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We clarified the genetic diversity of  Trypanosoma  spp. within the Kafue ecosystem, using PCR targeting the internal transcribed spacer 1 and the cathepsin L-like cysteine protease (CatL) sequences. The overall prevalence of  Trypanosoma  spp. in cattle and tsetse flies was 12.65 and 26.85%, respectively. Cattle positive for  Trypanosoma vivax  had a significantly lower packed cell volume, suggesting that  T. vivax  is the dominant  Trypanosoma  spp. causing anemia in this area. Among the 12 operational taxonomic units (OTUs) of  T. vivax  CatL sequences detected, one was from a known  T. vivax  lineage, two OTUs were from known  T. vivax -like lineages, and nine OTUs were considered novel  T. vivax -like lineages. These findings support previous reports that indicated the extensive diversity of  T. vivax -like lineages. The findings also indicate that combining CatL PCR with next generation sequencing is useful in assessing  Trypanosoma  spp. diversity, especially for  T. vivax  and  T. vivax -like lineages. In addition, the 5.42% prevalence of  Trypanosoma brucei rhodesiense  found in cattle raises concern in the community and requires careful monitoring of human African trypanosomiasis.

Genetic Diversity of African Trypanosomes in Tsetse Flies and Cattle From the Kafue Ecosystem