Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance in western Thailand

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Artemisinin-based combination therapies are the first line of treatment for <jats:italic>Plasmodium falciparum</jats:italic> infections worldwide, but artemisinin resistance (ART-R) has risen rapidly in in Southeast Asia over the last decade. Mutations in <jats:italic>kelch13</jats:italic> have been associated with artemisinin (ART) resistance in this region. To explore the power of longitudinal genomic surveillance to detect signals in <jats:italic>kelch13</jats:italic> and other loci that contribute to ART or partner drug resistance, we retrospectively sequenced the genomes of 194 <jats:italic>P. falciparum</jats:italic> isolates from five sites in Northwest Thailand, bracketing the era in which there was a rapid increase in ART-R in this region (2001–2014).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We evaluated statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance should increase frequency over this period. After <jats:italic>Kelch13-</jats:italic>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.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>This 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 the <jats:italic>kelch13</jats:italic> locus 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.</jats:p></jats:sec>