Longitudinal genomic surveillance ofPlasmodium falciparummalaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand

AbstractBackgroundArtemisinin-based combination therapies are the first line of treatment forPlasmodium falciparuminfections worldwide, but artemisinin resistance (ART-R) has risen rapidly in in Southeast Asia over the last decade. Mutations inkelch13have been associated with artemisinin (ART) resistance in this region. To explore the power of longitudinal genomic surveillance to detect signals inkelch13and other loci that contribute to ART or partner drug resistance, we retrospectively sequenced the genomes of 194P. falciparumisolates from five sites in Northwest Thailand, bracketing the era in which there was a rapid increase in ART-R in this region (2001–2014).ResultsWe evaluated statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance should increase frequency over this period. AfterKelch13-C580Y, the strongest temporal change was seen at a SNP in phosphatidylinositol 4-kinase (PI4K), situated in a pathway recently implicated in the ART-R mechanism. However, other loci exhibit temporal signatures nearly as strong, and warrant further investigation for involvement in ART-R evolution. Through genome–wide association analysis we also identified a variant in a kelch-domain–containing gene on chromosome 10 that may epistatically modulate ART-R.ConclusionsThis analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated loci and improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of thekelch13locus associated with ART-R parasites may yield new molecular markers for resistance surveillance and may retard the emergence or spread of ART-R in African parasite populations.