Abstract:
Background: The first models of malaria transmission assumed a completely mixed and
homogeneous population of parasites. Recent models include spatial heterogeneity and
variably mixed populations. However, there are few empiric estimates of parasite mixing
with which to parametize such models. Methods: Here we genotype 276 single
nucleotide polymorphisms (SNPs) in 5199 P. falciparum isolates from two Kenyan sites
(Kilifi county and Rachuonyo South district) and one Gambian site (Kombo coastal
districts) to determine the spatio-temporal extent of parasite mixing, and use Principal
Component Analysis (PCA) and linear regression to examine the relationship between
genetic relatedness and distance in space and time for parasite pairs. Results: Using 107,
177 and 82 SNPs that were successfully genotyped in 133, 1602, and 1034 parasite
isolates from The Gambia, Kilifi and Rachuonyo South district, respectively, we show
that there are no discrete geographically restricted parasite sub-populations, but instead
we see a diffuse spatio-temporal structure to parasite genotypes. Genetic relatedness of
sample pairs is predicted by relatedness in space and time. Conclusions: Our findings
suggest that targeted malaria control will benefit the surrounding community, but
unfortunately also that emerging drug resistance will spread rapidly through the
population.