{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T08:27:46Z","timestamp":1793694466896,"version":"4.5.1"},"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T00:00:00Z","timestamp":1707696000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009227","name":"Iowa State University","doi-asserted-by":"publisher","award":["IOWA5434; IOWA5615"],"award-info":[{"award-number":["IOWA5434; IOWA5615"]}],"id":[{"id":"10.13039\/100009227","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>An accurate diagnostic test is an essential aspect of successfully monitoring and managing wildlife diseases. Lymphoproliferative Disease Virus (LPDV) is an avian retrovirus that was first identified in domestic turkeys in Europe and was first reported in a Wild Turkey (<jats:italic>Meleagris gallopavo<\/jats:italic>) in the United States in 2009. It has since been found to be widely distributed throughout North America. The majority of studies have utilized bone marrow and PCR primers targeting a 413-nucleotide sequence of the <jats:italic>gag<\/jats:italic> gene of the provirus to detect infection. While prior studies have evaluated the viability of other tissues for LPDV detection (whole blood, spleen, liver, cloacal swabs) none to date have studied differences in detection rates when utilizing different genomic regions of the provirus. This study examined the effectiveness of another section of the provirus, a 335-nucleotide sequence starting in the U3 region of the <jats:italic>LTR<\/jats:italic> (Long Terminal Repeat) and extending into the Matrix of the <jats:italic>gag<\/jats:italic> region (henceforth <jats:italic>LTR<\/jats:italic>), for detecting LPDV. Bone marrow samples from hunter-harvested Wild Turkeys (n = 925) were tested for LPDV with the <jats:italic>gag<\/jats:italic> gene and a subset (n = 417) including both those testing positive and those where LPDV was not detected was re-tested with <jats:italic>LTR<\/jats:italic>. The positive percent agreement (PPA) was 97.1% (68 of 70 <jats:italic>gag<\/jats:italic> positive samples tested positive with <jats:italic>LTR<\/jats:italic>) while the negative percent agreement (NPA) was only 68.0% (236 of 347 <jats:italic>gag<\/jats:italic> negative samples tested negative with <jats:italic>LTR<\/jats:italic>). Cohen\u2019s Kappa (\u03ba = 0.402, Z = 10.26, p&lt;0.0001) and the McNemar test (OR = 55.5, p&lt;0.0001) indicated weak agreement between the two gene regions. We found that in Iowa Wild Turkeys use of the <jats:italic>LTR<\/jats:italic> region identified LPDV in many samples in which we failed to detect LPDV using the <jats:italic>gag<\/jats:italic> region and that <jats:italic>LTR<\/jats:italic> may be more appropriate for LPDV surveillance and monitoring. However, neither region of the provirus resulted in perfect detection and additional work is necessary to determine if <jats:italic>LTR<\/jats:italic> is more reliable in other geographic regions where LPDV occurs.<\/jats:p>","DOI":"10.1371\/journal.pone.0296856","type":"journal-article","created":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T18:29:11Z","timestamp":1707762551000},"page":"e0296856","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Detection of lymphoproliferative disease virus in Iowa Wild Turkeys (Meleagris gallopavo): Comparison of two sections of the proviral genome"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9177-7709","authenticated-orcid":true,"given":"Kelsey C.","family":"Smith","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie A.","family":"Blanchong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,2,12]]},"reference":[{"issue":"2","key":"pone.0296856.ref001","first-page":"165","article-title":"Importance of wildlife disease surveillance","volume":"4","author":"JL Belant","year":"2010","journal-title":"Hum Wildl Interact"},{"issue":"2","key":"pone.0296856.ref002","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1111\/j.2041-210X.2011.00156.x","article-title":"Site-occupancy modelling as a novel framework for assessing test sensitivity and estimating wildlife disease prevalence from imperfect diagnostic tests: Occupancy models for disease prevalence estimates","volume":"3","author":"S Lachish","year":"2012","journal-title":"Methods Ecol Evol"},{"issue":"9","key":"pone.0296856.ref003","doi-asserted-by":"crossref","first-page":"e0237309","DOI":"10.1371\/journal.pone.0237309","article-title":"How sure are you? A web-based application to confront imperfect detection of respiratory pathogens in bighorn sheep","volume":"15","author":"JT Paterson","year":"2020","journal-title":"PLoS One"},{"key":"pone.0296856.ref004","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.virol.2013.11.037","article-title":"Avian oncogenesis induced by lymphoproliferative disease virus: A neglected or emerging retroviral pathogen?","volume":"450\u2013451","author":"AB Allison","year":"2014","journal-title":"Virology"},{"issue":"3","key":"pone.0296856.ref005","doi-asserted-by":"crossref","first-page":"499","DOI":"10.7589\/2016-06-137","article-title":"Risk factors for and spatial distribution of lymphoproliferative disease virus (LPDV) in wild turkeys (Meleagris gallopavo) in New York state, USA","volume":"53","author":"K Alger","year":"2017","journal-title":"J Wildl Dis"},{"issue":"3","key":"pone.0296856.ref006","article-title":"Pathogen survey and predictors of lymphoproliferative disease virus infection in wild turkeys (Meleagris gallopavo)","volume":"58","author":"SA Shea","year":"2022","journal-title":"J Wildl Dis"},{"issue":"2","key":"pone.0296856.ref007","article-title":"Prevalence of lymphoproliferative disease virus in wild turkeys (Melagris gallopavo) in North Carolina","volume":"46","author":"CD Kreh","year":"2022","journal-title":"Wildl Soc Bull"},{"issue":"4","key":"pone.0296856.ref008","doi-asserted-by":"crossref","first-page":"e0122644","DOI":"10.1371\/journal.pone.0122644","article-title":"Molecular surveillance for lymphoproliferative disease virus in wild turkeys (Meleagris gallopavo) from the Eastern United States","volume":"10","author":"JM Thomas","year":"2015","journal-title":"PLoS One"},{"issue":"4","key":"pone.0296856.ref009","first-page":"909","article-title":"Molecular surveillance for lymphoproliferative disease virus and reticuloendotheliosis virus in Rio Grande Wild Turkeys (Meleagris gallopavo intermedia) in Texas, USA","volume":"58","author":"F Cox","year":"2022","journal-title":"J Wildl Dis"},{"issue":"1","key":"pone.0296856.ref010","doi-asserted-by":"crossref","first-page":"113","DOI":"10.7589\/2018-01-013","article-title":"Detection of lymphoproliferative disease virus in Canada in a survey for viruses in Ontario wild turkeys (Meleagris gallopavo)","volume":"55","author":"AM MacDonald","year":"2019","journal-title":"J Wildl Dis"},{"issue":"3","key":"pone.0296856.ref011","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1637\/aviandiseases-D-19-00102","article-title":"Lymphoproliferative disease virus in wild turkeys (Meleagris gallopavo) from Manitoba and Quebec, Canada","volume":"63","author":"AM MacDonald","year":"2019","journal-title":"Avian Dis"},{"issue":"1","key":"pone.0296856.ref012","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1080\/03079457808418265","article-title":"Lymphoproliferative disease of turkeys I. clinical aspects","volume":"7","author":"PM Biggs","year":"1978","journal-title":"Avian Pathol"},{"issue":"4","key":"pone.0296856.ref013","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1638\/2015-0037.1","article-title":"Diagnosing lymphoproliferative disease virus in live wild turkeys (Meleagris gallopavo) using whole blood","volume":"46","author":"K Alger","year":"2015","journal-title":"J Zoo Wildl Med"},{"key":"pone.0296856.ref014","volume-title":"Medical Microbiology","author":"MW Cloyd","year":"1996","edition":"4"},{"issue":"suppl B","key":"pone.0296856.ref015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jac\/37.suppl_B.1","article-title":"Retrovirus classification and cell interactions","volume":"37","author":"RA Weiss","year":"1996","journal-title":"J Antimicrob Chemother"},{"key":"pone.0296856.ref016","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/rwvi.1999.0174","volume-title":"Encyclopedia of Virology","author":"A Gazit","year":"1999","edition":"2"},{"issue":"2","key":"pone.0296856.ref017","doi-asserted-by":"crossref","first-page":"e1280","DOI":"10.1002\/wsb.1280","article-title":"Detecting lymphoproliferative disease virus in wild turkeys using cloacal swabs","volume":"46","author":"SA Shea","year":"2022","journal-title":"Wildl Soc Bull"},{"issue":"1","key":"pone.0296856.ref018","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1759-8753-4-5","article-title":"Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).","volume":"4","author":"F Benachenhou","year":"2013","journal-title":"Mob DNA"},{"issue":"2","key":"pone.0296856.ref019","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/0378-1119(91)90122-R","article-title":"Lymphoproliferative disease virus of turkeys: sequence analysis and transcriptional activity of the long terminal repeat","volume":"99","author":"E Gak","year":"1991","journal-title":"Gene"},{"issue":"1","key":"pone.0296856.ref020","doi-asserted-by":"crossref","first-page":"6","DOI":"10.22456\/1679-9216.81074","article-title":"Teixeira MFDS. Detection of maedi-visna virus from sheep bronchoalveolar lavage by nested PCR evaluation of different primers pairs.","volume":"44","author":"RC Marinho","year":"2016","journal-title":"Acta Sci Vet"},{"key":"pone.0296856.ref021","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.bjm.2018.04.013","article-title":"Duplex nested-PCR for detection of small ruminant lentiviruses","volume":"49","author":"RC Marinho","year":"2018","journal-title":"Braz J Microbiol"},{"key":"pone.0296856.ref022","unstructured":"Eriksen RE, Brown TA, Scott KB, Hughes TW, Akridge MD, Penner CS. Status and distribution of wild turkeys in the United States: 2014 status. In: Miller DA, editor. Proceedings of the Eleventh National Wild Turkey Symposium. Tuscon, Arizona: The National Wild Turkey Federation; 2016. p. 7\u201318."},{"issue":"2","key":"pone.0296856.ref023","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/ajcp\/93.2.252","article-title":"Evaluating Diagnostic Tests with Imperfect Standards","volume":"93","author":"PN Valenstein","year":"1990","journal-title":"Am J Clin Pathol"},{"issue":"11","key":"pone.0296856.ref024","doi-asserted-by":"crossref","first-page":"3153","DOI":"10.1128\/JCM.00977-17","article-title":"Sensitivity and Specificity or Positive and Negative Percent Agreement? A Micro-Comic Strip","volume":"55","author":"AJ McAdam","year":"2017","journal-title":"J Clin Microbiol"},{"issue":"5","key":"pone.0296856.ref025","doi-asserted-by":"crossref","first-page":"e0217146","DOI":"10.1371\/journal.pone.0217146","article-title":"The effect of uncertainty in patient classification on diagnostic performance estimations","volume":"14","author":"LC McHugh","year":"2019","journal-title":"PLoS One"},{"issue":"3","key":"pone.0296856.ref026","doi-asserted-by":"crossref","first-page":"276","DOI":"10.11613\/BM.2012.031","article-title":"Interrater reliability: the kappa statistic","volume":"22","author":"ML McHugh","year":"2012","journal-title":"Biochem Med (Zagreb)"},{"issue":"1","key":"pone.0296856.ref027","doi-asserted-by":"crossref","first-page":"23","DOI":"10.20982\/tqmp.08.1.p023","article-title":"Computing Inter-Rater Reliability for Observational Data: An Overview and Tutorial","volume":"8","author":"KA Hallgren","year":"2012","journal-title":"Tutor Quant Methods Psychol"},{"key":"pone.0296856.ref028","author":"D Meyer","year":"2021","journal-title":"Visualizing Categorical Data. Version 1.4.9"},{"key":"pone.0296856.ref029","volume-title":"Version 4.1.1","author":"R Core Team","year":"2021"},{"issue":"11","key":"pone.0296856.ref030","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s00265-020-02916-y","article-title":"Effective use of the McNemar test","volume":"74","author":"MQR Pembury Smith","year":"2020","journal-title":"Behav Ecol Sociobiol"},{"issue":"1","key":"pone.0296856.ref031","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1471-2288-13-91","article-title":"The McNemar test for binary matched-pairs data: mid-p and asymptotic are better than exact conditional","volume":"13","author":"MW Fagerland","year":"2013","journal-title":"BMC Med Res Methodol"},{"issue":"1","key":"pone.0296856.ref032","doi-asserted-by":"crossref","first-page":"53","DOI":"10.32614\/RJ-2010-008","article-title":"Two-sided Exact Tests and Matching Confidence Intervals for Discrete Data","volume":"2","author":"M. Fay","year":"2010","journal-title":"R J"},{"key":"pone.0296856.ref033","article-title":"Exact2x2: Exact Tests and Confidence Intervals for 2x2 Tables","author":"MP Fay","year":"2021","journal-title":"Version 1.6.6 [software]"},{"key":"pone.0296856.ref034","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/978-3-319-27104-0_49","volume-title":"Clinical Data Analysis on a Pocket Calculator: Understanding the Scientific Methods of Statistical Reasoning and Hypothesis Testing","author":"TJ Cleophas","year":"2016"},{"key":"pone.0296856.ref035","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2020.01092","article-title":"Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution","volume":"11","author":"L Rubio","year":"2020","journal-title":"Front Plant Sci"},{"issue":"1","key":"pone.0296856.ref036","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1038\/s41467-019-09235-5","article-title":"Low genetic variation is associated with low mutation rate in the giant duckweed","volume":"10","author":"S Xu","year":"2019","journal-title":"Nat Commun"},{"key":"pone.0296856.ref037","unstructured":"Shea SA. Retroviral Infection Dynamics in Maine\u2019s Wild Turkeys. Ph.D Dissertation, University of Maine. 2021. Available from: https:\/\/digitalcommons.library.umaine.edu\/cgi\/viewcontent.cgi?article=4568&context=etd"},{"key":"pone.0296856.ref038","unstructured":"Alger K. Lymphoproliferative disease virus (LPDV) in wild turkeys (Meleagris gallopavo) in New York State: Diagnostic methods, prevalence, and spatial distribution of a newly discovered pathogen. M.Sc. Thesis, State University of New York. 2015."},{"key":"pone.0296856.ref039","unstructured":"Smith KC. Lymphoproliferative disease virus (LPDV) in Iowa\u2019s Wild Turkeys (Meleagris gallopavo).M.Sc. Thesis, Iowa State University. 2022. Available from: https:\/\/www.proquest.com\/openview\/b95c0d0e689d528c34c679578d3112c8\/1"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0296856","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T18:29:32Z","timestamp":1707762572000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0296856"}},"subtitle":[],"editor":[{"given":"Elisabetta","family":"Pilotti","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,2,12]]},"references-count":39,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2024,2,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0296856","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,12]]}}}