Rapid detection of G6PD deficiency SNPs using a novel amplicon-based minion sequencing assay

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.