Characterizing Plasmodium falciparum genetic diversity and complexity of infections in clinical malaria infections in Western and Coastal Kenya using the poly-alpha microsatellite marker

BackgroundGenotyping P. falciparum polymorphic merozoite genes to describe parasite genetic diversity and the complexity of malaria infections (COI) is routinely used to assess the effectiveness of malaria control interventions. They are also utilized in anti-malarial drug therapeutic efficacy studies (TES) to differentiate recrudescent parasites from new infections. However, these polymorphic genes are usually under selection. Therefore, neutral microsatellite markers are preferred as they are also easier to genotype. The current study investigated the genetic diversity and COI using the poly- microsatellite marker to provide background information on circulating genotypes before its applied to TES in Kenya. MethodologyDried blood spot (DBS) samples were obtained from 93 participants from a TES in Busia County in 2016 and 92 participants from a malaria monitoring study conducted in Kilifi in 2020. Genotyping of the poly- microsatellite was done by PCR, capillary electrophoresis and the fragment data analyzed using GeneMarker. ResultsAbout 96.7% and 87% of the samples from Busia and Kilifi, respectively, were successfully genotyped. The infections in Busia were mainly polyclonal (80%) with a significantly higher mean COI of 2.9 (p < 0.0001), while those in Kilifi were mostly monoclonal (52.5%) with a mean COI of 1.7. Despite on average a younger population and lower parasite density, both regions had similar expected heterozygosity (He) (Busia = 0.92; Kilifi = 0.90) while Busia recorded a slightly higher number of effective alleles (Ne) (Busia = 10.8; Kilifi = 9.3). ConclusionThe poly- microsatellite genotyping revealed high genetic diversity of malaria parasites in Busia and Kilifi. These findings define the genotypes (fragment sizes) observed in the two Kenyan populations, providing a proof of concept for the utility of poly- in TES studies as a molecular correction tool and for the evaluation of the effectiveness of malaria interventions in Kenya.