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In this study, we investigated the diversity and phylogenetic relationships of trypanosomes infecting bats in Uganda and the Central African Republic (CAR) using molecular tools. A total of 22 distinct genotypes were identified, clustering into seven well-supported phylogroups, including known species such as <jats:italic>Trypanosoma dionisii<\/jats:italic>, <jats:italic>T. livingstonei<\/jats:italic>, <jats:italic>T. vespertilionis<\/jats:italic>, and <jats:italic>T. erneyi<\/jats:italic>, alongside several novel lineages. Notably, <jats:italic>T. erneyi<\/jats:italic> was restricted to <jats:italic>Mops condylurus<\/jats:italic>, reaffirming its narrow host specificity. Phylogenetic analyses revealed substantial intraspecific diversity in <jats:italic>T. livingstonei<\/jats:italic> and <jats:italic>T. vespertilionis<\/jats:italic>, suggesting potential cryptic species, while <jats:italic>T. dionisii<\/jats:italic> exhibited limited genetic divergence across a broad geographic range. Intriguingly, a unique and highly diverse phylogroup was detected exclusively in fruit bats (Pteropodidae) from Uganda, closely related to the Australian <jats:italic>T. teixeirae<\/jats:italic>, and likely represents a novel species. The absence of trypanosomes in fruit bats from CAR, despite similar sampling effort, hints at ecological or evolutionary factors shaping parasite distribution. Our findings expand the current knowledge of bat-trypanosome diversity and highlight the importance of African bat populations in understanding the evolutionary dynamics of trypanosomes.\n<\/jats:p>","DOI":"10.1007\/s00436-025-08547-4","type":"journal-article","created":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T03:28:45Z","timestamp":1757561325000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Hidden diversity and host specificity of bat trypanosomes in East and Central Africa"],"prefix":"10.1007","volume":"124","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9586-6944","authenticated-orcid":false,"given":"Sadic Waswa","family":"Babyesiza","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3319-8394","authenticated-orcid":false,"given":"Alena","family":"Forn\u016fskov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdul","family":"Katakweba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Kigai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Krist\u00fdna","family":"Hadov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean Luther","family":"Ngbangui Kaguendo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Labo Dieu-b\u00e9ni Sosth\u00e8ne","family":"Bonaventure","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Primael","family":"Tabiti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0470-0878","authenticated-orcid":false,"given":"Thierry","family":"Aebischer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5831-6284","authenticated-orcid":false,"given":"Jo\u00eblle Go\u00fcy","family":"de Bellocq","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0516-7742","authenticated-orcid":false,"given":"Josef","family":"Bryja","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0552-9363","authenticated-orcid":false,"given":"Jan","family":"Vot\u00fdpka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,9,11]]},"reference":[{"key":"8547_CR1","doi-asserted-by":"publisher","unstructured":"Aregawi WG, Agga GE, Abdi RD, B\u00fcscher P (2019) Systematic review and meta-analysis on the global distribution, host range, and prevalence of Trypanosoma evansi. 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UWA\/COD\/96\/05, 11 October 2022), the National Forest Authority (NFA, License no. 377, 3 October 2022), and the Uganda National Council for Science and Technology (UNCST, Ref. no. NS301ES, 17 October 2022). Research conducted in the Central African Republic was authorized by the Minist\u00e8re de l\u2019\u00c9levage et de la Sant\u00e9 Animale, Bangui, (License no. 031, 26 June 2024) and Minist\u00e8re des Eaux, Forets, Chasse et Peche (License no. 01\u201316, 24 June 2024).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All authors have read and approved the final version of the manuscript and consent to its submission for publication. The manuscript has not been published previously and is not under consideration for publication elsewhere.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"101"}}