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<p>Abstract</p> <p>Background</p> <p>Atovaquone is part of the antimalarial drug combination atovaquone-proguanil (Malarone^®) and inhibits the cytochrome bc₁complex of the electron transport chain in <it>Plasmodium </it>spp. Molecular modelling showed that amino acid mutations are clustered around a putative atovaquone-binding site resulting in a reduced binding affinity of atovaquone for plasmodial <it>cytochrome b</it>, thus resulting in drug resistance.</p> <p>Methods</p> <p>The prevalence of <it>cytochrome b </it>point mutations possibly conferring atovaquone resistance in <it>Plasmodium falciparum </it>isolates in atovaquone treatment-naïve patient cohorts from Lambaréné, Gabon and from South Western Ethiopia was assessed.</p> <p>Results</p> <p>Four/40 (10%) mutant types (four different single polymorphisms, one leading to an amino acid change from M to I in a single case) in Gabonese isolates, but all 141/141 isolates were wild type in Ethiopia were found.</p> <p>Conclusion</p> <p>In the absence of drug pressure, spontaneous and possibly resistance-conferring mutations are rare.</p>