Abdul Rashid Kassim, Priscilla Akuba Younge, Ignatus Nunana Dorvi, Samirah Saiid, Mona-Liza Ebiere Sakyi, Osumanu Ahmed, Albert Yao Kudakpo, Stephen Tetteh Addo, Silas Nkansah Yeboah, Charles Mensah, Isaiah Debrah, Collins M. Morang’a, Dominic S. Y. Amuzu, Gordon A. Awandare, Yaw Aniweh, Lucas Amenga–Etego
Abstract Background In Ghana, artemether-lumefantrine (AL), and artesunate-amodiaquine (AS-AQ) are the main first-line ACTs for uncomplicated malaria, with dihydroartemisinin-piperaquine (DHA-PPQ) as an alternative treatment regimen. Copy Number Polymorphisms (CNPs) in Plasmodium falciparum multidrug resistance 1 ( pfmdr1 ) and plasmepsin 2 ( pfpm2 ) genes, as well as specific pfmdr1 haplotypes have been implicated in resistance to AL and DHA-PPQ partner drugs. Methods This study characterised pfmdr1 and pfpm2 CNPs and pfmdr1 haplotypes in 900 clinical malaria samples across three transmission zones in Ghana. Using a SYBR Green-based Quantitative real-time Polymerase Chain Reaction (qPCR) assay, followed by targeted amplicon sequencing. Results Successful pfmdr1 and pfpm2 amplifications were detected in 32.0% (n = 288) and 27.8% (n = 250) isolates respectively. No significant difference in the prevalence of these gene amplifications was observed across the three eco-epidemiological zones ( pfmdr1 : p = 0.888; pfpm2 : p = 0.081). Furthermore, a weak positive correlation was observed between pfmdr1 and pfpm2 copy numbers (ρ = 0.196), suggesting limited co-selection of these loci. Pfmdr1 haplotype analysis at codons N86Y, Y184F, and D1246Y revealed a high prevalence (55.6%) of the NFD haplotype linked to lumefantrine selection. Interestingly, this haplotype allele was equally prevalent among isolates carrying single or multiple gene copy numbers. Conclusion Taken together, this study observed increased prevalence of pfmdr1 and pfpm2 gene amplification in Ghana. Also, a high frequency of the single mutant NFD pfmdr1 haplotype suggesting ongoing selection pressure potentially driven by widespread AL use in Ghana. In addition, pfpm2 CNP has been associated with piperaquine resistance. These findings provide a critical baseline for ongoing molecular surveillance as an early warning for ACT partner drug resistance in Ghana.