Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages
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 < 0.12) and IBD-based networks illustrate strong clustering by geography. IBD analysis in the RCT demonstrates a lower frequency of suspected relapses or recrudescence in patients treated with primaquine compared to those without primaquine; the impact is greater when paired with chloroquine than with artemether-lumefantrine. Our results demonstrate the potential to derive new information on P. vivax treatment and transmission using IBD generated by amplicon sequencing data that can be further improved with time-to-event models.
Authors
- Edwin Sutanto (ORCID: https://orcid.org/0000-0002-2997-4648)
- Richard D. Pearson (ORCID: https://orcid.org/0000-0002-7386-3566)
- Nguyễn Hoàng Châu (ORCID: https://orcid.org/0000-0002-7826-3850)
- Thuy-Nhien Nguyen (ORCID: https://orcid.org/0000-0002-4101-5706)
- Aimee R. Taylor (ORCID: https://orcid.org/0000-0002-2337-8992)
- Mohammad Shafiul Alam (ORCID: https://orcid.org/0000-0001-8330-5499)
- Anjana Rai (ORCID: https://orcid.org/0000-0001-7430-3424)
- Ric N. Price (ORCID: https://orcid.org/0000-0003-2000-2874)
- Ghulam Rahim Awab (ORCID: https://orcid.org/0000-0002-7380-1197)
- Sarah Auburn (ORCID: https://orcid.org/0000-0002-4638-536X)
- Dagimawie Tadesse Abate (ORCID: https://orcid.org/0000-0002-3770-1957)
- Timothy William (ORCID: https://orcid.org/0000-0002-2195-6736)
- Angela Rumaseb (ORCID: https://orcid.org/0000-0003-3939-0678)
- Paulo Manrique (ORCID: https://orcid.org/0000-0003-3412-0249)
- Rintis Noviyanti (ORCID: https://orcid.org/0000-0003-1383-3274)
- Tamiru Degaga (ORCID: https://orcid.org/0000-0002-0976-5558)
- Matthew J. Grigg (ORCID: https://orcid.org/0000-0001-9914-8352)
- Ayodhia Pitaloka Pasaribu (ORCID: https://orcid.org/0000-0002-3830-8073)
- Ashenafi Assefa (ORCID: https://orcid.org/0000-0001-6093-6685)
- Ernest Diez Benavente (ORCID: https://orcid.org/0000-0002-4313-4290)
- Tatiana M. Lopera-Mesa (ORCID: https://orcid.org/0000-0002-9401-2779)
- Inge Sutanto (ORCID: https://orcid.org/0000-0003-2488-5133)
- Daniel E. Neafsey (ORCID: https://orcid.org/0000-0002-1665-9323)
- Diego Echeverri (ORCID: https://orcid.org/0000-0003-0301-4478)
- Trent Peters
- Ashley Osborne (ORCID: https://orcid.org/0000-0002-2804-8298)
- Zuleima Pava (ORCID: https://orcid.org/0000-0002-4802-0647)
- Roberto Amato (ORCID: https://orcid.org/0000-0001-8633-9221)
- Dominic Kwiatkowski (ORCID: https://orcid.org/0000-0002-5023-0176)
- Georgia Whitton (ORCID: https://orcid.org/0009-0001-9456-6376)
- Hidayat Trimarsanto (ORCID: https://orcid.org/0000-0003-2436-8283)
- Nicholas John White (ORCID: https://orcid.org/0000-0002-1897-1978)
- Sasha V. Siegel (ORCID: https://orcid.org/0000-0002-1458-4348)
- Mariana Kleinecke
- David Hawkes
- Kian Soon Hoon (ORCID: https://orcid.org/0000-0002-2310-3403)
- Nicholas P. J. Day
- Nicholas M. Anstey
Institutions
- Broad Institute (US)
- Harvard University (US)
- Institut Pasteur (FR)
- International Centre for Diarrhoeal Disease Research (BD)
- Mahidol University (TH)
- Universitas Sumatera Utara (ID)
- Angkor Hospital for Children (KH)
- Eijkman Institute for Molecular Biology (ID)
- Wellcome Sanger Institute (GB)
- University of Indonesia (ID)
- Charles Darwin University (AU)
- University Medical Center Utrecht (NL)
- Universidad de Antioquia (CO)
- University of Oxford (GB)
- Menzies School of Health Research (AU)
- Ethiopian Public Health Institute (ET)
- Mahidol Oxford Tropical Medicine Research Unit (TH)
- Oxford University Clinical Research Unit (VN)
- AGRF Ltd (AU)
- Hospital for Tropical Diseases (VN)
- Queen Elizabeth Hospital (MY)
- Arba Minch University (ET)
- National Research and Innovation Agency (ID)
- Universidad del Valle (CO)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-05
- DOI
- https://doi.org/10.1038/s41467-025-62357-x
- Citations
- 8
- Primary Topic
- Vector-borne infectious diseases
- Type
- article
- Field-Weighted Citation Impact
- 16.38
Funders
- Bill and Melinda Gates Foundation
- Wellcome Trust
- Menzies School of Health Research
- Department for International Development
- Medical Research Council
- National Health and Medical Research Council