Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

Sarah Auburn, Ernest D. Benavente, Olivo Miotto, Richard D. Pearson, Roberto Amato, Matthew J. Grigg, Bridget E. Barber, Timothy William, Irene Handayuni, Jutta Marfurt, Hidayat Trimarsanto, Rintis Noviyanti, Kanlaya Sriprawat, Francois Nosten, Susana Campino, Taane G. Clark, Nicholas M. Anstey, Dominic P. Kwiatkowski, Ric N. Price

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    Abstract

    The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.

    Original languageEnglish
    Article number2585
    Pages (from-to)1-12
    Number of pages12
    JournalNature Communications
    Volume9
    Issue number1
    DOIs
    Publication statusPublished - 3 Jul 2018

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    Auburn, S., Benavente, E. D., Miotto, O., Pearson, R. D., Amato, R., Grigg, M. J., Barber, B. E., William, T., Handayuni, I., Marfurt, J., Trimarsanto, H., Noviyanti, R., Sriprawat, K., Nosten, F., Campino, S., Clark, T. G., Anstey, N. M., Kwiatkowski, D. P., & Price, R. N. (2018). Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. Nature Communications, 9(1), 1-12. [2585]. https://doi.org/10.1038/s41467-018-04965-4