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Background: With the current treatment options for visceral leishmaniasis (VL), recrudescence of the parasite is seen in a proportion of patients. Understanding parasite dynamics is crucial to improving treatment efficacy and predicting patient relapse in cases of VL. This study aimed to characterize the kinetics of circulating Leishmania parasites in the blood, during and after different antileishmanial therapies, and to find predictors for clinical relapse of disease. Methods: Data from three clinical trials, in which Eastern African VL patients received various antileishmanial regimens, were combined in this study. Leishmania kinetoplast DNA was quantified in whole blood with real-time quantitative PCR (qPCR) before, during, and up to six months after treatment. An integrated population pharmacokinetic-pharmacodynamic model was developed using non-linear mixed effects modelling. Results: Parasite proliferation was best described by an exponential growth model, with an in vivo parasite doubling time of 7.8 days (RSE 12%). Parasite killing by fexinidazole, liposomal amphotericin B, sodium stibogluconate, and miltefosine was best described by linear models directly relating drug concentrations to the parasite elimination rate. After treatment, parasite growth was assumed to be suppressed by the host immune system, described by an Emax model driven by the time after treatment. No predictors for the high variability in onset and magnitude of the immune response could be identified. Model-based individual predictions of blood parasite load on Day 28 and Day 56 after start of treatment were predictive for clinical relapse of disease. Conclusion: This semi-mechanistic pharmacokinetic-pharmacodynamic model adequately captured the blood parasite dynamics during and after treatment, and revealed that high blood parasite loads on Day 28 and Day 56 after start of treatment are an early indication for VL relapse, which could be a useful biomarker to assess treatment efficacy of a treatment regimen in a clinical trial setting. Author summary: After primary treatment of visceral leishmaniasis (VL), relapse of disease occurs in a proportion of patients. Understanding parasite dynamics is crucial to improving treatment efficacy and predicting disease relapse at an early stage. Leishmania kinetoplast DNA loads in blood from East African VL patients from three clinical trials, treated with five different treatment regimens, were used to develop a semi-mechanistic model to integrate in vivo parasite replication in the host, parasite clearance by different VL drug regimens, and suppression of parasite regrowth by the host immune system after treatment. This model deepened our understanding of the parasite-drug-host interaction and described the in vivo parasite growth rate in human for the first time. Moreover, the model revealed that high blood parasite loads on Day 28 and Day 56 after start of treatment are an early indication for VL relapse, which could serve as a biomarker to predict long-term clinical outcome, an important new tool for optimizing future VL treatment regimens. [ABSTRACT FROM AUTHOR]