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Flies serve as intermediate hosts. In recent years, reports on bovine parafilariosis have become more frequent, corroborating the necessity of reliable diagnostic interventions especially since no molecular or serological test has been available. We aimed to establish a polymerase chain reaction assay to detect DNA of<jats:italic>P. bovicola<\/jats:italic>in flies, skin biopsies and serohemorraghic exudates of bleeding spots.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>PCRs targeting the cytochrome<jats:italic>c<\/jats:italic>oxidase subunit 1 (<jats:italic>cox<\/jats:italic>1) gene and the internal transcribed spacer region (ITS) of the ribosomal RNA gene cluster were evaluated for their diagnostic sensitivity as well as performance and specificity on biopsy and serohemorrhagic exudate samples from<jats:italic>P. bovicola-<\/jats:italic>infected cattle.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Using serohemorrhagic exudates (<jats:italic>n<\/jats:italic>\u2009=\u20096), biopsies (<jats:italic>n<\/jats:italic>\u2009=\u20092) and flies (<jats:italic>n<\/jats:italic>\u2009=\u20091), the PCR targeting the<jats:italic>cox<\/jats:italic>1 gene resulted in a gel band of almost 700 bp. Cloning, sequencing, and removal of primer sequences yielded a 649-bp fragment of the<jats:italic>P. bovicola cox<\/jats:italic>1 gene. The PCR targeting the ITS region showed a band of about 1100 bp. Cloning, sequencing, and removal of primer sequences resulted in a 1083 bp stretch of the<jats:italic>P. bovicola<\/jats:italic>ITS region. Testing samples from presumably affected animals, the<jats:italic>cox<\/jats:italic>1-PCR resulted in bands with the expected size and they were all confirmed as<jats:italic>P. bovicola<\/jats:italic>by sequencing. In contrast, the ITS-PCR proved to be less sensitive and less specific and additionally amplified the ITS region of<jats:italic>Musca domestica<\/jats:italic>or buttercup DNA. When analysing for sensitivity, the<jats:italic>cox<\/jats:italic>1-PCR yielded visible bands up to 2 ng of genomic DNA, whereas the ITS-PCR produced bands up to 3 ng. In a plasmid dilution series, the minimum number of target DNA copies was 10<jats:sup>2<\/jats:sup>for the<jats:italic>cox<\/jats:italic>1-PCR and 10<jats:sup>1<\/jats:sup>in the ITS-PCR.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The evaluated<jats:italic>cox<\/jats:italic>1-PCR enables reliable detection of<jats:italic>P. bovicola<\/jats:italic>DNA in skin biopsies and serohemorrhagic exudates. This PCR and, to a limited extent, the ITS-PCR, may help evaluate different therapeutic approaches. Furthermore, the<jats:italic>cox<\/jats:italic>1-PCR may be useful for epidemiological studies on the geographical distribution of<jats:italic>P. bovicola<\/jats:italic>. Further understanding of the epidemiology of this parasite will help develop and implement effective control strategies.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13071-019-3838-4","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T16:04:04Z","timestamp":1576080244000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Diagnosing bovine parafilariosis: utility of the cytochrome c oxidase subunit 1 gene and internal transcribed spacer region for PCR detection of Parafilaria bovicola in skin biopsies and serohemorrhagic exudates of cattle"],"prefix":"10.1186","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2709-8541","authenticated-orcid":false,"given":"Andreas W.","family":"Oehm","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Stoll","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cornelia","family":"Silaghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annette","family":"Pfitzner-Friedrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Knubben-Schweizer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Strube","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,11]]},"reference":[{"key":"3838_CR1","first-page":"115","volume":"55","author":"MA Tubangui","year":"1934","unstructured":"Tubangui MA. 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