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medRxiv
MEDRXIV
medRxiv
Cold Spring Harbor Laboratory

10.1101/2024.09.07.24313132
preprint
1
Article
Population Genomics of Plasmodium malariae from Four African Countries
Popkin-Hall Zachary R. http://orcid.org/0000-0002-8308-5294

Carey-Ewend Kelly http://orcid.org/0000-0002-3200-1644

Aghakhanian Farhang http://orcid.org/0000-0002-5491-8293

Oriero Eniyou C. http://orcid.org/0000-0002-7911-6457

Seth Misago D. http://orcid.org/0000-0002-6743-4108

Kashamuka Melchior M. http://orcid.org/0000-0002-3871-1751

Ngasala Billy http://orcid.org/0000-0001-9300-7719

Ali Innocent M. http://orcid.org/0000-0002-1112-6376

Mukomena Eric Sompwe http://orcid.org/0000-0001-7083-4770

Mandara Celine I. http://orcid.org/0000-0003-4317-4425

Kharabora Oksana
Sendor Rachel http://orcid.org/0000-0001-7259-1514

Simkin Alfred http://orcid.org/0000-0001-9408-0053

Amambua-Ngwa Alfred http://orcid.org/0000-0003-4478-3601

Tshefu Antoinette http://orcid.org/0000-0001-7657-6901

Fola Abebe A. http://orcid.org/0000-0001-5392-2859

Ishengoma Deus S. http://orcid.org/0000-0003-2040-3416

Bailey Jeffrey A. http://orcid.org/0000-0002-6899-8204

Parr Jonathan B. http://orcid.org/0000-0002-4465-9830

Lin Jessica T. http://orcid.org/0000-0002-4516-723X

Juliano Jonathan J. http://orcid.org/0000-0002-0591-0850

09 9 2024
2024.09.07.24313132https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://medrxiv.org/lookup/doi/10.1101/2024.09.07.24313132
nihpp-2024.09.07.24313132.pdf
Abstract

Plasmodium malariae is geographically widespread but neglected and may become more prevalent as P. falciparum declines. We completed the largest genomic study of African P. malariae to-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-localized P. falciparum isolates, 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 African P. malariae is recovering from a bottleneck. Altogether, these results suggest that P. malariae is genomically atypical among human Plasmodium spp. and panmictic in Africa.
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