Genomic analysis of local variation and recent evolution in Plasmodium vivax

Richard D Pearson, Roberto Amato, Sarah Auburn, Olivo Miotto, Jacob Almagro-Garcia, Chanaki Amaratunga, Seila Suon, Sivanna Mao, Rintis Noviyanti, Hidayat Trimarsanto, Jutta Marfurt, Nicholas M. Anstey, Timothy WILLIAM, MacIej F. Boni, Christiane Dolecek, Hien Tinh Tran, Nicholas J White, Pascal Michon, Peter Siba, Livingstone TavulGabrielle Harrison, Alyssa E. Barry, Ivo Mueller, Marcelo U. Ferreira, Nadira Karunaweera, Milijaona Randrianarivelojosia, Qi Gao, Christina Hubbart, Lee Hart, Ben Jeffery, Eleanor Drury, Daniel Mead, Mihir Kekre, Susana Campino, Magnus Manske, Victoria J. Cornelius, Bronwyn MacInnis, Kirk A. Rockett, Alistair Miles, Julian C. Rayner, Rick M. Fairhurst, Francois Nosten, Ric N. Price, Dominic P. Kwiatkowski

    Research output: Contribution to journalArticle

    Abstract

    The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for the elimination of malaria. To characterize the genetic diversity of this parasite in individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region and analyzed data on >300,000 SNPs and nine regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at new loci, and these varied markedly between geographical locations. These findings demonstrate a dynamic landscape of local evolutionary adaptation in the parasite population and provide a foundation for genomic surveillance to guide effective strategies for control and elimination of P. vivax.

    Original languageEnglish
    Pages (from-to)959-964
    Number of pages6
    JournalNature Genetics
    Volume48
    Issue number8
    DOIs
    Publication statusPublished - 1 Aug 2016

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  • Cite this

    Pearson, R. D., Amato, R., Auburn, S., Miotto, O., Almagro-Garcia, J., Amaratunga, C., Suon, S., Mao, S., Noviyanti, R., Trimarsanto, H., Marfurt, J., Anstey, N. M., WILLIAM, T., Boni, M. F., Dolecek, C., Tran, H. T., White, N. J., Michon, P., Siba, P., ... Kwiatkowski, D. P. (2016). Genomic analysis of local variation and recent evolution in Plasmodium vivax. Nature Genetics, 48(8), 959-964. https://doi.org/10.1038/ng.3599