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

    Fingerprint

    Plasmodium vivax
    Malaysia
    elimination
    Genes
    Chloroquine
    Antimalarials
    Population
    Cambodia
    Thailand
    parasites
    Indonesia
    genome
    cues
    infectious diseases
    loci
    genes
    grade
    drugs
    incidence
    expansion

    Cite this

    Auburn, Sarah ; Benavente, Ernest D. ; Miotto, Olivo ; Pearson, Richard D. ; Amato, Roberto ; Grigg, Matthew J. ; Barber, Bridget E. ; William, Timothy ; Handayuni, Irene ; Marfurt, Jutta ; Trimarsanto, Hidayat ; Noviyanti, Rintis ; Sriprawat, Kanlaya ; Nosten, Francois ; Campino, Susana ; Clark, Taane G. ; Anstey, Nicholas M. ; Kwiatkowski, Dominic P. ; Price, Ric N. / Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. In: Nature Communications. 2018 ; Vol. 9, No. 1. pp. 1-12.
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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.",
    author = "Sarah Auburn and Benavente, {Ernest D.} and Olivo Miotto and Pearson, {Richard D.} and Roberto Amato and Grigg, {Matthew J.} and Barber, {Bridget E.} and Timothy William and Irene Handayuni and Jutta Marfurt and Hidayat Trimarsanto and Rintis Noviyanti and Kanlaya Sriprawat and Francois Nosten and Susana Campino and Clark, {Taane G.} and Anstey, {Nicholas M.} and Kwiatkowski, {Dominic P.} and Price, {Ric N.}",
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    Auburn, S, Benavente, ED, Miotto, O, Pearson, RD, Amato, R, Grigg, MJ, Barber, BE, William, T, Handayuni, I, Marfurt, J, Trimarsanto, H, Noviyanti, R, Sriprawat, K, Nosten, F, Campino, S, Clark, TG, Anstey, NM, Kwiatkowski, DP & Price, RN 2018, 'Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics', Nature Communications, vol. 9, no. 1, 2585, pp. 1-12. https://doi.org/10.1038/s41467-018-04965-4

    Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. / Auburn, Sarah; Benavente, Ernest D.; Miotto, Olivo; Pearson, Richard D.; Amato, Roberto; Grigg, Matthew J.; Barber, Bridget E.; William, Timothy; Handayuni, Irene; Marfurt, Jutta; Trimarsanto, Hidayat; Noviyanti, Rintis; Sriprawat, Kanlaya; Nosten, Francois; Campino, Susana; Clark, Taane G.; Anstey, Nicholas M.; Kwiatkowski, Dominic P.; Price, Ric N.

    In: Nature Communications, Vol. 9, No. 1, 2585, 03.07.2018, p. 1-12.

    Research output: Contribution to journalArticleResearchpeer-review

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    AU - Trimarsanto, Hidayat

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    AU - Nosten, Francois

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    AU - Clark, Taane G.

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