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Background  Trypanosomes cause disease in humans and livestock in sub-Saharan Africa and rely on tsetse flies as their main insect vector. Nigeria is the most populous country in Africa; however, only limited information about the occurrence and diversity of trypanosomes circulating in the country is available.    Methods  Tsetse flies were collected from five different locations in or adjacent to protected areas, i.e. national parks and game reserves, in Nigeria. Proboscis and gut samples were analysed for trypanosome DNA by molecular amplification of the internal transcribed spacer 1 (ITS1) region and part of the trypanosome specific glycosomal glyceraldehyde-3-phosphate dehydrogenase ( gGAPDH ) gene.    Results  The most abundant  Trypanosoma  species found in the tsetse gut was  T. grayi , a trypanosome infecting crocodiles. It was ubiquitously distributed throughout the country, accounting for over 90% of all cases involving trypanosomes.  Trypanosoma congolense  was detected in gut samples from all locations except Cross River National Park, but not in the proboscis, while  T. brucei  ( sensu lato ) was not detected at all. In proboscis samples,  T. vivax  was the most prominent. The sequence diversity of  gGAPDH  suggests that  T. vivax  and  T. grayi  represent genetically diverse species clusters. This implies that they are highly dynamic populations.    Conclusions  The prevalence of animal pathogenic trypanosomes throughout Nigeria emphasises the role of protected areas as reservoirs for livestock trypanosomes. The genetic diversity observed within  T. vivax  and  T. grayi  populations might be an indication for changing pathogenicity or host range and the origin and consequences of this diversity has to be further investigated.

Genetic diversity of trypanosome species in tsetse flies (Glossina spp.) in Nigeria