Compensatory Substitutions Restore Normal Core Assembly in Simian Immunodeficiency Virus Isolates with Gag Epitope Cytotoxic T-Lymphocyte Escape Mutations

Abstract

The evolution of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) as they replicate in infected individuals reflects a balance between the pressure on the virus to mutate away from recognition by dominant epitope-specific cytotoxic T lymphocytes (CTL) and the structural constraints on the virus' ability to mutate. To gain a further understanding of the strategies employed by these viruses to maintain replication competency in the face of the intense selection pressure exerted by CTL, we have examined the replication fitness and morphological ramifications of a dominant epitope mutation and associated flanking amino acid substitutions on the capsid protein (CA) of SIV/simian-human immunodeficiency virus (SHIV). We show that a residue 2 mutation in the immunodominant p11C, C-M epitope (T47I) of SIV/SHIV not only decreased CA protein expression and viral replication, but it also blocked CA assembly in vitro and virion core condensation in vivo. However, these defects were restored by the introduction of upstream I26V and/or downstream I71V substitutions in CA. These findings demonstrate how flanking compensatory amino acid substitutions can facilitate viral escape from a dominant epitope-specific CTL response through the effects of these associated mutations on the structural integrity of SIV/SHIV.

Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A

“…Thus, a revised model of control is that HLA-B57 commonly selects a less fit viral variant containing T 242 N and that compensation for this capsid defect results in higher viremia and progressive disease. This model is consistent with the work of Gao et al (32), demonstrating that the protective effect of HLA-B57 occurs at early stages of disease and accumulating data indicating the importance of compensatory mutations coincident with or subsequent to CTL epitope escape (24,30,41,67). In addition to the potential for unknown compensatory mutations, control of HIV-1 likely is due to CTL pressure against multiple epitopes, which may be the case for HLA-B57 in particular, for which numerous CTL responses against Gag and other proteins have been described.…”

“…Two putative compensatory mutations have been associated with T 242 N, namely, a Gly-to-Ala (G 248 A) change at position 9 within the epitope and an upstream His-to-Gln (H 219 Q) mutation within the CypA-binding loop (44). Because viral escape may require multiple compensatory mutations (30,55,56,67), we first investigated whether additional sequence changes were associated with T 242 N by using data from studies by Migueles et al (49,50) that identified variations in Gag CTL epitopes in B57 ϩ individuals with progressive disease. Note that in contrast to plasma viral sequences obtained for the viremic individuals, data for subjects with an undetectable viral load (Ͻ50 copies/ ml) were derived from cellular proviral DNA using a limiting dilution technique.…”

“…Reversion of certain CTL escape mutations upon transmission to a new host is a well-characterized phenomenon (5,29,43,44,61), and several CTL escape mutations now have been shown to occur at a substantial cost to viral replicative capacity (29,46,67). The important role that viral fitness plays in control of HIV-1 also is supported by reversion of transmitted drug resistance mutations in the absence of highly active antiretroviral therapy and observations of inherent intra-and intersubtype differences in viral replication capacity (12,14).…”

Structural and Biological Basis of CTL Escape in Coronavirus-Infected Mice

“…Moreover, many of those that do become selected are postulated to negatively affect virus fitness, as evidenced by rapid reversion to WT sequence when transmitted to hosts that lack the appropriate restriction element, or the requirement for co-selection of compensatory mutations that restore virus fitness (8,49,50). In a few cases, deleterious effects on virus fitness have been demonstrated directly in in vitro assays, using tissue culture cells or virus replicons (11,50,51). Consequently, a conclusion from these studies is that only a few mutations are selected because, despite their ability to evade CTL recognition, the vast majority negatively impact virus fitness.…”

The Dynamics of HIV-1 Adaptation in Early Infection

“…These double mutants would take longer to arise than single beneficial mutants. Fitness interactions of this type, more generally known as fitness epistasis, are common and strong in HIV-1 in the context of its adaptation to an alternative host-cell coreceptor (Da Silva et al 2010) and have been reported for the evolution of escape mutants in response to CD8 + T cell selection (Yeh et al 2006;Schneidewind et al 2008).…”