Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates

Harold Ocholla, Mark D. Preston, Mwapatsa Mipando, Anja T.R. Jensen, Susana Campino, Bronwyn Macinnis, Daniel Alcock, Anja Terlouw, Issaka Zongo, Jean Bosco Oudraogo, Abdoulaye A. Djimde, Samuel Assefa, Ogobara K. Doumbo, Steffen Borrmann, Alexis Nzila, Kevin Marsh, Rick M. Fairhurst, Francois Nosten, Tim J.C. Anderson, Dominic P. KwiatkowskiAlister Craig, Taane G. Clark, Jacqui Montgomery

    Research output: Contribution to journalArticle

    24 Scopus citations

    Abstract

    Background: Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. Methods: We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. Results. High genetic diversity (π = 2.4 × 10-4), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known drugresistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. Conclusions: The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.

    Original languageEnglish (US)
    Pages (from-to)1991-2000
    Number of pages10
    JournalJournal of Infectious Diseases
    Volume210
    Issue number12
    DOIs
    StatePublished - 2014

    Keywords

    • Genetic epidemiology
    • Genomes
    • Malawi
    • Plasmodium falciparum

    ASJC Scopus subject areas

    • Immunology and Allergy
    • Infectious Diseases

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    Ocholla, H., Preston, M. D., Mipando, M., Jensen, A. T. R., Campino, S., Macinnis, B., Alcock, D., Terlouw, A., Zongo, I., Oudraogo, J. B., Djimde, A. A., Assefa, S., Doumbo, O. K., Borrmann, S., Nzila, A., Marsh, K., Fairhurst, R. M., Nosten, F., Anderson, T. J. C., ... Montgomery, J. (2014). Whole-genome scans provide evidence of adaptive evolution in malawian Plasmodium falciparum isolates. Journal of Infectious Diseases, 210(12), 1991-2000. https://doi.org/10.1093/infdis/jiu349