes represent regions of the virus where sequences could not be obtained.