Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal

Stephen F. Schaffner, Aida Badiane, Akanksha Khorgade, Medoune Ndiop, Jules Gomis, Wesley Wong, Yaye Die Ndiaye, Younouss Diedhiou, Julie Thwing, Mame Cheikh Seck, Angela Early, Mouhamad Sy, Awa Deme, Mamadou Alpha Diallo, Ngayo Sy, Aita Sene, Tolla Ndiaye, Djiby Sow, Baba Dieye, Ibrahima Mbaye Ndiaye, Amy Gaye, Aliou Ndiaye, Katherine E. Battle, Joshua L. Proctor, Caitlin Bever, Fatou Ba Fall, Ibrahima Diallo, Seynabou Gaye, Doudou Sene, Daniel L. Hartl, Dyann F. Wirth, Bronwyn MacInnis, Daouda Ndiaye and Sarah K. Volkman ()
Additional contact information
Stephen F. Schaffner: The Broad Institute
Aida Badiane: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Akanksha Khorgade: The Broad Institute
Medoune Ndiop: Programme National de Lutte Contre le Paludisme (PNLP)
Jules Gomis: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Wesley Wong: Harvard T. H. Chan School of Public Health
Yaye Die Ndiaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Younouss Diedhiou: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Julie Thwing: Centers for Disease Control and Prevention
Mame Cheikh Seck: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Angela Early: The Broad Institute
Mouhamad Sy: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Awa Deme: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Mamadou Alpha Diallo: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Ngayo Sy: Section de Lutte Anti-Parasitaire (SLAP) Clinic
Aita Sene: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Tolla Ndiaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Djiby Sow: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Baba Dieye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Ibrahima Mbaye Ndiaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Amy Gaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Aliou Ndiaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Katherine E. Battle: Bill and Melinda Gates Foundation
Joshua L. Proctor: Bill and Melinda Gates Foundation
Caitlin Bever: Bill and Melinda Gates Foundation
Fatou Ba Fall: Programme National de Lutte Contre le Paludisme (PNLP)
Ibrahima Diallo: Programme National de Lutte Contre le Paludisme (PNLP)
Seynabou Gaye: Programme National de Lutte Contre le Paludisme (PNLP)
Doudou Sene: Programme National de Lutte Contre le Paludisme (PNLP)
Daniel L. Hartl: Harvard University
Dyann F. Wirth: The Broad Institute
Bronwyn MacInnis: The Broad Institute
Daouda Ndiaye: de Formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
Sarah K. Volkman: The Broad Institute

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study’s goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.

Date: 2023
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DOI: 10.1038/s41467-023-43087-4

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