{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T07:44:48Z","timestamp":1790063088749,"version":"4.0.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,12,4]],"date-time":"2021-12-04T00:00:00Z","timestamp":1638576000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Atypical porcine pestivirus (APPV), an RNA virus member of the Flaviviridae family, has been associated with congenital tremor in newborn piglets. Previously reported quantitative polymerase chain reaction (qPCR)\u2013based assays were unable to detect APPV in novel cases of congenital tremor originated from multiple farms from U.S. Midwest (MW). These assays targeted the viral polyprotein coding genes, which were shown to display substantial variation, with sequence identity ranging from 58.2% to 70.7% among 15 global APPV strains. In contrast, the 5\u2032-untranslated region (5\u2032 UTR) was found to have a much higher degree of sequence conservation. In order to obtain the complete 5\u2032 UTR of the APPV strains originated from MW, the 5\u2032 end of the viral cDNA was obtained by using template switching approach followed by amplification and dideoxy sequencing. Eighty one percent of the 5\u2032 UTR was identical across 14 global and 5 MW strains with complete or relatively complete 5\u2032 UTR. Notably, some of the most highly conserved 5\u2032 UTR segments overlapped with potentially important regions of an internal ribosome entry site (IRES), suggesting their functional role in viral protein translation. A newly designed single qPCR assay, targeting 100% conserved 5\u2032 UTR regions across 19 strains, was able to detect APPV in samples of well documented cases of congenital tremor which originated from five MW farm sites (1\u201318 samples\/site). As these fully conserved 5\u2032 UTR sequences may have functional importance, we expect that assays targeting this region would broadly detect APPV strains that are diverse in space and time.<\/jats:p>","DOI":"10.1093\/jas\/skab360","type":"journal-article","created":{"date-parts":[[2021,12,5]],"date-time":"2021-12-05T09:52:50Z","timestamp":1638697970000},"source":"Crossref","is-referenced-by-count":3,"title":["Genetic diversity and detection of atypical porcine pestivirus infections"],"prefix":"10.1093","volume":"100","author":[{"given":"Kylee M","family":"Sutton","sequence":"first","affiliation":[{"name":"Animal Science Department, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"},{"name":"School of Biological Sciences, University of Nebraska\u2013Lincoln, Lincoln, NE 68502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian W","family":"Eaton","sequence":"additional","affiliation":[{"name":"Animal Science Department, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"},{"name":"School of Veterinary Medicine and Biomedical Sciences, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tudor","family":"Borza","sequence":"additional","affiliation":[{"name":"Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, B2N 5E3, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6341-2403","authenticated-orcid":false,"given":"Thomas E","family":"Burkey","sequence":"additional","affiliation":[{"name":"Animal Science Department, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benny E","family":"Mote","sequence":"additional","affiliation":[{"name":"Animal Science Department, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Dustin","family":"Loy","sequence":"additional","affiliation":[{"name":"Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7301-1339","authenticated-orcid":false,"given":"Daniel C","family":"Ciobanu","sequence":"additional","affiliation":[{"name":"Animal Science Department, University of Nebraska\u2013Lincoln, Lincoln, NE 68583, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,12,4]]},"reference":[{"key":"2022011515192730300_CIT0001","doi-asserted-by":"crossref","first-page":"e0150104","DOI":"10.1371\/journal.pone.0150104","article-title":"Identification of a divergent lineage porcine pestivirus in nursing piglets with congenital tremors and reproduction of disease following experimental inoculation","volume":"11","author":"Arruda","year":"2016","journal-title":"PLoS One"},{"issue":"5","key":"2022011515192730300_CIT0002","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1111\/tbed.12532","article-title":"High prevalence of highly variable atypical porcine pestiviruses found in Germany","volume":"64","author":"Beer","year":"2017","journal-title":"Transbound Emerg Dis"},{"key":"2022011515192730300_CIT0003","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1006\/viro.1998.9425","article-title":"Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus","volume":"251","author":"Chon","year":"1998","journal-title":"Virology"},{"issue":"22","key":"2022011515192730300_CIT0004","doi-asserted-by":"crossref","first-page":"10,881","DOI":"10.1093\/nar\/16.22.10881","article-title":"Multiple sequence alignment with hierarchical clustering","volume":"16","author":"Corpet","year":"1988","journal-title":"Nucleic Acid Res"},{"key":"2022011515192730300_CIT0005","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1093\/nar\/21.8.1949","article-title":"5\u2019 and 3\u2019 untranslated regions of pestivirus genome: primary and secondary structure analyses","volume":"21","author":"Deng","year":"1993","journal-title":"Nucleic Acids Res"},{"key":"2022011515192730300_CIT0501","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2022011515192730300_CIT0006","doi-asserted-by":"crossref","first-page":"5024","DOI":"10.1128\/JVI.76.10.5024-5033.2002","article-title":"Pestivirus internal ribosome entry site (IRES) structure and function: elements in the 5\u2019 untranslated region important for IRES function","volume":"76","author":"Fletcher","year":"2002","journal-title":"J. Virol"},{"issue":"10","key":"2022011515192730300_CIT0007","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.3390\/v12101080","article-title":"Atypical porcine pestivirus circulation and molecular evolution within an affected swine herd","volume":"12","author":"Folgueiras-Gonz\u00e1lez","year":"2020","journal-title":"Viruses"},{"key":"2022011515192730300_CIT0008","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.virol.2005.01.007","article-title":"Hepatitis C virus and the related bovine viral diarrhea virus considerably differ in the functional organization of the 5\u2019 non-translated region: implications for the viral life cycle","volume":"333","author":"Grassmann","year":"2005","journal-title":"Virology"},{"issue":"10","key":"2022011515192730300_CIT0009","doi-asserted-by":"crossref","first-page":"271","DOI":"10.3390\/v8100271","article-title":"Atypical porcine pestivirus: a possible cause of congenital tremor type A-II in newborn piglets","volume":"8","author":"de Groof","year":"2016","journal-title":"Viruses"},{"key":"2022011515192730300_CIT0010","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1099\/jgv.0.000251","article-title":"Discovery of a novel putative atypical porcine pestivirus in pigs in the USA","volume":"96","author":"Hause","year":"2015","journal-title":"J. Gen. Virol"},{"key":"2022011515192730300_CIT0011","doi-asserted-by":"crossref","first-page":"5850","DOI":"10.1128\/JVI.02403-06","article-title":"A distinct group of hepacivirus\/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination","volume":"81","author":"Hellen","year":"2007","journal-title":"J. Virol"},{"issue":"7","key":"2022011515192730300_CIT0012","doi-asserted-by":"crossref","first-page":"653","DOI":"10.3390\/v11070653","article-title":"Long-term circulation of Atypical Porcine Pestivirus (APPV) within Switzerland","volume":"11","author":"Kaufmann","year":"2019","journal-title":"Viruses"},{"key":"2022011515192730300_CIT0013","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1017\/S1355838200000662","article-title":"Ribosomal binding to the internal ribosomal entry site of classical swine fever virus","volume":"6","author":"Kolupaeva","year":"2000","journal-title":"Rna"},{"key":"2022011515192730300_CIT0014","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol"},{"key":"2022011515192730300_CIT0015","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol. Biol"},{"key":"2022011515192730300_CIT0016","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1111\/tbed.12753","article-title":"Presence of atypical porcine pestivirus (APPV) in Brazilian pigs","volume":"65","author":"M\u00f3sena","year":"2018","journal-title":"Transbound. Emerg. Dis"},{"key":"2022011515192730300_CIT0017","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.virol.2018.12.002","article-title":"Identification of BVDV2b and 2c subgenotypes in the United States: genetic and antigenic characterization","volume":"528","author":"Neill","year":"2019","journal-title":"Virology"},{"key":"2022011515192730300_CIT0019","first-page":"16","article-title":"Development of a sensitive and reliable diagnostic assay to detect atypical porcine pestivirus (APPV) in Swine.","volume-title":"Diagnostic assay catalog","author":"Peddireddi","year":"2020"},{"key":"2022011515192730300_CIT0020","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/S0014-5793(99)00662-6","article-title":"Mutational analysis of a conserved tetraloop in the 5\u2019 untranslated region of hepatitis C virus identifies a novel RNA element essential for the internal ribosome entry site function","volume":"453","author":"Psaridi","year":"1999","journal-title":"FEBS Lett"},{"key":"2022011515192730300_CIT0021","doi-asserted-by":"crossref","first-page":"7645","DOI":"10.1128\/JVI.77.13.7645-7654.2003","article-title":"Classical swine fever virus interferes with cellular antiviral defense: evidence for a novel function of N(pro)","volume":"77","author":"Ruggli","year":"2003","journal-title":"J. Virol"},{"key":"2022011515192730300_CIT0022","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13567-016-0406-1","article-title":"Congenital infection with atypical porcine pestivirus (APPV) is associated with disease and viral persistence","volume":"48","author":"Schwarz","year":"2017","journal-title":"Vet. Res"},{"key":"2022011515192730300_CIT0023","doi-asserted-by":"crossref","first-page":"4775","DOI":"10.1128\/JVI.72.6.4775-4782.1998","article-title":"Specific interaction of eukaryotic translation initiation factor 3 with the 5\u2019 nontranslated regions of hepatitis C virus and classical swine fever virus RNAs","volume":"72","author":"Sizova","year":"1998","journal-title":"J. Virol"},{"key":"2022011515192730300_CIT0024","doi-asserted-by":"crossref","first-page":"7088","DOI":"10.1128\/jvi.67.12.7088-7095.1993","article-title":"Processing of pestivirus polyprotein: cleavage site between autoprotease and nucleocapsid protein of classical swine fever virus","volume":"67","author":"Stark","year":"1993","journal-title":"J. Virol"},{"issue":"10","key":"2022011515192730300_CIT0025","doi-asserted-by":"crossref","first-page":"4093","DOI":"10.1093\/jas\/skz267","article-title":"Detection of atypical porcine pestivirus genome in newborn piglets affected by congenital tremor and high preweaning mortality","volume":"97","author":"Sutton","year":"2019","journal-title":"J. Anim. Sci"},{"key":"2022011515192730300_CIT0026","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol. Biol. Evol"},{"key":"2022011515192730300_CIT0027","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/viro.1993.1097","article-title":"RNA-stimulated NTPase activity associated with the p80 protein of the pestivirus bovine viral diarrhea virus","volume":"193","author":"Tamura","year":"1993","journal-title":"Virology"},{"key":"2022011515192730300_CIT0029","doi-asserted-by":"crossref","first-page":"7681","DOI":"10.1128\/JVI.72.9.7681-7684.1998","article-title":"Classical swine fever virus leader proteinase Npro is not required for viral replication in cell culture","volume":"72","author":"Tratschin","year":"1998","journal-title":"J. Virol"},{"key":"2022011515192730300_CIT0030","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1128\/jvi.69.3.1720-1726.1995","article-title":"Pestivirus NS3 (p80) protein possesses RNA helicase activity","volume":"69","author":"Warrener","year":"1995","journal-title":"J. Virol"},{"key":"2022011515192730300_CIT0031","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1186\/1743-422X-6-185","article-title":"Bovine viral diarrhea virus NS4B protein is an integral membrane protein associated with Golgi markers and rearranged host membranes","volume":"6","author":"Weiskircher","year":"2009","journal-title":"Virol. J"},{"key":"2022011515192730300_CIT0032","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/0042-6822(91)90850-B","article-title":"Pestivirus gene expression: protein p80 of bovine viral diarrhea virus is a proteinase involved in polyprotein processing","volume":"184","author":"Wiskerchen","year":"1991","journal-title":"Virology"},{"key":"2022011515192730300_CIT0502","doi-asserted-by":"crossref","first-page":"114220","DOI":"10.1016\/j.jviromet.2021.114220","article-title":"Development of a quantitative real time RT-PCR assay for sensitive and rapid detection of emerging Atypical Porcine Pestivirus associated with congenital tremor in pigs","volume":"296","author":"Yuan","year":"2021","journal-title":"J. Virol. Methods"},{"key":"2022011515192730300_CIT0033","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Animal Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/100\/1\/skab360\/42201735\/skab360.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/100\/1\/skab360\/42201735\/skab360.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,15]],"date-time":"2022-01-15T15:20:06Z","timestamp":1642260006000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jas\/article\/doi\/10.1093\/jas\/skab360\/6449490"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,4]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,12,4]]},"published-print":{"date-parts":[[2022,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jas\/skab360","relation":{},"ISSN":["0021-8812","1525-3163"],"issn-type":[{"value":"0021-8812","type":"print"},{"value":"1525-3163","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,12,4]]},"article-number":"skab360"}}