{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T23:39:00Z","timestamp":1790293140311,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pntd.0009877","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000}}],"reference-count":45,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T00:00:00Z","timestamp":1635120000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Academy of Sciences, USA"},{"DOI":"10.13039\/501100008391","name":"UBS Optimus Foundation","doi-asserted-by":"publisher","award":["496600"],"award-info":[{"award-number":["496600"]}],"id":[{"id":"10.13039\/501100008391","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["1037304"],"award-info":[{"award-number":["1037304"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["613671"],"award-info":[{"award-number":["613671"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Elimination and control of <jats:italic>Schistosoma japonicum<\/jats:italic>, the most virulent of the schistosomiasis-causing blood flukes, requires the development of sensitive and specific diagnostic tools capable of providing an accurate measurement of the infection prevalence in endemic areas. Typically, detection of <jats:italic>S<\/jats:italic>. <jats:italic>japonicum<\/jats:italic> has occurred using the Kato-Katz technique, but this methodology, which requires skilled microscopists, has been shown to radically underestimate levels of infection. With the ever-improving capabilities of next-generation sequencing and bioinformatic analysis tools, identification of satellite sequences and other highly repetitive genomic elements for use as real-time PCR diagnostic targets is becoming increasingly common. Assays developed using these targets have the ability to improve the sensitivity and specificity of results for epidemiological studies that can in turn be used to inform mass drug administration and programmatic decision making.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methodology\/Principal findings<\/jats:title>\n<jats:p>Utilizing Tandem Repeat Analyzer (TAREAN) and RepeatExplorer2, a cluster-based analysis of the <jats:italic>S<\/jats:italic>. <jats:italic>japonicum<\/jats:italic> genome was performed and a tandemly arranged genomic repeat, which we named SjTR1 (<jats:underline><jats:italic>S<\/jats:italic><\/jats:underline><jats:italic>chistosoma<\/jats:italic> <jats:underline><jats:italic>j<\/jats:italic><\/jats:underline><jats:italic>aponicum<\/jats:italic> <jats:underline>T<\/jats:underline>andem <jats:underline>R<\/jats:underline>epeat <jats:underline>1<\/jats:underline>), was selected as the target for a real-time PCR diagnostic assay. Based on these analyses, a primer\/probe set was designed and the assay was optimized. The resulting real-time PCR test was shown to reliably detect as little as 200 ag of <jats:italic>S<\/jats:italic>. <jats:italic>japonicum<\/jats:italic> genomic DNA and as little as 1 egg per gram of human stool. Based on these results, the index assay reported in this manuscript is more sensitive than previously published real-time PCR assays for the detection of <jats:italic>S<\/jats:italic>. <jats:italic>japonicum<\/jats:italic>.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Conclusions\/Significance<\/jats:title>\n<jats:p>The extremely sensitive and specific diagnostic assay described in this manuscript will facilitate the accurate detection of <jats:italic>S<\/jats:italic>. <jats:italic>japonicum<\/jats:italic>, particularly in regions with low levels of endemicity. This assay will be useful in providing data to inform programmatic decision makers, aiding disease control and elimination efforts.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pntd.0009877","type":"journal-article","created":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T17:34:05Z","timestamp":1635183245000},"page":"e0009877","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Development of a novel real-time polymerase chain reaction assay for the sensitive detection of Schistosoma japonicum in human stool"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0586-8573","authenticated-orcid":true,"given":"Sara","family":"Halili","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0725-202X","authenticated-orcid":true,"given":"Jessica R.","family":"Grant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8447-7425","authenticated-orcid":true,"given":"Nils","family":"Pilotte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1509-5220","authenticated-orcid":true,"given":"Catherine A.","family":"Gordon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4881-7496","authenticated-orcid":true,"given":"Steven A.","family":"Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,10,25]]},"reference":[{"issue":"9936","key":"pntd.0009877.ref001","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1016\/S0140-6736(13)61949-2","article-title":"Human schistosomiasis","volume":"383","author":"DG Colley","year":"2014","journal-title":"The Lancet"},{"issue":"7","key":"pntd.0009877.ref002","doi-asserted-by":"crossref","first-page":"e0005749","DOI":"10.1371\/journal.pntd.0005749","article-title":"Geographic strain differentiation of Schistosoma japonicum in the Philippines using microsatellite markers","volume":"11","author":"KJ Moendeg","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0009877.ref003","doi-asserted-by":"crossref","first-page":"18058","DOI":"10.1038\/srep18058","article-title":"Co-dispersal of the blood fluke Schistosoma japonicum and Homo sapiens in the Neolithic Age","volume":"5","author":"M. 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