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BackgroundGenotyping Plasmodium falciparum subpopulations in malaria infections is an important aspect of malaria molecular epidemiology to understand within-host diversity and the frequency of drug resistance markers.MethodsWe characterized P. falciparum genetic diversity in asymptomatic infections and subsequent first febrile infections using amplicon sequencing (AmpSeq) of ama1 in Coastal Kenya. We also examined temporal changes in haplotype frequencies of mdr1, a drug-resistant marker.ResultsWe found >60% of the infections were polyclonal (complexity of infection [COI] >1) and there was a reduction in COI over time. Asymptomatic infections had a significantly higher mean COI than febrile infections based on ama1 sequences (2.7 [95% confidence interval {CI}, 2.65-2.77] vs 2.22 [95% CI, 2.17-2.29], respectively). Moreover, an analysis of 30 paired asymptomatic and first febrile infections revealed that many first febrile infections (91%) were due to the presence of new ama1 haplotypes. The mdr1-YY haplotype, associated with chloroquine and amodiaquine resistance, decreased over time, while the NY (wild type) and the NF (modulates response to lumefantrine) haplotypes increased.ConclusionsThis study emphasizes the utility of AmpSeq in characterizing parasite diversity as it can determine relative proportions of clones and detect minority clones. The usefulness of AmpSeq in antimalarial drug resistance surveillance is also highlighted.

Original publication

DOI

10.1093/infdis/jiac144

Type

Journal article

Journal

The Journal of infectious diseases

Publication Date

09/2022

Volume

226

Pages

920 - 927

Addresses

Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.

Keywords

Humans, Plasmodium falciparum, Malaria, Malaria, Falciparum, Protozoan Proteins, Antimalarials, Drug Resistance, Asymptomatic Infections