Population Genomics ofPlasmodium malariaefrom Four African Countries

Abstract

AbstractPlasmodium malariaeis geographically widespread but neglected and may become more prevalent asP. falciparumdeclines. We completed the largest genomic study of AfricanP. malariaeto-date by performing hybrid capture and sequencing of 77 isolates from Cameroon (n=7), the Democratic Republic of the Congo (n=16), Nigeria (n=4), and Tanzania (n=50) collected between 2015 and 2021. There is no evidence of geographic population structure. Nucleotide diversity was significantly lower than in co-localizedP. falciparumisolates, while linkage disequilibrium was significantly higher. Genome-wide selection scans identified no erythrocyte invasion ligands or antimalarial resistance orthologs as top hits; however, targeted analyses of these loci revealed evidence of selective sweeps around four erythrocyte invasion ligands and six antimalarial resistance orthologs. Demographic inference modeling suggests that AfricanP. malariaeis recovering from a bottleneck. Altogether, these results suggest thatP. malariaeis genomically atypical among humanPlasmodiumspp. and panmictic in Africa.