Background:  HIV-1 infected individuals who develope resistance to antiretroviral drugs may derive virologic and immunologic benefit from continued treatment for 2 reasons: Drug-resistant viruses can retain partial susceptibility to drugs in the regimen, and drug selection pressure favors resistant viruses with reduced replication capacity relative to the archived, drug-sensitive viruses.

Methods:  To distinguish these two effects, we developed a novel single-cell level phenotypic assay in which patient-derived gag-pol sequences were cloned into an HIV-1 reporter construct that expresses an ER-retained EGFP protein. Viral replication in the absence and presence of drug combinations can be measured on a single-cell level over a 4 log dynamic range by flow cytometry.

Results:  We partitioned the treatment benefit into partial suppression and selection for diminished replication capacity. Three patterns were observed in viremic patients under treatment:  In some patients, resistant viruses showed no susceptibility to the drug regimen and a replication capacity equivalent to the archived, wild type viruses. In this case, continued treatment has not benefit. In other patients, the resistant viruses exhibited significant susceptibility. In a third pattern, the resistant viruses showed little drug susceptibility yet significantly diminished replication capacity.

Conclusions:  Using a novel single-cell level phenotypic assay, we have shown that failing drug regimens can provide treatment benefit either from residual suppression of viral replication or selection for resistant viruses with diminished replication capacity.  Understanding the relative contribution of these effects may help guide salvage therapy.

Keywords: HIV-1; drug-resistance; replication capacity