Mutations in the Plasmodium falciparum K13-propeller domain have recently been shown to be important determinants of artemisinin resistance in Southeast Asia. This study investigated the prevalence of K13-propeller polymorphisms across sub-Saharan Africa. A total of 1212 P. falciparum samples collected from 12 countries were sequenced. None of the K13-propeller mutations previously reported in Southeast Asia were found, but 22 unique mutations were detected, of which 7 were nonsynonymous. Allele frequencies ranged between 1% and 3%. Three mutations were observed in >1 country, and the A578S was present in parasites from 5 countries. This study provides the baseline prevalence of K13-propeller mutations in sub-Saharan Africa.

Elucidation of the evolutionary history and interrelatedness of Plasmodium species that infect humans has been hampered by a lack of genetic information for three human-infective species: P. malariae and two P. ovale species (P. o. curtisi and P. o. wallikeri)1. These species are prevalent across most regions in which malaria is endemic2,3 and are often undetectable by light microscopy4, rendering their study in human populations difficult5. The exact evolutionary relationship of these species to the other human-infective species has been contested6,7. Using a new reference genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to accurately place these species within the Plasmodium phylogeny. Sequencing of a P. malariae relative that infects chimpanzees reveals similar signatures of selection in the P. malariae lineage to another Plasmodium lineage shown to be capable of colonization of both human and chimpanzee hosts. Molecular dating suggests that these host adaptations occurred over similar evolutionary timescales. In addition to the core genome that is conserved between species, differences in gene content can be linked to their specific biology. The genome suggests that P. malariae expresses a family of heterodimeric proteins on its surface that have structural similarities to a protein crucial for invasion of red blood cells. The data presented here provide insight into the evolution of the Plasmodium genus as a whole.

Plasmodium falciparum remains a relevant global health pathogen with high levels of genomic variation and gene flow that could undermine malaria elimination strategies, especially in the high burden regions of Africa. Infections with P. falciparum remain complex across most of sub-Saharan Africa. SNP variants from 2263 isolates from 24 malaria endemic settings within 15 African countries classified into western, central and eastern ancestry, plus a divergent Ethiopian population. The parasite populations are interbred and share genomic haplotypes especially across drug resistance loci. Haplotypes across drug resistance associated loci showed the strongest recent identity-by-descent between populations and endogenous haplotypes have spread to and from all populations. A recent signature of selection on chromosome 12 with candidate resistance loci against artemisinin derivatives is evident in Ghana and Malawi. Such selection and emerging sub-structure may affect intervention strategies and the efficacy of drugs and vaccines for malaria elimination. Formatted: Font: +Body (Calibri) Formatted: Line spacing: Multiple 1.15 li