Multiple adaptive trajectories shape antimalarial resistance evolution in Ethiopian Plasmodium falciparum

Plasmodium falciparum malaria continues to impose a substantial public health burden across sub-Saharan Africa, with Ethiopia experiencing a recent resurgence in malaria cases. We analysed whole genome data from 120 P. falciparum isolates collected in 2024 across five ecologically and epidemiologically diverse transmission settings in Ethiopia and placed these in the context of 1,220 publicly available genomes. Parasite populations were highly structured within Ethiopia, while Horn of Africa isolates formed a genetically distinct regional cluster relative to East and West African populations. We identified evidence of recent positive selection surrounding the artemisinin resistance associated PfK13 R622I variant and detected co-occurrence with Pfcrt mutations together with recurrent selection signals at genes within the PfK13-associated haemoglobin endocytosis pathway, including Pfmca2, Pfkic7, Pfkic8 and Pfkic9. We further observed the emergence of the PfPX1 D384A-PIN haplotype, with shared identity-by-descent linking Ethiopian and Ugandan carriers, supporting a recent introduction followed by local selection. Widespread Pfhrp2/3 deletions occurred on diverse genetic backgrounds. Together, these findings reveal a complex adaptive landscape shaped by antimalarial and diagnostic selection pressures and suggest that parasite evolution in the Horn of Africa proceeds through multiple adaptive trajectories, rather than through the spread of a single dominant lineage.