Sub-national Variation and Heterogeneity of Malaria transmission and Antimalarial Drug Utilization in Fifteen Endemic Sub-Regions of Uganda

Background: Uganda is the third largest contributor to the global malaria burden. Despite decades of investment in control interventions, the entire population remains at risk of exposure to infective mosquito bites, malaria morbidity and mortality. The WHO recommends epidemiological stratification and sub-national tailoring of malaria interventions based on local transmission given the heterogeneity of malaria transmission, however current malaria transmission data at sub-national level is often lacking. Methods: From October 2024 to April 2025 using a cross-sectional design, blood samples were collected from children <5 years for Rapid Diagnostic Tests (RDTs) and thick blood smears to assess presence of malaria parasites. Interviews were conducted with caretakers in household using an electronic Questionnaire to collect respondents’ demographic variables as well as the antimalarial drug use pattern. Data were analysed with STATA and the Geographical Information System (ArcGIS) software and reported as proportions and geospatial maps at sub-national levels. Results: Throughout the study period, interviews were completed in 9,238 caretakers while blood samples were collected from 6,802 children. Based on blood smear microscopy 13% of children were positive for malaria parasites. At sub-national level, there was substantial variation in parasite prevalence with the highest seen in Lango (32%), Karamoja (26%), Acholi (23%), Teso (23%) and Busoga (21%) while Kampala (<1%) and Kigezi (1%) had the lowest. Artemisinin based combination therapy (ACT) was the major drug used for malaria treatment (87%), however the use of artemisinin monotherapies and non-artemisinin compounds for treatment of malaria was reported among respondents. Conclusion: The study provides current estimates of parasite prevalence at national scale and demonstrates wide variation and heterogeneity of malaria transmission across the subregions in Uganda. The substantial regional variation and high heterogeneity of malaria transmission observed across the subregions suggests the need for malaria epidemiological stratification and sub-national tailoring of interventions by the national malaria program in Uganda. Key words: Malaria parasites, Malaria transmission, sub-national parasite estimates, stratification and sub-national tailoring