A Novel A675T Mutation and High Levels of Chloroquine and Sulfadoxine-Pyrimethamine Resistance in Burundi.

Antimalarial resistance, including failure of artemisinin combination therapy, is increasing in Africa. Molecular surveillance of markers of drug resistance is essential to monitoring drug resistance. isolates from Cibitoke Province, Burundi were sequenced for ten markers of resistance (including potential background markers conferring 13mediated artemisinin partial resistance) by Illumina or Nanopore sequencing. and copy number variations were typed by digital PCR. Among 157 isolates, no validated mutations linked to artemisinin partial resistance (ART-R) were detected. However, a novel mutation, A675T, was identified. A mutation in the same position (A675V) had been found and validated in neighboring Rwanda previously. Background mutations were frequent, including D193Y (45.9%) and V127M (11.5%). Sulfadoxine-pyrimethamine (SP) resistance was widespread, with quintuple haplotypes detected in 82.3% and sextuple haplotypes in 12.3% of mono-infections. The IET triple mutant haplotype (94.9%) and N-F-D mutant haplotype (57.9%) indicate sustained CQ resistance and efficacy of artemether-lumefantrine (AL). No duplications but rare amplifications (1.8%) were identified. These findings indicate substantial SP resistance, posing a threat to the efficacy of IPTp and SMC strategies in Burundi. The findings also show potential ART-R and partner drug resistance in Burundi, highlighting the need for strengthened surveillance and coordinated regional efforts to mitigate resistance and sustain malaria control.