{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T01:59:14Z","timestamp":1762221554583,"version":"build-2065373602"},"reference-count":46,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100021171","name":"Basic and Applied Basic Research Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2024A1515012840"],"award-info":[{"award-number":["2024A1515012840"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Virology"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1016\/j.virol.2025.110528","type":"journal-article","created":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T02:18:56Z","timestamp":1744165136000},"page":"110528","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Genetic diversity of canine coronavirus identified in dogs in yulin city, southern China"],"prefix":"10.1016","volume":"608","author":[{"given":"Chun-Yang","family":"Lian","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin-Yan","family":"Yao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi-Hang","family":"Lv","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xue-Lian","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9548-3831","authenticated-orcid":false,"given":"Jian-Wei","family":"Shao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.virol.2025.110528_bib1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.virol.2025.110528_bib2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/s00705-009-0547-x","article-title":"Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses (2009)","volume":"155","author":"Carstens","year":"2010","journal-title":"Arch. Virol."},{"key":"10.1016\/j.virol.2025.110528_bib3","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/s12985-024-02425-8","article-title":"A systematic review and meta-analysis of canine enteric coronavirus prevalence in dogs of mainland China","volume":"21","author":"Chen","year":"2024","journal-title":"Virol. J."},{"key":"10.1016\/j.virol.2025.110528_bib4","doi-asserted-by":"crossref","first-page":"i884","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.virol.2025.110528_bib5","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/bs.aivir.2018.01.001","article-title":"Hosts and sources of endemic human coronaviruses","volume":"100","author":"Corman","year":"2018","journal-title":"Adv. Virus Res."},{"key":"10.1016\/j.virol.2025.110528_bib6","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"Cui","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib7","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.vetmic.2008.06.007","article-title":"An update on canine coronaviruses: viral evolution and pathobiology","volume":"132","author":"Decaro","year":"2008","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib8","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1128\/JVI.01937-08","article-title":"Recombinant canine coronaviruses related to transmissible gastroenteritis virus of swine are circulating in dogs","volume":"83","author":"Decaro","year":"2009","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2025.110528_bib9","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.virusres.2006.12.006","article-title":"Molecular characterisation of the virulent canine coronavirus CB\/05 strain","volume":"125","author":"Decaro","year":"2007","journal-title":"Virus Res."},{"key":"10.1016\/j.virol.2025.110528_bib10","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.jviromet.2004.03.012","article-title":"Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR","volume":"119","author":"Decaro","year":"2004","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.virol.2025.110528_bib11","doi-asserted-by":"crossref","DOI":"10.1016\/j.prevetmed.2022.105792","article-title":"Epidemiological investigation of canine coronavirus infection in Chinese domestic dogs: a systematic review and data synthesis","volume":"209","author":"Dong","year":"2022","journal-title":"Prev. Vet. Med."},{"key":"10.1016\/j.virol.2025.110528_bib12","doi-asserted-by":"crossref","first-page":"vev023","DOI":"10.1093\/ve\/vev023","article-title":"MERS-CoV recombination: implications about the reservoir and potential for adaptation","volume":"2","author":"Dudas","year":"2016","journal-title":"Virus Evol"},{"key":"10.1016\/j.virol.2025.110528_bib13","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.virusres.2008.12.009","article-title":"Sequence analysis of divergent canine coronavirus strains present in a UK dog population","volume":"141","author":"Erles","year":"2009","journal-title":"Virus Res."},{"key":"10.1016\/j.virol.2025.110528_bib14","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"10.1016\/j.virol.2025.110528_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2020.104209","article-title":"Etiology and genetic evolution of canine coronavirus circulating in five provinces of China, during 2018\u20132019","volume":"145","author":"He","year":"2020","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.virol.2025.110528_bib16","doi-asserted-by":"crossref","first-page":"4508","DOI":"10.1128\/JVI.72.5.4508-4514.1998","article-title":"Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus","volume":"72","author":"Herrewegh","year":"1998","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2025.110528_bib17","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/s41579-020-00459-7","article-title":"Characteristics of SARS-CoV-2 and COVID-19","volume":"19","author":"Hu","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006698","article-title":"Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus","volume":"13","author":"Hu","year":"2017","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.virol.2025.110528_bib19","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1056\/NEJMoa030781","article-title":"A novel coronavirus associated with severe acute respiratory syndrome","volume":"348","author":"Ksiazek","year":"2003","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.virol.2025.110528_bib20","doi-asserted-by":"crossref","first-page":"e1184","DOI":"10.1093\/cid\/ciab924","article-title":"Isolation of a novel recombinant canine coronavirus from a visitor to Haiti: further evidence of transmission of coronaviruses of zoonotic origin to humans","volume":"75","author":"Lednicky","year":"2022","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.virol.2025.110528_bib21","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.virol.2025.110528_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.cimid.2023.101956","article-title":"Prevalence and genetic diversity of canine coronavirus in northeastern China during 2019-2021","volume":"94","author":"Li","year":"2023","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"10.1016\/j.virol.2025.110528_bib23","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.3201\/eid1803.120002","article-title":"New variants of porcine epidemic diarrhea virus, China, 2011","volume":"18","author":"Li","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.virol.2025.110528_bib24","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s11427-016-5038-1","article-title":"Genetic and antigenic characterization of recombinant nucleocapsid proteins derived from canine coronavirus and canine respiratory coronavirus in China","volume":"59","author":"Lu","year":"2016","journal-title":"Sci. China Life Sci."},{"key":"10.1016\/j.virol.2025.110528_bib25","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41579-023-00878-2","article-title":"The evolution of SARS-CoV-2","volume":"21","author":"Markov","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib26","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol"},{"key":"10.1016\/j.virol.2025.110528_bib27","first-page":"418","article-title":"Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions","volume":"3","author":"Nei","year":"1986","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.virol.2025.110528_bib28","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1128\/JCM.42.4.1797-1799.2004","article-title":"Two genotypes of canine coronavirus simultaneously detected in the fecal samples of dogs with diarrhea","volume":"42","author":"Pratelli","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib29","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S0166-0934(99)00017-8","article-title":"Development of a nested PCR assay for the detection of canine coronavirus","volume":"80","author":"Pratelli","year":"1999","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.virol.2025.110528_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2022.105548","article-title":"Detection and molecular characteristics of canine coronavirus in Chengdu city, southwest China from 2020 to 2021","volume":"166","author":"Sha","year":"2022","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.virol.2025.110528_bib47","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.3390\/v13112206","article-title":"A novel subtype of bovine hepacivirus identified in ticks reveals the genetic diversity and evolution of bovine hepacivirus","volume":"13","author":"Shao","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.virol.2025.110528_bib31","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nrmicro2614","article-title":"Why do RNA viruses recombine?","volume":"9","author":"Simon-Loriere","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib32","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/78132","article-title":"Molecular breeding of viruses","volume":"25","author":"Soong","year":"2000","journal-title":"Nat. Genet."},{"key":"10.1016\/j.virol.2025.110528_bib33","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1016\/j.cell.2020.08.012","article-title":"Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding","volume":"182","author":"Starr","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.virol.2025.110528_bib34","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.tim.2016.03.003","article-title":"Epidemiology, genetic recombination, and pathogenesis of coronaviruses","volume":"24","author":"Su","year":"2016","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.virol.2025.110528_bib35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0106534","article-title":"Emergence of pathogenic coronaviruses in cats by homologous recombination between feline and canine coronaviruses","volume":"9","author":"Terada","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.virol.2025.110528_bib36","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Briefings Bioinf."},{"key":"10.1016\/j.virol.2025.110528_bib37","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1292\/jvms.16-0538","article-title":"Characterization of canine coronavirus spread among domestic dogs in Vietnam","volume":"79","author":"van Nguyen","year":"2017","journal-title":"J. Vet. Med. Sci."},{"key":"10.1016\/j.virol.2025.110528_bib38","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1093\/cid\/ciab456","article-title":"Novel canine coronavirus isolated from a hospitalized patient with pneumonia in East Malaysia","volume":"74","author":"Vlasova","year":"2022","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.virol.2025.110528_bib39","doi-asserted-by":"crossref","first-page":"veac046","DOI":"10.1093\/ve\/veac046","article-title":"Coronaviruses in wild animals sampled in and around Wuhan at the beginning of COVID-19 emergence","volume":"8","author":"Wang","year":"2022","journal-title":"Virus Evol"},{"key":"10.1016\/j.virol.2025.110528_bib40","article-title":"Co-circulation of canine coronavirus I and IIa\/b with high prevalence and genetic diversity in Heilongjiang province, northeast China","volume":"11","author":"Wang","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.virol.2025.110528_bib41","doi-asserted-by":"crossref","first-page":"3995","DOI":"10.1128\/JVI.06540-11","volume":"86","author":"Woo","year":"2012","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2025.110528_bib42","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.virol.2025.110528_bib43","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2023.105463","article-title":"Molecular epidemiology and genetic diversity of canine coronavirus from domestic dogs in Chengdu, China from 2020 to 2021 using a multiplex RT-PCR","volume":"112","author":"Wu","year":"2023","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.virol.2025.110528_bib44","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1056\/NEJMoa1211721","article-title":"Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia","volume":"367","author":"Zaki","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.virol.2025.110528_bib45","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"}],"container-title":["Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682225001412?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682225001412?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T01:57:40Z","timestamp":1762221460000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0042682225001412"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":46,"alternative-id":["S0042682225001412"],"URL":"https:\/\/doi.org\/10.1016\/j.virol.2025.110528","relation":{},"ISSN":["0042-6822"],"issn-type":[{"type":"print","value":"0042-6822"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genetic diversity of canine coronavirus identified in dogs in yulin city, southern China","name":"articletitle","label":"Article Title"},{"value":"Virology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.virol.2025.110528","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"110528"}}