Population genomics of Plasmodium ovale species in sub-Saharan Africa

Kelly Carey-Ewend; Zachary R. Popkin-Hall; Alfred Simkin; Meredith Muller; Christopher M. Hennelly; Wenqiao He; Kara A. Moser; Claudia Gaither; Karamoko Niaré; Farhang F. Aghakhanian; Sindew Mekasha Feleke; Bokretsion Gidey Brhane; Fernandine Phanzu; Kashamuka Mwandagalirwa; Özkan Aydemir; Colin J. Sutherland; Deus S. Ishengoma; Innocent Mbulli Ali; Billy Ngasala; Albert Ntumba Kalonji; Antoinette Kitoto Tshefu; Jonathan B. Parr; Jeffrey A. Bailey; Jonathan J. Juliano; Jessica T. Lin

doi:10.1101/2024.04.10.588912

GenomicsbioRxivApr 10, 2024

Preprint

Population genomics of Plasmodium ovale species in sub-Saharan Africa

Kelly Carey-Ewend iD, Zachary R. Popkin-Hall iD, Alfred Simkin iD, Meredith Muller, Christopher M. Hennelly iD, Wenqiao He iD, Kara A. Moser iD, Claudia Gaither iD, Karamoko Niaré iD, Farhang F. Aghakhanian iD, Sindew Mekasha Feleke iD, Bokretsion Gidey Brhane iD, Fernandine Phanzu, Kashamuka Mwandagalirwa iD, Özkan Aydemir iD, Colin J. Sutherland iD, Deus S. Ishengoma iD, Innocent Mbulli Ali iD, Billy Ngasala iD, Albert Ntumba Kalonji iD, Antoinette Kitoto Tshefu iD, Jonathan B. Parr iD, Jeffrey A. Bailey iD, Jonathan J. Juliano iD, Jessica T. Lin iD

Abstract

Plasmodium ovale curtisi (Poc) and Plasmodium ovale wallikeri (Pow) are relapsing malaria parasites endemic to Africa and Asia that were previously thought to represent a single species. Amid increasing detection of ovale malaria in sub-Saharan Africa, we performed a population genomic study of both species across the continent. We conducted whole-genome sequencing of 25 isolates from Central and East Africa and analyzed them alongside 20 previously published African genomes. Isolates were predominantly monoclonal (43/45), with their genetic similarity aligning with geography. Pow showed lower average nucleotide diversity (1.8x10-4) across the genome compared to Poc (3.0x10-4) (p < 0.0001). Signatures of selective sweeps involving the dihydrofolate reductase gene were found in both species, as were signs of balancing selection at the merozoite surface protein 1 gene. Differences in the nucleotide diversity of Poc and Pow may reflect unique demographic history, even as similar selective forces facilitate their resilience to malaria control interventions.

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