{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T07:15:21Z","timestamp":1776669321723,"version":"3.51.2"},"reference-count":55,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T00:00:00Z","timestamp":1746057600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T00:00:00Z","timestamp":1746057600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T00:00:00Z","timestamp":1741305600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008771","name":"Animal and Plant Quarantine Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008771","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Poultry Science"],"published-print":{"date-parts":[[2025,5]]},"DOI":"10.1016\/j.psj.2025.105007","type":"journal-article","created":{"date-parts":[[2025,3,10]],"date-time":"2025-03-10T12:48:54Z","timestamp":1741610934000},"page":"105007","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["The complete genome sequence of quail coronavirus identified in disease surveillance on quail farms in South Korea"],"prefix":"10.1016","volume":"104","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8926-2298","authenticated-orcid":false,"given":"Hye-Ryoung","family":"Kim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6300-2609","authenticated-orcid":false,"given":"So-Hyeon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hoang Duc","family":"Le","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7409-9941","authenticated-orcid":false,"given":"Jae-Kyeom","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moon","family":"Her","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.psj.2025.105007_bib0001","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2021.104831","article-title":"Mutations in SARS-CoV-2; consequences in structure, function, and pathogenicity of the virus","volume":"154","author":"Bakhshandeh","year":"2021","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.psj.2025.105007_bib0002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/03079457.2010.542575","article-title":"Pullorum disease and fowl typhoid\u2014New thoughts on old diseases: a review","volume":"40","author":"Barrow","year":"2011","journal-title":"Avian Pathol."},{"key":"10.1016\/j.psj.2025.105007_bib0003","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.3390\/v4061011","article-title":"Mechanisms of coronavirus cell entry mediated by the viral spike protein","volume":"4","author":"Belouzard","year":"2012","journal-title":"Viruses"},{"key":"10.1016\/j.psj.2025.105007_bib0004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1297-9716-44-23","article-title":"Pathobiology and transmission of highly and low pathogenic avian influenza viruses in European quail (Coturnix c. coturnix)","volume":"44","author":"Bertran","year":"2013","journal-title":"Vet. Res."},{"key":"10.1016\/j.psj.2025.105007_bib0005","doi-asserted-by":"crossref","first-page":"212","DOI":"10.2307\/1588003","article-title":"Diseases of Japanese quail (Coturnix coturnix japonica): a flock survey and experimental transmission of selected avian pathogens","volume":"9","author":"Bigland","year":"1965","journal-title":"Avian Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0006","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.psj.2025.105007_bib0007","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1099\/jgv.0.000338","article-title":"First complete genome sequence of European turkey coronavirus suggests complex recombination history related with US turkey and guinea fowl coronaviruses","volume":"97","author":"Brown","year":"2016","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.psj.2025.105007_bib0008","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.jviromet.2006.07.018","article-title":"Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens","volume":"138","author":"Callison","year":"2006","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.psj.2025.105007_bib0009","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.mcp.2004.04.003","article-title":"Development of a multiplex PCR for detection of avian adenovirus, avian reovirus, infectious bursal disease virus, and chicken anemia virus","volume":"18","author":"Caterina","year":"2004","journal-title":"Mol. Cell. Probes."},{"key":"10.1016\/j.psj.2025.105007_bib0010","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1051\/vetres:2006055","article-title":"Coronavirus avian infectious bronchitis virus","volume":"38","author":"Cavanagh","year":"2007","journal-title":"Vet. Res."},{"key":"10.1016\/j.psj.2025.105007_bib0011","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.psj.2025.105007_bib0012","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1080\/03079450701344738","article-title":"Coronavirus associated with an enteric syndrome on a quail farm","volume":"36","author":"Circella","year":"2007","journal-title":"Avian Pathol."},{"key":"10.1016\/j.psj.2025.105007_bib0013","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1080\/03079450020023140","article-title":"An in vitro and in vivo evaluation of the virulence of egg drop syndrome virus for the chicken reproductive tract","volume":"30","author":"Dhinakar Raj","year":"2001","journal-title":"Avian Pathol."},{"key":"10.1016\/j.psj.2025.105007_bib0014","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/s11262-019-01639-1","article-title":"Whole genome characterisation of quail deltacoronavirus detected in Poland","volume":"55","author":"Doma\u0144ska-Blicharz","year":"2019","journal-title":"Virus Genes"},{"key":"10.1016\/j.psj.2025.105007_bib0015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.psj.2021.101018","article-title":"Recombinant turkey coronavirus: are some S gene structures of gammacoronaviruses especially prone to exchange?","volume":"100","author":"Domanska-Blicharz","year":"2021","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0016","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1007\/s11262-015-1183-z","article-title":"Full genome sequence of guinea fowl coronavirus associated with fulminating disease","volume":"50","author":"Ducatez","year":"2015","journal-title":"Virus Genes"},{"key":"10.1016\/j.psj.2025.105007_bib0017","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1016\/j.psj.2020.01.026","article-title":"Molecular and pathogenicity of infectious bronchitis virus (Gammacoronavirus) in Japanese quail (Coturnix japonica)","volume":"99","author":"Fadhilah","year":"2020","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0018","series-title":"Diseases of Poultry","first-page":"167","article-title":"Infectious bronchitis","author":"Jackwood","year":"2020"},{"key":"10.1016\/j.psj.2025.105007_bib0019","doi-asserted-by":"crossref","first-page":"53","DOI":"10.4142\/jvs.2009.10.1.53","article-title":"Experimental infection of chickens, ducks and quails with the highly pathogenic H5N1 avian influenza virus","volume":"10","author":"Jeong","year":"2009","journal-title":"J. Vet. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0020","first-page":"40","article-title":"Viral metagenomic analysis of Japanese quail (Coturnix japonica) with enteritis in the Republic of Korea","volume":"65","author":"Kim","year":"2021","journal-title":"Avian Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0021","doi-asserted-by":"crossref","first-page":"3469","DOI":"10.3390\/ani13223469","article-title":"Intrahepatic cholangiocarcinoma identified in a zoo-housed sandhill crane (Grus canadensis): an anatomopathological and metagenomic study","volume":"13","author":"Kim","year":"2023","journal-title":"Animals"},{"key":"10.1016\/j.psj.2025.105007_bib0022","doi-asserted-by":"crossref","first-page":"480","DOI":"10.3201\/1803.111490","article-title":"Highly pathogenic avian influenza (H5N1) outbreaks in wild birds and poultry, South Korea","volume":"18","author":"Kim","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0023","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1637\/0005-2086(2007)51[540:DOORTC]2.0.CO;2","article-title":"Development of one-step reverse transcriptase\u2013polymerase chain reaction to detect duck hepatitis virus type 1","volume":"51","author":"Kim","year":"2007","journal-title":"Avian Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0024","series-title":"The UFAW Handbook on the Care and Management of Laboratory and Other Research Animals 9th ed.","first-page":"762","article-title":"The Japanese quail","author":"Lansford","year":"2024"},{"key":"10.1016\/j.psj.2025.105007_bib0025","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/v16040515","article-title":"An amplicon-based application for the whole-genome sequencing of GI-19 lineage infectious bronchitis virus directly from clinical samples","volume":"16","author":"Le","year":"2024","journal-title":"Viruses"},{"key":"10.1016\/j.psj.2025.105007_bib0026","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.17582\/journal.aavs\/2022\/10.7.1481.1491","article-title":"Phylogenetic and histopathological characterization of newcastle disease virus (VII. 1.1) recently isolated from naturally infected quails in Egypt","volume":"10","author":"Lebdah","year":"2022","journal-title":"Adv. Anim. Vet. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0027","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.psj.2025.105007_bib0028","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.psj.2025.105007_bib0029","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"10.1016\/j.psj.2025.105007_bib0030","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"10.1016\/j.psj.2025.105007_bib0031","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1080\/03079457.2011.551936","article-title":"First full-length sequences of the S gene of European isolates reveal further diversity among turkey coronaviruses","volume":"40","author":"Maurel","year":"2011","journal-title":"Avian Pathol."},{"key":"10.1016\/j.psj.2025.105007_bib0032","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1007\/s11259-009-9321-5","article-title":"Characterization of Newcastle disease viruses isolated from chicken, gamefowl, pigeon and quail in Mexico","volume":"33","author":"Merino","year":"2009","journal-title":"Vet. Res. Commun."},{"key":"10.1016\/j.psj.2025.105007_bib0033","unstructured":"Mizutani, M., 2003. The Japanese quail. Available online: https:\/\/www.angrin.tlri.gov.tw\/apec2003\/chapter5jpquail.pdf . (accessed on 20 November 2024)."},{"key":"10.1016\/j.psj.2025.105007_bib0034","series-title":"Diseases of Poultry","first-page":"548","article-title":"Neoplastic diseases","author":"Nair","year":"2020"},{"key":"10.1016\/j.psj.2025.105007_bib0035","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1080\/03079459208418823","article-title":"Detection of chicken anaemia virus by DNA hybridization and polymerase chain reaction","volume":"21","author":"Noteborn","year":"1992","journal-title":"Avian Pathol."},{"key":"10.1016\/j.psj.2025.105007_bib0036","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.psj.2025.105007_bib0037","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1136\/vr.146.10.273","article-title":"Causes of mortality and culling in adult pheasants","volume":"146","author":"Pennycott","year":"2000","journal-title":"Vet. Rec."},{"key":"10.1016\/j.psj.2025.105007_bib0038","series-title":"Diseases of Poultry","first-page":"401","article-title":"Viral enteric infections","author":"Saif","year":"2020"},{"key":"10.1016\/j.psj.2025.105007_bib0039","first-page":"17","article-title":"ITIS (The Integrated Taxonomic Information System)","volume":"29","author":"Shaw","year":"2004","journal-title":"Navigating Shoals: Evolving User Serv. Aquatic Marine Sci. Lib.: Proc. 29th Annu. Conf. Int. Assoc. Aquatic Marine Sci. Lib. Inform. Centers (IAMSLIC)"},{"key":"10.1016\/j.psj.2025.105007_bib0040","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.3382\/ps\/pew217","article-title":"Molecular characterization of quail bronchitis virus isolated from bobwhite quail in Minnesota","volume":"95","author":"Singh","year":"2016","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0041","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/S0168-1702(98)00022-7","article-title":"Development and application of polymerase chain reaction (PCR) tests for the detection of subgroup J avian leukosis virus","volume":"54","author":"Smith","year":"1998","journal-title":"Virus. Res."},{"key":"10.1016\/j.psj.2025.105007_bib0042","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.psj.2021.01.009","article-title":"Simultaneous detection of infectious laryngotracheitis virus, fowlpox virus, and reticuloendotheliosis virus in chicken specimens","volume":"100","author":"Song","year":"2021","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0043","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1136\/vr.113.15.354","article-title":"Isolation of infectious bronchitis virus from pheasants","volume":"113","author":"Spackman","year":"1983","journal-title":"Vet. Rec."},{"key":"10.1016\/j.psj.2025.105007_bib0044","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.psj.2025.105007_bib0045","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.cimid.2018.01.001","article-title":"Novel reassortant H5N6 highly pathogenic influenza A viruses in Vietnamese quail outbreaks","volume":"56","author":"Thanh","year":"2018","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0046","doi-asserted-by":"crossref","first-page":"717","DOI":"10.3382\/ps\/pew332","article-title":"Gamma and Deltacoronaviruses in quail and pheasants from Northern Italy","volume":"96","author":"Torres","year":"2017","journal-title":"Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0047","doi-asserted-by":"crossref","first-page":"925","DOI":"10.3923\/ijps.2008.925.931","article-title":"The Japanese quail: a review","volume":"7","author":"Vali","year":"2008","journal-title":"Int. J. Poult. Sci."},{"key":"10.1016\/j.psj.2025.105007_bib0048","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12985-017-0775-8","article-title":"A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination","volume":"14","author":"van Beurden","year":"2017","journal-title":"Virol. J."},{"key":"10.1016\/j.psj.2025.105007_bib0049","doi-asserted-by":"crossref","first-page":"315","DOI":"10.2165\/00063030-200822050-00004","article-title":"The impact of PEGylation on biological therapies","volume":"22","author":"Veronese","year":"2008","journal-title":"BioDrugs"},{"key":"10.1016\/j.psj.2025.105007_bib0050","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1006\/mcpr.1997.0108","article-title":"Multiplex PCR for avian pathogenic mycoplasmas","volume":"11","author":"Wang","year":"1997","journal-title":"Mol. Cell. Probes."},{"key":"10.1016\/j.psj.2025.105007_bib0051","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.psj.2025.105007_bib0052","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1637\/9668-012711-ResNote.1","article-title":"Rapid detection of Marek's disease virus in feather follicles by loop-mediated amplification","volume":"55","author":"Wo\u017aniakowski","year":"2011","journal-title":"Avian Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0053","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1637\/7307-111804R","article-title":"Reverse transcriptase-polymerase chain reaction to detect avian encephalomyelitis virus","volume":"49","author":"Xie","year":"2005","journal-title":"Avian Dis."},{"key":"10.1016\/j.psj.2025.105007_bib0054","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.mcp.2006.01.003","article-title":"A multiplex RT-PCR for detection of type A influenza virus and differentiation of avian H5, H7, and H9 hemagglutinin subtypes","volume":"20","author":"Xie","year":"2006","journal-title":"Mol. Cell. Probes."},{"key":"10.1016\/j.psj.2025.105007_bib0055","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/0042-6822(70)90218-7","article-title":"Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification","volume":"40","author":"Yamamoto","year":"1970","journal-title":"Virol"}],"container-title":["Poultry Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579125002469?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0032579125002469?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T06:33:22Z","timestamp":1776666802000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0032579125002469"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5]]},"references-count":55,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2025,5]]}},"alternative-id":["S0032579125002469"],"URL":"https:\/\/doi.org\/10.1016\/j.psj.2025.105007","relation":{},"ISSN":["0032-5791"],"issn-type":[{"value":"0032-5791","type":"print"}],"subject":[],"published":{"date-parts":[[2025,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The complete genome sequence of quail coronavirus identified in disease surveillance on quail farms in South Korea","name":"articletitle","label":"Article Title"},{"value":"Poultry Science","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.psj.2025.105007","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc. on behalf of Poultry Science Association Inc.","name":"copyright","label":"Copyright"}],"article-number":"105007"}}