Spatial and temporal description of antimalarial drug resistance markers in Ghana using targeted amplicon deep sequencing.

Molecular markers give evidence of Plasmodium falciparum resistance to antimalarials. We determined the spatial and temporal distribution of antimalarial drug resistance markers in the P. falciparum population in Ghana using targeted amplicon deep sequencing. We contextualized our findings within the framework that duration of drug exposure and transmission intensity drive trends in molecular markers. About 87% (901/1,037) of samples collected from children ≤9 years with uncomplicated malaria from 2018 to 2023 were sequenced. There was a decreasing trend in the amodiaquine/lumefantrine pfmdr1 NFSND haplotype in the Coastal zone. For chloroquine, the pfcrt CVIET haplotype showed a decreasing trend in all zones. For sulfadoxine-pyrimethamine, the pfdhps SGKAA haplotype showed increasing trends in all zones in contrast with the pfdhps AGKAA, pfdhfr IRN, and quintuple IRN + AGKAA haplotypes. Finally, validated markers of artemisinin resistance P441L (1/709), M476I (1/709), N537I (1/709), A481V (1/709), P574L (1/709), C469Y (2/709), P553L (2/709), R561H (2/709), A578S (4/709), and A675V (5/709) were identified. Zonal differences in trends for pfmdr1 NFSND haplotype are likely due to lower amodiaquine drug pressure in the Coastal zone. Policy review of amodiaquine/lumefantrine antimalarial use might help reduce the increasing trends seen in the Forest and Savannah zones. The declining prevalence of the pfcrt mutant CVIET after two decades of chloroquine disuse in Ghana suggests the return of chloroquine-sensitive parasites. Therapeutic efficacy studies must be done to verify this observation. The opposing trends of sulfadoxine-pyrimethamine molecular markers highlight concern for its use in malaria prophylaxis in pregnancy and children. Molecular surveillance remains vital to mitigating the risk of artemisinin-resistant parasites evolving in malaria-endemic regions.