The study is the operational research component of a larger project funded by the Global Fund 5% Initiative through the Italian Agency of Development Cooperation. The project title is “Enhancement of Malaria response in South Sudan through the improvement in access, utilization and quality of preventive/diagnostic/curative services and their integration to the three levels of care of the health system of West Equatoria, South Sudan” and the coordinator is the NGO Doctors With Africa CUAMM.

The general aim of the study is the improvement of malaria prevention, diagnosis and treatment in South Sudan. Specific objectives are:

• Equip laboratories and train personnel for malaria diagnosis at three peripheral health centres (Mudri, Nvolo, Lakoumadi) in Western Equatoria, South Sudan
• Perform malaria diagnosis by RTD, microscopy and molecular assays on outpatient children aged less than 5 years and on pregnant women attending ante-natal care visits during the high malaria transmission season (1000-1500 samples)
• Compare results of different diagnostic methods (RTD, microscopy, sequencing) to monitor the quality of diagnosis
• Assess the prevalence of infection for different Plasmodium species among high-risk and sentinel population groups
• Assess frequency of markers of resistance to sulfadoxine-pyrimethamine, artesunate and amodiaquine
• Assess frequency of hrp2/hrp3 deletion
• Describe variation of var2csa
• Share data with the national malaria control programme of South Sudan and discuss evidence-based changes in policies
• Contribute to research in malaria genomic epidemiology