Duration of prophylaxis and impact on clinical incidence in under 5-year-old children of using AS-AQ rather than AL as first-line treatment, estimated by the transmission model analysis, contrasting areas with low (a–c) or high (d–f) pfmdr1 86Y and pfcrt 76T prevalence. a The estimated proportion of individuals protected over time since treatment by AL or AS-AQ in Gourcy, Burkina Faso, where 86Y and 76T prevalences are low (18% and 25%, respectively) and amodiaquine provides longer chemoprophylaxis than lumefantrine or d Nimba, Liberia, where 86Y and 76T prevalences are high (69% and 95%, respectively) and the prophylactic times are reversed so that lumefantrine provides longer chemoprophylaxis than amodiaquine. b, c The model-estimated impact in children aged 0–5 years of using AS-AQ rather than AL as first-line treatment in the whole population, using the prophylactic profiles in a. The outcomes are b the difference and c the % difference in the cumulative number of clinical episodes occurring during the 5 years after implementing either drug at 80% coverage; here AS-AQ is predicted to decrease clinical incidence compared with AL. Orange bars show the impact in non-seasonal settings, while red shows the impact in a seasonal setting (see “Methods”). e, f The corresponding results using the prophylactic profiles in d; here AS-AQ is predicted to increase clinical incidence compared with AL