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Background  While Human African Trypanosomiasis (HAT) is in decline on the continent of Africa, the disease still remains a major health problem in Uganda. There are recurrent sporadic outbreaks in the traditionally endemic areas in south-east Uganda, and continued spread to new unaffected areas in central Uganda. We evaluated the evolutionary dynamics underpinning the origin of new foci and the impact of host species on parasite genetic diversity in Uganda. We genotyped 269  Trypanosoma brucei  isolates collected from different regions in Uganda and southwestern Kenya at 17 microsatellite loci, and checked for the presence of the SRA gene that confers human infectivity to  T. b. rhodesiense .    Results  Both Bayesian clustering methods and Discriminant Analysis of Principal Components partition  Trypanosoma brucei  isolates obtained from Uganda and southwestern Kenya into three distinct genetic clusters. Clusters 1 and 3 include isolates from central and southern Uganda, while cluster 2 contains mostly isolates from southwestern Kenya. These three clusters are not sorted by subspecies designation ( T. b. brucei  vs  T. b. rhodesiense ), host or date of collection. The analyses also show evidence of genetic admixture among the three genetic clusters and long-range dispersal, suggesting recent and possibly on-going gene flow between them.    Conclusions  Our results show that the expansion of the disease to the new foci in central Uganda occurred from the northward spread of  T. b. rhodesiense  ( Tbr ). They also confirm the emergence of the human infective strains ( Tbr ) from non-infective  T. b. brucei  ( Tbb ) strains of different genetic backgrounds, and the importance of cattle as  Tbr  reservoir, as confounders that shape the epidemiology of sleeping sickness in the region.

Genetic Diversity and Population Structure of Trypanosoma brucei in Uganda: Implications for the Epidemiology of Sleeping Sickness and Nagana