Geographical Heterogeneity in Antimalarial Resistance Markers Revealed by Genomic Surveillance in Angola, 2023

Abstract Plasmodium falciparum malaria remains a leading cause of mortality in Angola, with emerging antimalarial resistance threatening treatment and prevention strategies. Efficacy of artemether-lumefantrine, one of the country’s preferred malaria treatments, has been reported below 90% in two provinces, underscoring the need for routine resistance surveillance and efficacy monitoring to guide policy decisions. Between March and July 2023, dried blood spots and demographic data were collected from P . falciparum -positive participants at 16 health facilities across 8 provinces. Multiplexed amplicon deep sequencing was used to characterize single nucleotide polymorphisms in 12 genes linked with resistance, estimate allele frequencies, and detect co-infecting non-falciparum Plasmodium species. Sequence data from 817 samples revealed significant geographic variation in resistance markers. In the southeast, artemisinin partial resistance markers ( k13 P574L, P441L), were detected at very low prevalence (<0.1%), while the quintuple dhps / dhfr haplotype, linked to sulfadoxine-pyrimethamine (SP) resistance, was very prevalent (>40% of samples). In the northwest, the sextuple dhps / dhfr haplotype, a marker of higher SP resistance, was most prevalent in Zaire (14.2%). The crt CVIET haplotype, associated with chloroquine resistance, had a national prevalence of 15.9%, detected in over 48% of samples from Zaire and Uíge. The mdr1 N86 genotype, linked to reduced lumefantrine susceptibility, was widespread, detected in 99.3% of samples. Co-infections of P . falciparum and non-falciparum species were rare with no clear geographic distribution. No P . vivax co-infections were detected. These findings highlight the need for continued monitoring to safeguard treatment efficacy, reinforcing the importance of molecular surveillance in malaria control strategies.