Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults

Abstract

Continued use of antiretroviral therapy despite the emergence of drug-resistant human immunodeficiency virus (HIV) has been associated with the durable maintenance of plasma HIV RNA levels below pretherapy levels. The factors that may account for this partial control of viral replication were assessed in a longitudinal observational study of 20 HIV-infected adults who remained on a stable protease inhibitor-based regimen despite ongoing viral replication (plasma HIV RNA levels consistently >500 copies/ml). Longitudinal plasma samples (n = 248) were assayed for drug susceptibility and viral replication capacity (measured by using a single-cycle recombinant-virus assay). The initial treatment-mediated decrease in plasma viremia was directly proportional to the reduction in replicative capacity (P = 0.01). Early virologic rebound was associated the emergence of a virus population exhibiting increased protease inhibitor phenotypic resistance, while replicative capacity remained low. During long-term virologic failure, plasma HIV RNA levels often remained stable or increased slowly, while phenotypic resistance continued to increase and replicative capacity decreased slowly. The emergence of primary genotypic mutations within protease (particularly V82A, I84V, and L90M) was temporally associated with increasing phenotypic resistance and decreasing replicative capacity, while the emergence of secondary mutations within protease was associated with more-gradual changes in both phenotypic resistance and replicative capacity. We conclude that HIV may be constrained in its ability to become both highly resistant and highly fit and that this may contribute to the continued partial suppression of plasma HIV RNA levels that is observed in some patients with drug-resistant viremia.

FIG. 1.

Time to virologic rebound to greater than 10,000 copies of RNA/ml. The proportion of patients maintaining plasma HIV RNA levels below 10,000 copies/ml is shown by using the Kaplan-Meier method. All 19 patients who had a plasma HIV RNA levels of <10,000 at the study baseline date are included. The first plasma HIV RNA level greater than 10,000 copies of RNA/ml was used as the failure end point.

FIG. 2.

Change in protease inhibitor susceptibility and replicative capacity in 11 patients who initiated a new protease inhibitor (PI) regimen and remained on that regimen despite incomplete viral suppression. Day 0 is defined by the study baseline date (earliest available sample during virologic failure of the study regimen). Patient data were censored at the time therapy was discontinued or modified. Replicative capacity is expressed as the ratio of the luciferase activity from vectors containing patient-derived sequences to the luciferase activity from vectors containing wild-type sequences.

FIG. 3.

The effect of primary versus secondary mutations within HIV protease on drug susceptibility and replicative capacity. Genotypic resistance sequences, phenotypic resistance levels, and replicative-capacity levels were available for 141 samples. The influence of a new primary or secondary protease inhibitor-associated mutation on change in drug susceptibility and replicative capacity is shown. A primary mutation within protease was defined based on published guidelines (most of the new mutations which emerged in this cohort were V82A, I84V, and L90M) (24). The changes in replicative capacity and phenotypic susceptibility were defined as the differences between the values obtained at the study visit immediately preceding the emergence of the new mutation and those at the study visit at which the new mutation was first observed. Replicative capacity is expressed as the ratio of the luciferase activity from vectors containing patient-derived sequences to the luciferase activity from vectors containing wild-type sequences.

FIG. 4.

Cross-resistance patterns during long-term virologic failure of combination antiretroviral therapy. The level of drug susceptibility is defined as IC₅₀ for the patient-derived virus/IC₅₀ of the wild-type reference (fold change).