High Prevalence of Molecular Markers Associated with Artemisinin, Sulphadoxine and Pyrimethamine Resistance in Northern Namibia

Artemisinin-based combination therapies are a cornerstone of Namibias efforts to eliminate malaria, which has had an over 90% reduction in cases since their introduction in 2005. However, their efficacy has not been routinely monitored, with malaria outbreaks regularly reported since 2016. The recent emergence of artemisinin partial resistance in Africa has highlighted the role of malaria molecular surveillance in complementing efficacy studies. This cross-sectional genomic surveillance study was nested within Namibias routine surveillance system and aimed to determine the prevalence of antimalarial drug resistance markers in northern Namibia. Dried blood spots (DBS) and epidemiological data were collected from confirmed Plasmodium falciparum cases presenting at health facilities in the highest malaria-burden regions (Zambezi, Kavango East, Kavango West, Ohangwena, and Omusati) from April to September 2023. 12 genes associated with resistance to 7 antimalarial drugs were genotyped from 264 DBS using multiplexed targeted amplicon sequencing. Multiple pfk13 mutations associated with artemisinin partial resistance were identified: the P441L candidate marker was the most abundant, at 33.2%, and the validated markers P574L and A675V were observed at 1.2%. The chloroquine resistance marker pfcrt CVIET haplotype was observed at 1%, while the pfmdr1 N86 genotype, selected by lumefantrine use, was found in all samples. Although sulphadoxine-pyrimethamine is not used in Namibia, a high proportion of sulphadoxine-pyrimethamine resistance-associated mutations in the pfdhps and pfdhfr genes were observed. This study underscores the need for routine genomic surveillance to monitor emerging drug resistance markers and calls for further research to define their clinical implications.