Partial escape of HIV-1 from cytotoxic T lymphocytes during chronic infection

Abstract

Viral mutational escape from CD8(+) cytotoxic T lymphocytes (CTLs) is typically considered to be a dichotomous process and uncommon during chronic HIV-1 infection. Ex vivo passaging of HIV-1 from persons with chronic infection, however, revealed the evolution of many fixed substitutions within and around CTL-targeted regions, with an associated increase in replicative capacity. This indicates an evolution of mutations during chronic HIV-1 infection that trade replicative fitness for incomplete evasion of CTLs, or "partial escape."

Fig 1

Summary of CTL targeting and associated amino acid changes. The black arrowheads mark the locations of CTL responses within the HIV-1 coding regions for each subject as determined by IFN-γ ELISpot mapping of CD8⁺ T lymphocytes using a consensus subtype B peptide library (no responses were seen against Vpu or Tat). The regions shaded in gray were sequenced before and after ex vivo passaging (see Fig. 2 for the exact sequence regions). Amino acid sites that changed with passaging are marked with open arrowheads. Amino acid sites that displayed evidence of positive selection with passaging are marked with shaded diamonds (see Tables 1 and 2 for the exact amino acid positions).

Fig 2

Changes in sequence diversity with passaging. (A) The average diversity of the initial ex vivo (black bars) and after passaging (gray bars) virus sequences was calculated and evaluated by 500 bootstrap replicates to give a mean and standard error. Significant differences in pre- and postpassaging values are marked with an asterisk (t test; P < 0.05). (B) A representative neighbor-joining phylogenetic tree for subject 25 p17 Gag (amino acids 1 to 155) shows that the passaged sequences have less diversity and form an independent cluster with 100% bootstrap support.

Fig 3

Comparison of the replication capacities of the ex vivo and passaged viruses. Recombinant NL4-3-based reporter viruses carrying the GagPol coding region from baseline and passaged viruses from subjects 17, 25, and 26 were created. Paired baseline and passaged samples, each with a different reporter, were grown simultaneously at low MOIs in coculture, and viral copy number was measured by qPCR on days 1, 3, and 5. The mean and standard deviation of the slope of the growth curve of each sample (log₁₀ copies/day) were calculated based on duplicate infections. P values for the differences between baseline and passaged virus replication rates are shown above each group of paired samples.