National genomic profiling of antimalarial resistance in Zambian children participating in the 2018 Malaria Indicator Survey.

The emergence of antimalarial drug resistance is a major threat to malaria control and elimination. Using whole genome sequencing of 282 samples collected during the 2018 Zambia National Malaria Indicator Survey, we determined the prevalence and spatial distribution of known and candidate antimalarial drug resistance mutations. High levels of genotypic resistance were found across Zambia to pyrimethamine, with over 94% (n=266) of samples having the triple mutant (N51, C59, and S108), and sulfadoxine, with over 84% (n=238) having the double mutant (A437 and K540). In northern Zambia, 5.3% (n=15) of samples also harbored the A581 mutation. Although 29 mutations were identified in , these mutations were present at low frequency (<2.5%), and only three were WHO-validated artemisinin partial resistance mutations: P441 (n=1, 0.35%), V568 (n=2, 0.7%) and R622 (n=1, 0.35%). Notably, 91 (32%) of samples carried the E431 mutation in the gene, which is associated with artemisinin resistance. No specimens carried any known mutations associated with chloroquine resistance in the gene (codons 72-76). strains circulating in Zambia were highly resistant to sulfadoxine and pyrimethamine but remained susceptible to chloroquine and artemisinin. Despite this encouraging finding, early genetic signs of developing artemisinin resistance highlight the urgent need for continued vigilance and expanded routine genomic surveillance to monitor these changes.