Molecular surveillance of Plasmodium falciparum drug-resistance markers in Vietnam using multiplex amplicon sequencing

To investigate Plasmodium falciparum drug resistance in Vietnam, we conducted a retrospective surveillance study in eight malaria-endemic administrative provinces during a 17-year period. A multiplex amplicon sequencing assay was designed to target 11 markers or modulators of drug resistance to artemisinin, piperaquine, mefloquine and chloroquine, plus 4 neutral microsatellite loci. The oligonucleotide probe panel was adapted to TruSeq (Illumina) sequencing chemistry for 250bp-length fragments, libraries were prepared using TruSeq Custom Amplicon Low Input Library Prep Kit (Illumina), and paired-end sequencing was conducted in a MiSeq instrument using MiSeq Reagent Kit v2 (300 cycles, Illumina).