Oxford Nanopore P. falciparum drug resistance marker gene sequencing

The emergence of drug-resistant clones of P. falciparum is a major public health concern, and the ability to detect and track the spread of these clones is crucial for effective control and treatment. However, in endemic settings, malaria infected people often carry more than one malaria clone simultaneously making it likely to miss drug resistant clones using traditional molecular screening methods. Our goal was to develop a bioinformatics pipeline for detecting all haplotypes in multiclonal samples, sequenced using the Oxford Nanopore Technology MinION platform. We developed the PHARE pipeline and validated it on three control datasets containing P. falciparum DNA of four laboratory strains at varying mixing ratios. Additionally, the pipeline was tested on clinical samples from children admitted to a paediatric hospital in the Central African Republic. The PHARE pipeline was tested with amplicons of the P. falciparum drug resistance marker genes pfdhps, pfdhfr, and pfk13.