title: Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.
abstract: Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p<0.0001) whereas Kisii had the least significant index of association values (0.03; p<0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.
authors.affiliation: Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya.
authors.forename: Luicer A
authors.initials: LA
authors.lastname: Ingasia
authors.affiliation: Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya.
authors.forename: Jelagat
authors.initials: J
authors.lastname: Cheruiyot
authors.affiliation: Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, United States; Atlanta Research and Education Foundation/VA Medical Center, Decatur, GA, United States.
authors.forename: Sheila Akinyi
authors.initials: SA
authors.lastname: Okoth
authors.affiliation: Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya.
authors.forename: Ben
authors.initials: B
authors.lastname: Andagalu
authors.affiliation: Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)/Walter Reed Project (WRP), Kisumu, Kenya. Electronic address: edwin.kamau.mil@mail.mil.
authors.forename: Edwin
authors.initials: E
authors.lastname: Kamau
mesh_terms: D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D062306:Geography, Medical; D006239:Haplotypes; D006801:Humans; D015994:Incidence; D007630:Kenya / Q000453:epidemiology; D015810:Linkage Disequilibrium; D016778:Malaria, Falciparum / Q000453:epidemiology* / Q000469:parasitology*; D018895:Microsatellite Repeats; D058885:Multilocus Sequence Typing; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics*
keywords: Genetic diversity; Kenya; Plasmodium falciparum; Population structure