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Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance

Author

Listed:
  • Gabrielle C. Ngwana-Joseph

    (London School of Hygiene and Tropical Medicine)

  • Jody E. Phelan

    (London School of Hygiene and Tropical Medicine)

  • Emilia Manko

    (London School of Hygiene and Tropical Medicine)

  • Jamille G. Dombrowski

    (London School of Hygiene and Tropical Medicine
    University of São Paulo)

  • Simone Silva Santos

    (Oswaldo Cruz Foundation – Fiocruz)

  • Martha Suarez-Mutis

    (Oswaldo Cruz Foundation – Fiocruz)

  • Gabriel Vélez-Tobón

    (Universidad de Antioquia)

  • Alberto Tobón Castaño

    (Universidad de Antioquia)

  • Ricardo Luiz Dantas Machado

    (Universidade Federal Fluminense)

  • Claudio R. F. Marinho

    (University of São Paulo)

  • Debbie Nolder

    (London School of Hygiene and Tropical Medicine)

  • François Nosten

    (University of Oxford
    Mahidol University)

  • Colin J. Sutherland

    (London School of Hygiene and Tropical Medicine
    London School of Hygiene and Tropical Medicine)

  • Susana Campino

    (London School of Hygiene and Tropical Medicine)

  • Taane G. Clark

    (London School of Hygiene and Tropical Medicine
    London School of Hygiene and Tropical Medicine)

Abstract

Increasing reports of chloroquine resistance (CQR) in Plasmodium vivax endemic regions have led to several countries, including Indonesia, to adopt dihydroarteminsin-piperaquine instead. However, the molecular drivers of CQR remain unclear. Using a genome-wide approach, we perform a genomic analysis of 1534 P. vivax isolates across 29 endemic countries, detailing population structure, patterns of relatedness, selection, and resistance profiling, providing insights into potential drivers of CQR. Selective sweeps in a locus proximal to pvmdr1, a putative marker for CQR, along with transcriptional regulation genes, distinguish isolates from Indonesia from those in regions where chloroquine remains highly effective. In 106 isolates from Indonesian Papua, the epicentre of CQR, we observe an increasing prevalence of novel SNPs in the candidate resistance gene pvmrp1 since the introduction of dihydroartemisinin-piperaquine. Overall, we provide novel markers for resistance surveillance, supported by evidence of regions under recent directional selection and temporal analysis in this continually evolving parasite.

Suggested Citation

  • Gabrielle C. Ngwana-Joseph & Jody E. Phelan & Emilia Manko & Jamille G. Dombrowski & Simone Silva Santos & Martha Suarez-Mutis & Gabriel Vélez-Tobón & Alberto Tobón Castaño & Ricardo Luiz Dantas Macha, 2024. "Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54964-x
    DOI: 10.1038/s41467-024-54964-x
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    References listed on IDEAS

    as
    1. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
    2. John C. Wootton & Xiaorong Feng & Michael T. Ferdig & Roland A. Cooper & Jianbing Mu & Dror I. Baruch & Alan J. Magill & Xin-zhuan Su, 2002. "Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum," Nature, Nature, vol. 418(6895), pages 320-323, July.
    3. Lucas E Buyon & Ana Maria Santamaria & Angela M Early & Mario Quijada & Itza Barahona & Jose Lasso & Mario Avila & Sarah K Volkman & Matthias Marti & Daniel E Neafsey & Nicanor Obaldia III, 2020. "Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination," PLOS Neglected Tropical Diseases, Public Library of Science, vol. 14(12), pages 1-16, December.
    4. Pardis C. Sabeti & Patrick Varilly & Ben Fry & Jason Lohmueller & Elizabeth Hostetter & Chris Cotsapas & Xiaohui Xie & Elizabeth H. Byrne & Steven A. McCarroll & Rachelle Gaudet & Stephen F. Schaffner, 2007. "Genome-wide detection and characterization of positive selection in human populations," Nature, Nature, vol. 449(7164), pages 913-918, October.
    5. Ernest Diez Benavente & Emilia Manko & Jody Phelan & Monica Campos & Debbie Nolder & Diana Fernandez & Gabriel Velez-Tobon & Alberto Tobón Castaño & Jamille G. Dombrowski & Claudio R. F. Marinho & Ann, 2021. "Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
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