Artemisinin resistance in Plasmodium falciparum is associated with nonsynonymous mutations in the Kelch 13 ( K13 ) propeller domain. We found that 12.1% (8/66) of clinical P. falciparum isolates from Huye district, Rwanda, exhibited K13 mutations, including R561H, a validated resistance marker. K13 mutations appear to be increasing in this region.

Plasmodium falciparum multidrug resistance-1 gene ( pfmdr1 ) polymorphisms associate with altered antimalarial susceptibility. Between 2010 and 2018/19, we observed that the prevalence of the wildtype allele N86 and the wildtype combination NYD increased ten-fold (4% versus 40%) and more than two-fold (18% versus 44%), respectively. Haplotypes other than NYD or NFD declined by up to >90%. Our molecular data suggest the pfmdr1 pattern to have shifted towards one associated with artemether-lumefantrine resistance.

Plasmodium vivax is the second-most common malaria pathogen globally, but is considered very rare in the predominantly Duffy-negative sub-Saharan African population. In 259 malaria patients from highland southern Rwanda, we assessed Plasmodium species and Duffy blood group status by polymerase chain reaction (PCR). Plasmodium falciparum, P. vivax, Plasmodium malariae, and Plasmodium ovale were seen in 90.7%, 8.1%, 11.6%, and 5.0%, respectively. Plasmodium vivax occurred more frequently as a monoinfection than in combination with P. falciparum. All P. vivax–infected individuals showed heterozygous Duffy positivity, whereas this was the case for only 3.1% of patients with P. falciparum monoinfection and malaria-negative control subjects (P < 0.01). Based on PCR diagnosis, P. vivax is not rare in southern Rwanda. All episodes of P. vivax were observed in heterozygous Duffy-positive patients, whereas elsewhere in Africa, P. vivax is also reported in Duffy-negative individuals. Refined mapping of Plasmodium species is required to establish control and elimination strategies including all malaria species.