Genetic surveillance of Plasmodium falciparum populations following treatment policy revisions in the Greater Mekong Subregion

Varanya Wasakul, Tess D. Verschuuren, Nguyen Thuy-Nhien, Ethan Booth, Huynh Hong Quang, Ngo Duc Thang, Keobouphaphone Chindavongsa, Siv Sovannaroth, Virasak Banouvong, Viengphone Sengsavath, Mayfong Mayxay, Nguyen Thi Kim Tuyen, Vo Ngoc Lam Phuong, Pham Duc Trung, Sónia Gonçalves, Soun Chen, Sonexay Phalivong, Saiamphone Xayvanghang, Supaporn Mahaphontrakoon, Richard D. Pearson, Paul N. Newton, Richard J. Maude, Elizabeth A. Ashley, Cristina V. Ariani, Victoria J. Simpson, Nicholas P. Day, Arjen M. Dondorp and Olivo Miotto ()
Additional contact information
Varanya Wasakul: Mahidol University
Tess D. Verschuuren: Mahidol University
Nguyen Thuy-Nhien: Oxford University Clinical Research Unit
Ethan Booth: Mahidol University
Huynh Hong Quang: Institute of Malariology, Parasitology and Entomology
Ngo Duc Thang: National Institute of Malariology, Parasitology and Entomology
Keobouphaphone Chindavongsa: Centre for Malariology, Parasitology and Entomology
Siv Sovannaroth: National Center for Parasitology, Entomology and Malaria Control
Virasak Banouvong: Centre for Malariology, Parasitology and Entomology
Viengphone Sengsavath: Centre for Malariology, Parasitology and Entomology
Mayfong Mayxay: Mahosot Hospital
Nguyen Thi Kim Tuyen: Oxford University Clinical Research Unit
Vo Ngoc Lam Phuong: Oxford University Clinical Research Unit
Pham Duc Trung: Oxford University Clinical Research Unit
Sónia Gonçalves: Wellcome Sanger Institute
Soun Chen: National Center for Parasitology, Entomology and Malaria Control
Sonexay Phalivong: Mahosot Hospital
Saiamphone Xayvanghang: Mahosot Hospital
Supaporn Mahaphontrakoon: Mahidol University
Richard D. Pearson: Wellcome Sanger Institute
Paul N. Newton: Mahosot Hospital
Richard J. Maude: Mahidol University
Elizabeth A. Ashley: Mahosot Hospital
Cristina V. Ariani: Wellcome Sanger Institute
Victoria J. Simpson: Wellcome Sanger Institute
Nicholas P. Day: Mahidol University
Arjen M. Dondorp: Mahidol University
Olivo Miotto: Mahidol University

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Genetic surveillance of Plasmodium falciparum (Pf) can track antimalarial-resistant strains, to inform decision-making by National Malaria Control Programmes (NMCPs). The GenRe-Mekong project prospectively collected 5982 samples in the Greater Mekong Subregion (GMS) between 2017 and 2022, genotyping drug resistance markers, and barcodes that recapitulate genetic variation. Genotypes were analyzed with the grcMalaria R package, first described in this paper, to translate genetic epidemiology data into actionable visual information. Since 2020, Pf incidences decreased rapidly, accompanied by a decline of dihydroartemisinin-piperaquine (DHA-PPQ) resistant lineages, previously dominant in the eastern GMS. The frequency of plasmepsin2/3 amplifications, conferring piperaquine resistance, dropped from 62% in 2017-2019 to 2% in 2022, coinciding with a switch in frontline therapy in Cambodia, Thailand, and Vietnam. While regional artemisinin resistance levels remained high, no evidence of emerging mefloquine resistance was found. Routine genetic surveillance proved valuable in monitoring rapid parasite population changes in response to public health interventions, providing actionable information for NMCPs.

Date: 2025
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DOI: 10.1038/s41467-025-59946-1

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