Amplicon sequencing as a potential surveillance tool for complexity of infection and drug resistance markers in Plasmodium falciparum asymptomatic infections.
Wamae K., Kimenyi KM., Osoti V., de Laurent ZR., Ndwiga L., Kharabora O., Hathaway NJ., Bailey JA., Juliano JJ., Bejon P., Ochola-Oyier LI.
IntroductionGenotyping Plasmodium falciparum sub-populations in malaria infections is an important aspect of malaria molecular epidemiology to understand within-host diversity and the frequency of drug resistance markers.MethodsWe characterised 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 more than 60% of the infections were polyclonal (complexity of infection >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% 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 (wildtype) and the NF (modulates response to lumefantrine) haplotypes increased.ConclusionThis study emphasizes the utility of AmpSeq in characterising 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.