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In neonates of domestic animals, it is associated with consistent diarrhea and dehydration. <jats:italic>Cryptosporidium<\/jats:italic> infection begins with the ingestion of sporulated oocytes disseminated by carrier animals that consistently contaminate the environment. Many diagnostic tests are available including microscopy and antigen trap\u2010ELISA, but none of the diagnostic tests available currently cannot differentiate between active and passive infection in the host. In the current study, to address this challenge an mRNA\u2010based\u00a0duplex TaqMan\u00ae probe PCR was developed to target the <jats:italic>Cryptosporidium<\/jats:italic> oocyst wall protein gene and <jats:italic>18SSU rRNA<\/jats:italic> gene in a single tube that can detect metabolically active cryptosporidial oocysts. The mRNA transcripts are the direct indicator of any actively replicating cell and they will help decipher the active stages of its lifecycle in a host. This diagnostic assay was standardized by computing transcript copy number\u2010based limit of detection (LOD). For <jats:italic>COWP<\/jats:italic> and <jats:italic>18SSU rRNA<\/jats:italic> genes, the LOD was 7.08\u2009\u00d7\u200910<jats:sup>04<\/jats:sup> and 5.95\u2009\u00d7\u200910<jats:sup>05<\/jats:sup>, respectively. During active infections, the oocyst wall protein will be active and so its <jats:italic>COWP<\/jats:italic> gene transcripts will act as a marker for active infection. While transcripts for <jats:italic>18SSU rRNA<\/jats:italic> are constitutively expressed in cryptosporidial life cycle. This current diagnostic assay will be a quantitative marker that will help assess the active stages of <jats:italic>Cryptosporidium<\/jats:italic> infection in neonates. The disease dynamics will help better understand to formulate the control strategies and contain infection among healthy animals.<\/jats:p>","DOI":"10.1002\/cbf.3759","type":"journal-article","created":{"date-parts":[[2022,10,18]],"date-time":"2022-10-18T03:15:09Z","timestamp":1666062909000},"page":"45-57","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Development of duplex real\u2010time PCR for quick detection of cryptosporidiosis in goats"],"prefix":"10.1002","volume":"41","author":[{"given":"Atul Kumar","family":"Sharma","sequence":"first","affiliation":[{"name":"Division of Animal Health ICAR\u2010Central Institute for Research on Goats Mathura Uttar Pradesh India"},{"name":"Department of Biotechnology GLA University Mathura Uttar Pradesh 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