EPPIcenter/imported-malaria-sw-uganda

doi: 10.64898/2026.01.25.26344810 # Imported malaria in southwestern Uganda doi: 10.64898/2026.01.25.26344810 This repository contains data, analysis scripts, figures, and supplementary materials for the project. ## Project overview: Malaria transmission in southwestern Uganda is relatively low compared to most regions of the country, yet persistent transmission continues to occur. This project investigates the contribution of imported malaria infections to transmission dynamics in three health facility catchment areas in southwestern Uganda: Maziba, Muko, and Kamwezi. The study integrates epidemiologic surveillance, travel history data, parasite genotyping, and transmission network analyses to distinguish imported from locally acquired malaria infections. Parasite genetic data were generated using the MAD4HatTeR multiplex amplicon sequencing panel, while analyses of complexity of infection, genetic relatedness, and transmission networks were performed using MOIRE, Dcifer, and Plasmotrack. ## Repository structure: - `Data/` contains raw from MAD4HatTeR and processed datasets (after quality control) used in the analyses - `Scripts/` contains analysis scripts used for data cleaning, statistical analyses, genomic analyses, and figure generation - `Figures/` contains all figure files and tables used in the manuscript. - `manuscript figures/` contains figures included in the main manuscript. - `supplementary_materials/` contains supplementary figures, tables, and additional materials not included in the main manuscript. - `Results/` contains intermediate outputs and summary results ## Data availability Data and code required to reproduce the analyses presented in the manuscript are provided in this repository. Sensitive or potentially identifiable information has been removed prior to sharing. ## References