Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health

Targeted amplicon sequencing is a powerful and efficient tool to interrogate the P . falciparum genome and generate actionable data from infections to complement traditional malaria epidemiology. For maximum impact, genomic tools should be multi-purpose, robust, sensitive and reproducible. We developed, characterized, and implemented MAD ⁴ HatTeR, an amplicon sequencing panel based on Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing, along with a bioinformatic pipeline for data analysis. MAD ⁴ HatTeR targets 165 highly diverse loci, focusing on multiallelic microhaplotypes; key markers for drug and diagnostic resistance, including duplications and deletions; and csp and potential vaccine targets. In addition, it can detect non- falciparum Plasmodium species. We used laboratory control and field sample data to demonstrate the high sensitivity and robustness of the panel. The successful implementation of this method in five laboratories, including three in malaria-endemic African countries, showcases its feasibility in generating reproducible data across laboratories. Finally, we introduce an analytical approach to detect gene duplications and deletions from amplicon sequencing data. MAD ⁴ HatTeR is thus a powerful research tool and a robust resource for malaria public health surveillance and control.