Background Antimalarial drug resistance represents an increasing public health concern in Africa. Indeed, since the introduction of IPTp-SP and SMC in moderate-to-high transmission settings, the prevalence of Sulfadoxine-Pyrimethamine and Amodiaquine resistance markers are increasing. This calls into question the effectiveness of these preventive strategies in the future. In this project, we aim to evaluate how NGS tools may contribute to the molecular surveillance of malaria drug resistance markers in target populations in Burkina Faso.

Methods The study will be conducted in Nanoro Health District in Burkina Faso. A retrospective analysis of archived samples collected in 2015 from pregnant women receiving IPTp-SP and in 2016 from their children within the ‘’COSMIC’’ trial. Archived samples collected in 2020 from children participating in a study known as ‘’In-Host’’ project will be included as well. In addition, prospective cross-sectional studies will be conducted in 2023 and 2025 in children and pregnant women, respectively. The identification of P. falciparum infections will be performed by microscopy and qPCR. Resistance markers will be investigated using the AmpliSeq Assay and a sequencer machine (MiSeq, Illumina, USA). The multiple nucleotide sequence alignments method will be used to identify the resistance markers.

Results The expected results include the impacts of IPTp-SP and SMC on the evolution of targeted resistance markers in pregnant women in a 10 year-time and in children under 5 years in a 6 year-time. In addition, the level of P. falciparum resistance to Artemisinin-based combination therapies will be known in the two study groups.

Conclusion Regarding the pressure of antimalarial drugs on the selection of resistance markers, it is necessary to use NGS techniques to monitor these markers and assess current strategies for target populations in order to inform and guide the national malaria control programs.