Viral escape from dominant simian immunodeficiency virus epitope-specific cytotoxic T lymphocytes in DNA-vaccinated rhesus monkeys

Abstract

Virus-specific cytotoxic T lymphocytes (CTL) are critical for control of human immunodeficiency virus type 1 replication. However, viral escape from CTL recognition can undermine this immune control. Here we demonstrate the high frequency and pattern of viral escape from dominant epitope-specific CTL in SIV gag DNA-vaccinated rhesus monkeys following a heterologous simian immunodeficiency virus (SIV) challenge. DNA-vaccinated monkeys exhibited initial effective control of the SIV challenge, but this early control was lost by serial breakthroughs of viral replication over a 3-year follow-up period. Increases in plasma viral RNA correlated temporally with declines of dominant SIV epitope-specific CD8(+) T-lymphocyte responses and the emergence of viral mutations that escaped recognition by dominant epitope-specific CTL. Viral escape from CTL occurred in a total of seven of nine vaccinated and control monkeys, including three animals that initially controlled viral replication to undetectable levels of plasma viral RNA. These data suggest that CTL exert selective pressure on viral replication and that viral escape from CTL may be a limitation of CTL-based AIDS vaccine strategies.

FIG. 1.

Plasma viral RNA levels and CD8⁺ T-lymphocyte responses following SIVsmE660 challenge. (A) Plasma viral RNA levels were determined for 3 years following challenge in the SIV gag DNA-vaccinated and control rhesus monkeys. The limit of detection of this assay was 500 RNA copies/ml. Asterisks denote animal deaths. (B) Gag p11C-specific CD8⁺ T-lymphocyte responses were determined for 3 years following challenge in the SIV gag DNA-vaccinated and control rhesus monkeys. The tetramer responses represent the percentages of gated CD3⁺ CD8⁺ T lymphocytes that bound tetramer. Functional CTL activity was confirmed by chromium release assays (data not shown).

FIG. 2.

Viral sequence evolution in SIV gag DNA-vaccinated animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes. Sequence analyses are shown for SIV gag DNA-vaccinated rhesus monkeys P091 (A), N529 (B), 92-98 (C), and T258 (D) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 3.

Viral sequence evolution in control animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes is shown. Sequence analyses are shown for control rhesus monkeys R468 (A), J8N (B), V299 (C), T720 (D), and P967 (E) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 3.

Viral sequence evolution in control animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes is shown. Sequence analyses are shown for control rhesus monkeys R468 (A), J8N (B), V299 (C), T720 (D), and P967 (E) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 3.

Viral sequence evolution in control animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes is shown. Sequence analyses are shown for control rhesus monkeys R468 (A), J8N (B), V299 (C), T720 (D), and P967 (E) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 3.

Viral sequence evolution in control animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes is shown. Sequence analyses are shown for control rhesus monkeys R468 (A), J8N (B), V299 (C), T720 (D), and P967 (E) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 3.

Viral sequence evolution in control animals. Viral sequence evolution over time in the Mamu-A^∗01-restricted Gag p11C, Gag LW9, Gag QI9, Env CL9, Env TL9, and Pol p68A CTL epitopes is shown. Sequence analyses are shown for control rhesus monkeys R468 (A), J8N (B), V299 (C), T720 (D), and P967 (E) at various time points following the challenge. The numbers of viral clones analyzed per time point are shown in parentheses.

FIG. 4.

CD8⁺ T-lymphocyte recognition of mutant peptides. Results of functional gamma interferon ELISPOT assays using PBMC from long-term nonprogressor monkey H443 and from study monkeys 92-98 and P967 at week 150 following challenge are shown. PBMC from these Mamu-A^∗01-positive animals were stimulated with either the wild-type (wt) or the mutant p11C or TL9 peptide at 8, 0.8, or 0.08 μg/ml. Mean numbers of SFC per 10⁶ PBMC are shown. Mean responses determined by assays performed in triplicate are shown. Control media were <25 SFC per 10⁶ PBMC.