Addressing the SNPs associated with malaria treatment failure of King Faisal hospital patients

Abstract

Malaria is a major health burden nationally and regionally, especially in sub-Saharan Africa which experiencing more than 94% of cases and 95% of deaths attributed to malaria, and Plasmodium falciparum being the most lethal parasite species. Rwanda, continues to have a high transmission of malaria despite the national commitment and malaria control programs. The major cause of this failure to malaria control strategies includes the Resistance of Plasmodium falciparum to antimalarial drugs, affecting more treatment programs globally including the use of Artemisinin-based combination therapies (ACTs). There is therefore an urgent need to improve the control strategy. This study focused on addressing Single Nucleotide Polymorphisms (SNPs) associated with malaria treatment failure. P. falciparum, the deadliest malaria parasite species, and the gene mutation associated with it, specifically in the Plasmodium falciparum Kelch 13 (PfK13), Plasmodium falciparum chloroquine resistance transporter (Pfcrt) and Plasmodium falciparum multidrug resistance 1(Pfmdr1) genes were studied. These genetic markers are widely implicated in resistance to drugs like chloroquine, lumefantrine, and amodiaquine. In Rwanda, as many other countries adopted ACTs as the first line therapy but the presence of mutation associated with PfK13 and pfmdr1 caused reduced treatment efficacy of ACTs. In this study, validation of oxford nanopore technology (ONT) findings by sanger sequencing were performed. In total 64 samples (collected in 2024) were sequenced by ONT and validated by sanger sequencing. Results obtained revealed the concordance of results to be 92.05 % and Cohen’s Kappa k=0.479, chi-square test (x2 = 25.000), p < 0.001 confirms concordance and the Pearson Chi-Square test also confirms a strong association of the ONT and Sanger sequencing and finally the Likelihood Ratio Test confirms the concordance (x2 = 8.397, p = 0.015). Next, another cohort of 43 samples (collected in 2025) were analyzed for prevalence, 36/43(83.7%) of samples presented SNPs associated with malaria treatment failure, PfK13R561H (51.2%) and PfMDR1-Y184F (60.5%) were the most prevalence SNPs identified. These mutations compromise rapid malaria parasites clearance thus causing ACT failure and plays a role in multidrug resistance and reduce the efficacy of ArtemetherLumefantrine (Coartem).