There is a need for adequate models of virus depletion in animals and humans as a function of drug dose in order to plan starting dose regimens in the clinic for new antiretroviral nucleoside agents. An indirect response pharmacodynamic model was fitted to link the plasma pharmacokinetics from a 28 day treatment with the nucleoside reverse transcription inhibitor emtricitabine [(-)-FTC], with the resulting virus depletion and recovery profiles in woodchucks chronically infected with woodchuck hepatitis B virus. In this approach it is assumed that the virus is eliminated from serum in a first order fashion and that the fraction of serum virus load produced per day is inhibited by the accumulation of nucleoside triphosphate in a manner that could be described using a Hill equation. Nadir virus load values were inversely related to pretreatment virus load levels within each dose group. A median inhibitory concentration value of 1.5 microM for (-)-FTC triphosphate, previously measured against the isolated viral polymerase of woodchuck hepatitis, was used in model fitting. The fitted value for concentration exponent eta of 3.46 indicated a greater than linear sensitivity of virus inhibition with dose. Since the post-treatment virus rebound was much greater than predictions of an initial model, a dose-dependent rebound factor was incorporated in the final model. The rebound factor was maximal at the end of (-)-FTC treatment and decayed mono-exponentially with a rate constant Kreb of 0.11/day. The model inferred decay half-life of (-)-FTC triphosphate in the apparent 'effect compartment' of the model was similar to the half-life value previously estimated for human hepatitis B virus-infected hepatocytes. The model described adequately the virus depletion and recovery profiles for the dose range tested and could be adapted for the selection of starting doses for future animal and human studies with emtricitabine and other nucleoside analogues in development.