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Clinical Research and Public HealthIn-Press PreviewInfectious diseaseMicrobiologyPublic Health Open Access | 10.1172/jci.insight.196322

Population genomics of Plasmodium malariae from four African countries

Zachary R. Popkin-Hall,1 Kelly Carey-Ewend,2 Farhang Aghakhanian,1 Eniyou C. Oriero,3 Misago D. Seth,4 Melchior M. Kashamuka,5 Billy Ngasala,6 Innocent M. Ali,7 Eric Mukomena SOMPWE,8 Celine I. Mandara,4 Oksana Kharabora,1 Rachel Sendor,2 Alfred Simkin,9 Alfred Amambua-Ngwa,3 Antoinette Tshefu,5 Abebe A. Fola,9 Deus S. Ishengoma,4 Jeffrey A. Bailey,9 Jonathan B. Parr,1 Jessica T. Lin,1 and Jonathan J. Juliano1

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Popkin-Hall, Z. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Carey-Ewend, K. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Aghakhanian, F. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Oriero, E. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Seth, M. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Kashamuka, M. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Ngasala, B. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Ali, I. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Mukomena SOMPWE, E. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Mandara, C. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Kharabora, O. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Sendor, R. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Simkin, A. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Amambua-Ngwa, A. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Tshefu, A. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Fola, A. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Ishengoma, D. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Bailey, J. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Parr, J. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Lin, J. in: PubMed | Google Scholar

1Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, United States of America

2Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, United States of America

3Disease Control and Elimination Theme, Medical Research Council Unit The Gambia at LSHTM, Fajara, Gambia

4National Institute for Medical Research, Dar es Salaam, Tanzania, United Republic of

5Kinshasa School of Public Health, Kinshasa, Congo

6Muhimbili University of Health and Allied Sciences, Bagamoyo, Tanzania, United Republic of

7Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon

8Programme nationale de lutte contre le paludism, Congo

9Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States of America

Find articles by Juliano, J. in: PubMed | Google Scholar

Published May 5, 2026 - More info

JCI Insight. https://doi.org/10.1172/jci.insight.196322.
Copyright © 2026, Popkin-Hall et al. This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Published May 5, 2026 - Version history
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Abstract

BACKGROUND. Malaria caused by Plasmodium malariae is geographically widespread and sometimes associated with prolonged infection, yet little is known about its genomic epidemiology.

METHODS. We performed hybrid capture and whole genome sequencing of 77 isolates collected from Cameroon (n=7), the Democratic Republic of the Congo (n=16), Nigeria (n=4), and Tanzania (n=50) between 2015 and 2021, and analyzing parasite genetic population structure and demography.

RESULTS. 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.

CONCLUSION.P. malariae is genomically atypical among human Plasmodium spp. and lacks strong population structure in Africa. The low diversity has potential impacts on understanding persistent versus new infection through genomic epidemiology.

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  • Version 1 (May 5, 2026): In-Press Preview
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