Geographical Variation in Antimalarial Drug Resistance Marker Prevalence across the Southern African Elimination Eight Region

ABSTRACT. Global efforts to control and eliminate malaria are threatened by antimalarial drug resistance. The WHO recommends molecular surveillance of resistance markers as a complementary approach to therapeutic efficacy studies. Here, the first regional analysis of antimalarial resistance markers across six southern African countries spanning diverse transmission intensities and geographies is reported. Dried blood spots, collected from rapid diagnostic test-positive individuals in Angola, Eswatini, Namibia, and Zambia in 2023, Mozambique in 2022, and South Africa between 2022 and 2024 using a standardized collection method, were analyzed using a Plasmodium falciparum -targeted amplicon sequencing protocol. The distribution of resistance markers was spatially heterogeneous. Validated markers of artemisinin partial resistance (ART-R) were rare. However, more than 30% of samples from eastern Namibia and Zambia’s Western and Central Provinces carried the candidate kelch13 P441L ART-R marker. Other ART-R markers ( kelch13 R515K, P553L, P574L, A675V) were detected at a prevalence rate 99%) across all countries, whereas the chloroquine resistance marker K76T, in the chloroquine resistance transporter ( crt ) was nearly absent in most districts. The sulfadoxine–pyrimethamine resistance dihydropteroate synthase ( dhps )-dihydrofolate reductase quintuple mutation was approaching fixation (>95%) in 35% of districts. Northern Angola was a clear outlier, with a lower dhps K540E prevalence (≤20%) but a higher crt K76T prevalence (48% to 56%). This pronounced spatial heterogeneity underscores the need for timely high-resolution local resistance data generation and sharing to safeguard antimalarial drug efficacy and guide malaria control and elimination strategies across the region.