Determinants of HIV-1 Mutational Escape From Cytotoxic T Lymphocytes

Abstract

CD8+ class I–restricted cytotoxic T lymphocytes (CTLs) usually incompletely suppress HIV-1 in vivo, and while analogous partial suppression induces antiretroviral drug-resistance mutations, epitope escape mutations are inconsistently observed. However, escape mutation depends on the net balance of selective pressure and mutational fitness costs, which are poorly understood and difficult to study in vivo. Here we used a controlled in vitro system to evaluate the ability of HIV-1 to escape from CTL clones, finding that virus replicating under selective pressure rapidly can develop phenotypic resistance associated with genotypic changes. Escape varied between clones recognizing the same Gag epitope or different Gag and RT epitopes, indicating the influence of the T cell receptor on pressure and fitness costs. Gag and RT escape mutations were monoclonal intra-epitope substitutions, indicating limitation by fitness constraints in structural proteins. In contrast, escape from Nef-specific CTL was more rapid and consistent, marked by a polyclonal mixture of epitope point mutations and upstream frameshifts. We conclude that incomplete viral suppression by CTL can result in rapid emergence of immune escape, but the likelihood is strongly determined by factors influencing the fitness costs of the particular epitope targeted and the ability of responding CTL to recognize specific epitope variants.

Evasion of cytotoxic T lymphocytes is a functional constraint maintaining HIV-1 Nef expression

“…This prediction was substantiated by our in vitro model of HIV-1 escape from CTL, in contrast to the observation that the Nef reading frame is highly maintained in vivo [22]. However, the model evaluated escape of HIV-1 from individual CTL clones, while HIV-1 encounters CTL of multiple specificities in vivo [27,28].…”

“…Given the involvement of MHC-I in recognition of target cells by CTL and the central role of CD8 + T cells in the control of viremia [14], a unifying explanation for maintenance of the Nef reading frame and the associated pathogenicity would be a selective advantage for virus containing Nef allowing evasion of the CTL response. Although Nef is perhaps the most highly CTLtargeted HIV-1 protein [20,21] and loss of its expression could favor escape from Nef-specific CTL [22], the HIV-1-specific response in almost all infected persons tends to recognize multiple proteins [27,28].…”

“…Not being directly required for viral replication, it might be expected that viral escape should rapidly occur by loss of epitope expression through nef reading frame disruption. Under selective pressure by CTL in vitro, it is indeed the case that HIV-1 rapidly evolves disrupted nef, rapidly becoming resistant to Nef-specific CTL [22]. However, this also results in loss of Nef MHC-I down-regulatory function, rendering the virus more sensitive to CTL of other specificities such as Gag and RT [23]; suggesting that this function of Nef contributes to its maintenance.…”

Simian-Human Immunodeficiency Virus Escape from Cytotoxic T-Lymphocyte Recognition at a Structurally Constrained Epitope

“…It has been suggested that early high-avidity CTL specific for Tat and Nef select for escape viruses more frequently than do late lowavidity CTL specific for Gag (26). This paradigm has, however, not been confirmed in in vitro studies with CTL clones with different avidities for the same epitope (37).…”

Long-term protection against SHIV89.6P replication in HIV-1 Tat vaccinated cynomolgus monkeys

“…Subsequent studies demonstrated that CTLs with high functional avidity for the early and intermediate proteins Tat, Nef and Vpr were the major factor driving the selection of immune escape variants during acute SIV infection [63]. More recent data measuring inhibition of HIV-1 replication by CTLs clones with known avidity and specificity indicate that, in vitro, the fine epitope specificity might be the most important factor at determining control of virus replication and selection of virus variants [64]. In both cases, CTLs against regulatory proteins were responsible of rapid selection of escape variants indicating a strong immune pressure.…”