28Emergence of Plasmodium falciparum resistance to antimalarial drugs is currently the primary rationale 29 supporting the development of new and well-tolerated drugs. In 2014-2015, a phase 2b clinical study 30 was conducted to evaluate the efficacy of a single oral dose of Artefenomel (OZ439)-piperaquine (PPQ) 31 in Asian and African patients presenting with uncomplicated falciparum malaria. Blood samples 32 collected before treatment offered the opportunity to investigate the proportion of multidrug resistant 33 parasite genotypes including P. falciparum Kelch13 mutations and copy number variation of both P. 34 falciparum plasmepsin2 (Pfpm2) and P. falciparum multidrug resistance 1 (Pfmdr1) genes. 35Validated Kelch13 resistance mutations including C580Y, I543T, P553L and V568G were only 36 detected in parasites from Vietnamese patients. In Africa, isolates with multiple copies of the Pfmdr1 37 gene were shown to be more frequent than previously reported (21.1%, range from 12.4% in Burkina 38Faso to 27.4% in Uganda). More strikingly, high proportions of isolates with multiple copies of the 39 Pfpm2 gene, associated to PPQ resistance, were frequently observed in the African sites, especially in 40 Burkina Faso and Uganda (>30%). 41 Our findings sharply contrast with the recent description of increased sensitivity to PPQ of Ugandan 42 parasite isolates. This emphasizes the necessity to decipher the genetic background associated with PPQ 43 resistance in Africa by investigating in vitro susceptibilities to PPQ of isolates with multiple copies of 44 the Pfpm2 gene and the urgent need to assess the risk of development of PPQ resistance, along with the 45 efficacy of both current frontline therapies and new antimalarial combinations. 46 47 48 49 50 51 52 Michael Ramharter) and MMV staff involved in study conduct, data collection and reporting (Helen 311 Demarest, Stephan Duparc, Sophie Biguenet). MMV would also like to acknowledge their development 312 partner Sanofi-Aventis.