Contribution of Gag and protease to variation in susceptibility to protease inhibitors between different strains of HIV-1

Recent reports have shown that HIV-1 Gag can directly affect susceptibility to protease inhibitors (PIs) in the absence of known resistance mutations in protease. Inclusion of co-evolved Gag alongside protease in phenotypic drug susceptibility assays can alter PI susceptibility in comparison to protease with a wild-type Gag. Using a single replication-cycle assay encompassing full-length Gag together with protease, we demonstrate significant variation in PI susceptibility between a number of PI-naïve subtype B viruses. Six publicly available subtype B molecular clones, namely HXB2, NL4-3, SF2, YU2, JRFL and 89.6, displayed up to 9-fold reduction in PI susceptibility. For two molecular clones, YU2 and JRFL, Gag contributed solely to the observed reduction in susceptibility. Gag and protease from treatment-naïve, patient-derived viruses also demonstrated significant variation in susceptibility, with up to a 17-fold reduction to atazanavir. In contrast to the molecular clones, protease was the main determinant of the reduced susceptibility. Common polymorphisms in protease including I13V, L63P and A71T were shown to contribute to this reduction in PI susceptibility, in the absence of major resistance mutations. The role of variation in PI susceptibility on LPV/r monotherapy treatment failure was investigated. The contribution of suboptimal adherence to treatment failure was shown and the development of reduced PI susceptibility during treatment observed. In addition, reduced PI susceptibility and single-round infectivity were associated with subsequent treatment failure. This study demonstrates significant variation in PI susceptibility of treatment-naïve patient viruses and provides further evidence of the independent role of Gag, the protease substrate, and in particular the amino terminus of Gag in PI susceptibility. It also highlights the importance of considering co-evolved Gag and protease when assessing PI susceptibility. These data indicate that reduced PI susceptibility at baseline may contribute to treatment failure on PI monotherapy