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Infections by these apicomplexan parasites limit performance and cause economic losses for the horse industry. Equine piroplasmosis is widespread in the northern regions of Nigeria, where an increasing portion of the animal population is composed of horses. This disease has remained epidemiologically challenging, especially as the movement of horses increases across Nigeria. In this study, blood samples from 300 horses were collected in three states of northwestern Nigeria. The presence of piroplasms was screened by nested PCR targeting 18S rDNA and positive samples were analyzed using species-specific-nested PCR-targeting genes including <jats:italic>ema1<\/jats:italic> (<jats:italic>T. equi<\/jats:italic>), <jats:italic>rap1<\/jats:italic> (<jats:italic>B. caballi<\/jats:italic>), and a gene coding a protein of unknown function (<jats:italic>T. haneyi<\/jats:italic>). Species-specific-nPCR results demonstrated that the prevalence of <jats:italic>T. equi<\/jats:italic> was 13.0% (39\/300), <jats:italic>B. caballi<\/jats:italic> was 3.3% (10\/300) and <jats:italic>T. haneyi<\/jats:italic> was 2.7% (8\/300). Mixed infections with <jats:italic>T. equi<\/jats:italic> and <jats:italic>B. caballi<\/jats:italic> was 2.7% (8\/300) while <jats:italic>T. equi<\/jats:italic>, <jats:italic>B. caballi<\/jats:italic>, and <jats:italic>T. haneyi<\/jats:italic> multiple infection prevalence was 0.6% (2\/300). We used 18S rDNA sequences to determine close relationships between <jats:italic>T. equi<\/jats:italic> by phylogenetic analysis and demonstrated that among 57 sequences of <jats:italic>Theileria<\/jats:italic> parasites, 28 samples belonged to clade A (49%), 13 samples were found to be clade C (22%), and 16 were clade D (28%). These results demonstrate the genetic diversity of <jats:italic>T. equi<\/jats:italic> circulating in horses from Nigeria.<\/jats:p>","DOI":"10.1007\/s00436-020-06797-y","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T01:03:34Z","timestamp":1594343014000},"page":"2955-2963","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Molecular detection of Theileria species and Babesia caballi from horses in Nigeria"],"prefix":"10.1007","volume":"119","author":[{"given":"Philip W.","family":"Mshelia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lowell","family":"Kappmeyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendell C.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caleb A.","family":"Kudi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Okubanjo O.","family":"Oluyinka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel O.","family":"Balogun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edeh E.","family":"Richard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Onoja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly P.","family":"Sears","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2680-6091","authenticated-orcid":false,"given":"Massaro W.","family":"Ueti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,10]]},"reference":[{"issue":"3","key":"6797_CR1","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.ttbdis.2012.11.008","volume":"4","author":"C Baptista","year":"2013","unstructured":"Baptista C, Lopes MS, Tavares AC, Rojer H, Kappmeyer L, Mendon\u00e7a D, da C\u00e2mara Machado A (2013) Diagnosis of Theileria equi infections in horses in the Azores using cELISA and nested PCR. 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