Plasmodium falciparum molecular surveillance in the Peruvian Amazon with Ampliseq assay

We designed a new highly-multiplexed deep sequencing assay (Pf AmpliSeq), compatible with benchtop sequencers, allowing for high accuracy sequencing at higher coverage and lower cost than WGS, targeting genomic regions of interest. The novelty of the assay is in its high number of targets multiplexed in one easy workflow, combining population genetic markers with 13 near full-length resistance genes, applicable for many different use cases. We provide a first proof-of-principle for hrp2 and hrp3 deletion detection using amplicon sequencing. The assay was validated with a retrospective sample collection from the Peruvian Amazon between 2003 and 2018.