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Despite the widespread distribution of the tsetse vectors and animal trypanosomiasis, human disease is only found in discrete foci which periodically give rise to epidemics followed by periods of endemicity A key to unravelling this puzzle is a detailed knowledge of the aetiological agents responsible for different patterns of disease \u2013 knowledge that is difficult to achieve using traditional microscopy. The science of molecular epidemiology has developed a range of tools which have enabled us to accurately identify taxonomic groups at all levels (species, subspecies, populations, strains and isolates). Using these tools, we can now investigate the genetic interactions within and between populations of <jats:italic>Trypanosoma brucei<\/jats:italic> and gain an understanding of the distinction between human- and nonhuman-infective subspecies. In this review, we discuss the development of these tools, their advantages and disadvantages and describe how they have been used to understand parasite genetic diversity, the origin of epidemics, the role of reservoir hosts and the population structure. Using the specific case of <jats:italic>T.b. rhodesiense<\/jats:italic> in Uganda, we illustrate how molecular epidemiology has enabled us to construct a more detailed understanding of the origins, generation and dynamics of sleeping sickness epidemics.<\/jats:p>","DOI":"10.1017\/s0031182009990333","type":"journal-article","created":{"date-parts":[[2009,6,26]],"date-time":"2009-06-26T05:36:39Z","timestamp":1245994599000},"page":"1491-1500","source":"Crossref","is-referenced-by-count":18,"title":["Molecular epidemiology of African sleeping sickness"],"prefix":"10.1017","volume":"136","author":[{"given":"G.","family":"HIDE","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"TAIT","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2009,6,26]]},"reference":[{"key":"S0031182009990333_ref047","first-page":"113","article-title":"Epidemiological studies on the animal reservoir of Gambiense sleeping sickness. 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