Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages

Mariana Kleinecke, Edwin Sutanto, Angela Rumaseb, Kian Soon Hoon, Hidayat Trimarsanto, Ashley Osborne, Paulo Manrique, Trent Peters, David Hawkes, Ernest Diez Benavente, Georgia Whitton, Sasha V. Siegel, Richard D. Pearson, Roberto Amato, Anjana Rai, Nguyen Thanh Thuy Nhien, Hoang Chau Nguyen, Ashenafi Assefa, Tamiru S. Degaga, Dagimawie Tadesse Abate, Awab Ghulam Rahim, Ayodhia Pitaloka Pasaribu, Inge Sutanto, Mohammad Shafiul Alam, Zuleima Pava, Tatiana Lopera-Mesa, Diego Echeverry, Tim William, Nicholas M. Anstey, Matthew J. Grigg, Nicholas P. Day, Nicholas J. White, Dominic P. Kwiatkowski, Aimee R. Taylor, Rintis Noviyanti, Daniel Neafsey, Ric N. Price and Sarah Auburn ()
Additional contact information
Mariana Kleinecke: Menzies School of Health Research and Charles Darwin University
Edwin Sutanto: Exeins Health Initiative
Angela Rumaseb: Menzies School of Health Research and Charles Darwin University
Kian Soon Hoon: Menzies School of Health Research and Charles Darwin University
Hidayat Trimarsanto: Menzies School of Health Research and Charles Darwin University
Ashley Osborne: Menzies School of Health Research and Charles Darwin University
Paulo Manrique: Harvard T.H. Chan School of Public Health
Trent Peters: Australian Genome Research Facility
David Hawkes: Australian Genome Research Facility
Ernest Diez Benavente: University Medical Center Utrecht
Georgia Whitton: Wellcome Sanger Institute
Sasha V. Siegel: Wellcome Sanger Institute
Richard D. Pearson: Wellcome Sanger Institute
Roberto Amato: Wellcome Sanger Institute
Anjana Rai: Menzies School of Health Research and Charles Darwin University
Nguyen Thanh Thuy Nhien: Hospital for Tropical Diseases
Hoang Chau Nguyen: Hospital for Tropical Diseases
Ashenafi Assefa: Ethiopian Public Health Institute
Tamiru S. Degaga: Arba Minch University
Dagimawie Tadesse Abate: Arba Minch University
Awab Ghulam Rahim: Afghan International Islamic University
Ayodhia Pitaloka Pasaribu: Universitas Sumatera Utara
Inge Sutanto: University of Indonesia
Mohammad Shafiul Alam: b)
Zuleima Pava: Menzies School of Health Research and Charles Darwin University
Tatiana Lopera-Mesa: Universidad de Antioquia
Diego Echeverry: Universidad del Valle
Tim William: Menzies School of Health Research and Charles Darwin University
Nicholas M. Anstey: Menzies School of Health Research and Charles Darwin University
Matthew J. Grigg: Menzies School of Health Research and Charles Darwin University
Nicholas P. Day: University of Oxford
Nicholas J. White: University of Oxford
Dominic P. Kwiatkowski: Wellcome Sanger Institute
Aimee R. Taylor: Infectious Disease Epidemiology and Analytics Unit
Rintis Noviyanti: National Research and Innovation Agency
Daniel Neafsey: Harvard T.H. Chan School of Public Health
Ric N. Price: Menzies School of Health Research and Charles Darwin University
Sarah Auburn: Menzies School of Health Research and Charles Darwin University

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Plasmodium vivax elimination is challenged by dormant liver stages (hypnozoites) that can reactivate months after initial infection resulting in relapses. Relapsing infections confound antimalarial clinical efficacy trials due to the inability to distinguish between recurrences arising from blood-stage treatment failure (recrudescence), reinfection or relapse. Genetic relatedness of paired parasite isolates, measured by identity-by-descent (IBD), can provide important information on whether individuals have had single or multiple mosquito inoculations, thus informing on recurrence origin. We developed a high-throughput amplicon sequencing assay comprising 93 multi-SNP (microhaplotype) markers to determine IBD between P. vivax clinical isolates. The assay was evaluated in 745 global infections, including 128 infection pairs from a randomized controlled trial (RCT) (ClinicalTrials.gov NCT01680406). Simulations demonstrate low error in pairwise IBD estimation at the panel (RMSE

Date: 2025
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DOI: 10.1038/s41467-025-62357-x

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