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High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes

Author

Listed:
  • Zachary R. Popkin-Hall

    (University of North Carolina)

  • Karamoko Niaré

    (Brown University)

  • Rebecca Crudale

    (Brown University)

  • Alfred Simkin

    (Brown University)

  • Abebe A. Fola

    (Brown University)

  • Juan F. Sanchez

    (U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH))

  • Danielle L. Pannebaker

    (U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH))

  • David J. Giesbrecht

    (Brown University)

  • Isaac E. Kim

    (The Warren Alpert Medical School of Brown University
    Brown University)

  • Özkan Aydemir

    (UMass Chan Medical School)

  • Jeffrey A. Bailey

    (Brown University
    Brown University)

  • Hugo O. Valdivia

    (U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH))

  • Jonathan J. Juliano

    (University of North Carolina
    University of North Carolina at Chapel Hill
    University of North Carolina at Chapel Hill
    University of North Carolina at Chapel Hill)

Abstract

Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for P. vivax. Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD[identity by descent]>0.99), copy number variation in Pvdbp and multiple Pvrbps, mutations in antimalarial resistance orthologs, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of P. vivax transmission.

Suggested Citation

  • Zachary R. Popkin-Hall & Karamoko Niaré & Rebecca Crudale & Alfred Simkin & Abebe A. Fola & Juan F. Sanchez & Danielle L. Pannebaker & David J. Giesbrecht & Isaac E. Kim & Özkan Aydemir & Jeffrey A. B, 2024. "High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54731-y
    DOI: 10.1038/s41467-024-54731-y
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    References listed on IDEAS

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    1. Nicholas F. Brazeau & Cedar L. Mitchell & Andrew P. Morgan & Molly Deutsch-Feldman & Oliver John Watson & Kyaw L. Thwai & Pere Gelabert & Lucy Dorp & Corinna Y. Keeler & Andreea Waltmann & Michael Emc, 2021. "The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    2. Sasha V. Siegel & Hidayat Trimarsanto & Roberto Amato & Kathryn Murie & Aimee R. Taylor & Edwin Sutanto & Mariana Kleinecke & Georgia Whitton & James A. Watson & Mallika Imwong & Ashenafi Assefa & Awa, 2024. "Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Robert Verity & Ozkan Aydemir & Nicholas F. Brazeau & Oliver J. Watson & Nicholas J. Hathaway & Melchior Kashamuka Mwandagalirwa & Patrick W. Marsh & Kyaw Thwai & Travis Fulton & Madeline Denton & And, 2020. "The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    4. 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 , 2018. "Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
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