Background: Mutations in HIV-1 that encode drug resistance may result in decreased viral replication capacity (RC). This has been well defined for some PI-associated resistance mutations, but the effects of NRTI-associated mutations (NAMs) or thymidine analog mutations (TAMs) are less clearly defined. The current study characterizes the RC of a large panel of clinical isolates with defined mutations in RT and/or protease.

Methods: Patient (pt) isolates with defined genotypes were selected from samples submitted to ViroLogic for routine genotypic, phenotypic, and RC analysis. Of 1,829 samples, 37.6% had no NAMs or TAMs (n = 688), 48.8% had TAMs (mutations at codons 41, 67, 70, 210, 215, or 219; n = 893), 11.5% had M184V without other NAMs (n = 211), 1.3% had Q151M complex or T69S insertions (n = 23), and 0.7% had K65R (n = 14). RC is reported as percentage of wild-type using a defined cohort without resistance mutations. Statistical comparisons were made between RT genotypic groups by the unpaired t-test.

Results: Without adjusting for PI-associated resistance mutations (PI-R), all RT genotypic groups showed significant reductions in RC compared to the no NAM control group (p < 0.05). However, among pt samples without PI-R (n = 1040) significant reductions in RC were observed only for isolates containing M184V alone or K65R alone (median RC 57% and 56%, respectively, p < 0.03). The few samples with K65R+M184V and no other NAMs had lower median RC (29%). Similarly, median RC for pt isolates with Q151M+M184V or T69S Ins+M184V was 28-29%. In the absence of K65R, M184V and PI-R, pt isolates with 1-2, 3-4, or > 4 TAMs showed a slight reduction in RC that was not significantly different than control. TAMs+M184V showed significantly reduced RC (47%–66%) that was comparable to samples with M184V but no TAMs.

Conclusions: In this sample set, TAMs were highly prevalent (49%) and the K65R was infrequent (< 1%). Pt isolates with K65R or M184V exhibit decreased RC and these effects on replication appear additive. Conversely, pt isolates with TAMs alone do not have significantly reduced RC. The results with K65R are consistent with the sustained reductions in HIV RNA observed among pts in clinical trials of tenofovir DF who had developed K65R. Although therapeutic strategies should attempt to avoid development of resistance, the clinical consequences of certain resistance mutations may be moderated by the reduced replication capacity of the mutant virus.