Zeleke AJ, Fola AA, Tollefson GA, Niaré K, Leonetti A, Taropawala O, Marglous J, Crudale R, Brhane BG, Assefa A, Kiyuka P, Parr JB, Hailu A, Tegegne MA, Bailey JA
PLoS Pathog. 2025;21
The rise of antimalarial drug-resistant Plasmodium falciparum threatens malaria elimination efforts. Mutations in the gene kelch13 (k13) confer artemisinin partial resistance (ART-R), compromising the efficacy of frontline artemisinin-based combination therapies (ACTs). The validated mutation k13 R622I has emerged and expanded rapidly in the Horn of Africa. We conducted a year-long genomic surveillance study in Gondar Zuria and Tach Armachiho, two ecologically distinct districts in northwestern Ethiopia where R622I was first identified. A total of 903 P. falciparum infections were sequenced using molecular inversion probe (MIP) panels targeting major drug resistance mutations and genome-wide informative SNPs. The R622I mutation was found in 44.3% of samples, more frequent in Gondar Zuria than Tach Armachiho (52% vs. 35%; p < 0.001), and persisted year-round in nearly all sites, indicating stable transmission with minimal seasonal variation. Histidine-rich protein 2 (HRP2) based rapid diagnostic test (RDT) negativity was also prevalent (39.3%), with significant district-level variation (48.7% vs. 27.6%; p < 0.001). Concerningly, R622I and HRP2-RDT co-occured in 22% of samples, higher in Gondar Zuria than in Tach Armachiho (28.9% vs. 12.9%; p < 0.001). Overall, HRP2-RDT negativity was significantly more common among R622I mutant parasites than wild-type (48.3% vs. 30.7%; p < 0.05). The k13 C580Y mutation was also detected at very low frequency (0.4%) in Gondar Zuria, representing the first report of this mutation in the Horn of Africa. Long-read whole-genome sequencing showed k13 flanking haplotypes of C580Y isolates were distinct from Southeast Asian lineages, suggesting a local, de novo emergence of African origin. These findings highlight the increasing prevalence and types of ART-R mutations, persistence of k13 R622I and its increasing association with HRP2-RDT negativity, representing a double threat to malaria control and elimination efforts.
