Rapid detection of G6PD deficiency SNPs using a novel amplicon-based minion sequencing assay
Year: 2025
Type: article
Abstract: Plasmodium vivax malaria remains a significant global health challenge, complicated by the parasite's ability to form dormant liver stages (hypnozoites) that cause relapses. Radical cure of P. vivax malaria requires administration of a hypnozoitocidal drug, such as primaquine or tafenoquine. However, these drugs can cause severe haemolysis in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. G6PD deficiency is caused by more than 230 different variants at the gene level that confer different degrees of deficiency phenotypically. Understanding the distribution of different G6PD variants in affected populations is essential to inform safer antimalarial treatment strategies. This study aimed to develop a cost-effective sequencing assay targeting key regions of the G6PD gene, suitable for field deployment. A novel assay based on Nanopore technology was designed to amplify two amplicons covering exon 3 to exon 13, focusing on known variants associated with enzyme deficiency. A total of 79 samples from individuals in Cambodia, Vietnam, Afghanistan, and China were sequenced, and a bioinformatics pipeline was created for the targeted variant calling of 192 G6PD SNP mutations. The assay demonstrated reliable detection of known variants, with high concordance between runs, within runs, and with Sanger sequencing. The Nanopore MinION long-amplicon sequencing assay offers a robust and portable solution for large-scale G6PD genotyping in low-resource settings, that will improve malaria control and elimination strategies by enabling safer antimalarial treatment.
Source: Scientific Reports
Authors: Costanza Tacoli, Mariana Kleinecke, Kian Soon Hoon, Hidayat Trimarsanto, Muhammad Nadeem, Rotha Eam, Nimol Khim, Angela Rumaseb, Benedikt Ley, Dean Sayre, Sochea Phok, Dysoley Lek, Benoit Witkowski, Jimee Hwang, Sarah Auburn, Ivo Mueller, Ric N. Price, Jean Popovici
Institutions: Walter and Eliza Hall Institute of Medical Research, Institut Pasteur du Cambodge, Charles Darwin University, Menzies School of Health Research, National Research and Innovation Agency, Centers for Disease Control and Prevention, U.S. President's Malaria Initiative, Population Services International, Cambodia National Malaria Center, Mahidol University, University of Oxford, Mahidol Oxford Tropical Medicine Research Unit, The University of Melbourne, Institut Pasteur
Language: English
Topic: Malaria Research and Control
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,690
Funders: Bill and Melinda Gates Foundation, Wellcome Trust, National Institute for Health and Care Research, Department for International Development, UK Government, Department for International Development, Université Paris-Saclay, National Institutes of Health, President's Malaria Initiative, Medical Research Council, National Health and Medical Research Council, National Institute of Allergy and Infectious Diseases
Awards: Improving the radical cure of vivax malaria: A multicentre randomised comparison of short and long course primaquine regimens, Menzies School of Health Research - to expand the safe and effective use of primaquine for radical cure in diverse locations, Interventions to eliminate Plasmodium vivax malaria, Novel genetic tools for tracking the origins and spread of Plasmodium vivax, G9000166282, G9000195522, Leveraging access to parasite natural diversity to identify Plasmodium vivax culture-adaptable strain.
OpenAlex ID: W7116631372