The CCR100136 (EPIC) study evaluated the antiviral activity of the novel CCR5 entry inhibitor aplaviroc in combination with lopinavir-ritonavir in drug-naïve human immunodeficiency virus type 1-infected subjects. Although the trial was stopped prematurely due to idiosyncratic hepatotoxicity, 11 subjects met the protocoldefined virologic failure criteria. Clonal analyses of the viral envelope tropism, aplaviroc susceptibility, and env sequencing were performed on plasma at day 1 and at the time of virologic failure. Molecular evolutionary analyses were also performed. Treatment-emergent resistance to aplaviroc or lopinavir-ritonavir was not observed at the population level. However, aplaviroc resistance was detected prior to therapy at both the clonal and population levels in one subject with virologic failure and in six subjects in a minority (<50%) of clones at day 1 or at the time of virologic failure. Reduced aplaviroc susceptibility manifested as a 50% inhibitory concentration curve shift and/or a plateau. Sequence changes in the clones with aplaviroc resistance were unique to each subject and scattered across the envelope coding region. Clones at day 1 and at the time of virologic failure were not phylogenetically distinct. Two subjects with virologic failure had a population tropism change from CCR5-to dual/mixed-tropic during treatment. Virologic failure during a regimen of aplaviroc and lopinavir-ritonavir may be associated with aplaviroc resistance, only at the clonal level, and/or, infrequently, tropism changes.Although highly active antiretroviral therapy results in a profound and sustained reduction in plasma human immunodeficiency virus type 1 (HIV-1) RNA in many individuals, the side effects of currently available antiretroviral therapy (ART) and the emergence of multidrug-resistant viral strains continue to represent major challenges for the management of HIV infection (7,29). The discovery that the chemokine receptors CCR5 and CXCR4 function as coreceptors that mediate HIV-1 entry into CD4 ϩ host cells (2) has led to the development of coreceptor inhibitors, which are currently being tested for use in ART.Unlike other drug classes, resistance to CCR5 entry inhibitors (CCR5 EIs) could involve the use of drug-bound CCR5 or a change in coreceptor usage. Much of the data on CCR5 EI resistance come from in vitro passage and short-term monotherapy studies. An analysis of virus envelopes (Env) during passage studies with CCR5 EIs demonstrated the maintenance of R5 tropism in a setting where the cells utilized expressed both CCR5 and CXCR4 (17,34,38). Resistance or reduced susceptibility to aplaviroc (APL) was slow to emerge in passage studies; the characterization of CCR5-tropic (R5-tropic) HIV-1 isolates from long-term passage (Ͼ48 weeks) showed marginal increases in the change (n-fold) in the 50% inhibitory concentration (FCIC 50 ) values, the standard measure by which resistance to other antiretroviral classes is detected (16,17).Another measure of drug susceptibility that has been suggested for CCR...