Background Effectiveness of ART regimens strongly depends upon complex
interactions between the selective pressure of drugs and the evolution of
mutations that allow or restrict drug resistance. Methods Four clinical
isolates from NRTI-exposed, NNRTI-naive subjects were passaged in increasing
concentrations of NVP in combination with 1 µM 3 TC and 2 µM ADV to assess
selective pressures of multi-drug treatment. A novel parameter inference
procedure, based on a stochastic viral growth model, was used to estimate
phenotypic resistance and fitness from in vitro combination passage
experiments. Results Newly developed mathematical methods estimated key
phenotypic parameters of mutations arising through selective pressure exerted
by 3 TC and NVP. Concentrations of 1 µM 3 TC maintained the M184V mutation,
which was associated with intrinsic fitness deficits. Increasing NVP
concentrations selected major NNRTI resistance mutations. The evolutionary
pathway of NVP resistance was highly dependent on the viral genetic
background, epistasis as well as stochasticity. Parameter estimation indicated
that the previously unrecognized mutation L228Q was associated with NVP
resistance in some isolates. Conclusion Serial passage of viruses in the
presence of multiple drugs may resemble the selection of mutations observed
among treated individuals and populations in vivo and indicate evolutionary
preferences and restrictions. Phenotypic resistance estimated here “in silico”
from in vitro passage experiments agreed well with previous knowledge,
suggesting that the unique combination of “wet-” and “dry-lab” experimentation
may improve our understanding of HIV-1 resistance evolution in the future