Genomic Levering of the Neglected Malaria Parasites using SWGA Approach.

Neglected malaria parasites, Plasmodium malariae and Plasmodium ovale species, remain challenging due to their low parasitemia, underestimation, and lack of comprehensive genetic analysis. We applied Selective Whole Genome Amplification (SWGA) using specifically designed primer sets targeting the pathogen genome to enrich parasite DNA from clinical samples, enabling cost-effective and high-quality Whole Genome Sequencing (WGS) of these neglected species. WGS on SWGA-treated samples demonstrated improved genome coverage, surpassing non-SWGA samples. For P. malariae, genome coverage increased from 6.89X to 331.16X post-SWGA, allowing better SNP identification. Parallel improvements in genome coverage were achieved for P. ovale spp., facilitating the detection of numerous additional SNPs that were barely detectable pre-SWGA. Additionally, leveraging the long DNA fragments generated by SWGA, we achieved successful genome assemblies for P. malariae and P. ovale curtisi. Our SWGA approach provides a powerful tool for enhancing genomic analysis of these neglected parasites, revealing population diversity, drug resistance markers, and hypervariable regions. This methodology constitutes a transformative tool to surmount the challenges of genomic analysis for neglected malaria parasites and can improve malaria research and control.