{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T03:51:02Z","timestamp":1790481062705,"version":"4.1.0"},"reference-count":23,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"\u201cAgence National de S\u00e9curit\u00e9 Sanitaire, de l\u2019Environnement et du travail\u201d (ANSES)","award":["180019"],"award-info":[{"award-number":["180019"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.<\/jats:p>","DOI":"10.3390\/v14071392","type":"journal-article","created":{"date-parts":[[2022,6,26]],"date-time":"2022-06-26T22:50:23Z","timestamp":1656283823000},"page":"1392","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens"],"prefix":"10.3390","volume":"14","author":[{"given":"Alexandre","family":"Flageul","sequence":"first","affiliation":[{"name":"Virology, Immunology, Parasitology, Aviaire et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chantal","family":"All\u00e9e","sequence":"additional","affiliation":[{"name":"Virology, Immunology, Parasitology, Aviaire et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3006-764X","authenticated-orcid":false,"given":"C\u00e9line","family":"Courtillon","sequence":"additional","affiliation":[{"name":"Virology, Immunology, Parasitology, Aviaire et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00e9ronique","family":"B\u00e9ven","sequence":"additional","affiliation":[{"name":"G\u00e9n\u00e9tique Virale et Bios\u00e9curit\u00e9, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9l\u00e8ne","family":"Quenault","sequence":"additional","affiliation":[{"name":"G\u00e9n\u00e9tique Virale et Bios\u00e9curit\u00e9, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yannick","family":"Blanchard","sequence":"additional","affiliation":[{"name":"G\u00e9n\u00e9tique Virale et Bios\u00e9curit\u00e9, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michel","family":"Amelot","sequence":"additional","affiliation":[{"name":"Service d\u2019Elevage et d\u2019Exp\u00e9rimentation Avicole et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Courtois","sequence":"additional","affiliation":[{"name":"Service d\u2019Elevage et d\u2019Exp\u00e9rimentation Avicole et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sjaak","family":"De Wit","sequence":"additional","affiliation":[{"name":"Royal GD, Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 7418 EZ Deventer, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Eterradossi","sequence":"additional","affiliation":[{"name":"Virology, Immunology, Parasitology, Aviaire et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Universit\u00e9 de Rennes 1, 22440 Ploufragan, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e9atrice","family":"Grasland","sequence":"additional","affiliation":[{"name":"Virology, Immunology, Parasitology, Aviaire et Cunicole, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratoire de Ploufragan-Plouzan\u00e9-Niort, 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Dis."},{"key":"ref_2","first-page":"413","article-title":"First Report of Infectious Bronchitis in North Dakota\u2014An Apparently New Respiratory Disease of Chicks","volume":"78","author":"Schalk","year":"1931","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1637\/10227-043012-Review.1","article-title":"Review of infectious bronchitis virus around the world","volume":"56","author":"Jackwood","year":"2012","journal-title":"Avian Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.meegid.2016.02.015","article-title":"S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification","volume":"39","author":"Valastro","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"993","DOI":"10.20506\/rst.34.3.2411","article-title":"Assessing the economic burden of avian infectious bronchitis on poultry farms in Brazil: -EN- -FR- \u00c9valuation de l\u2019impact \u00e9conomique de la bronchite infectieuse aviaire dans les \u00e9levages de volailles br\u00e9siliens -ES- Determinaci\u00f3n de la carga econ\u00f3mica que impone la bronquitis infecciosa aviar a las explotaciones av\u00edcolas del Brasil","volume":"34","author":"Colvero","year":"2015","journal-title":"Revue Scientifique et Technique"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"6388","DOI":"10.3382\/ps\/pez473","article-title":"Vaccine or field strains: The jigsaw pattern of infectious bronchitis virus molecular epidemiology in Poland","volume":"98","author":"Legnardi","year":"2019","journal-title":"Poult. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1016\/j.meegid.2012.05.003","article-title":"Molecular evolution and emergence of avian gammacoronaviruses","volume":"12","author":"Jackwood","year":"2012","journal-title":"Infect. Genet. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1637\/10072-020212-Review.1","article-title":"Genetic diversity and selection regulates evolution of infectious bronchitis virus","volume":"56","author":"Toro","year":"2012","journal-title":"Avian Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1080\/03079450400013154","article-title":"Development and use of the H strain of avian infectious bronchitis virus from the Netherlands as a vaccine: A review","volume":"33","author":"Bijlenga","year":"2004","journal-title":"Avian Pathol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1080\/03079457.2011.599060","article-title":"Induction of cystic oviducts and protection against early challenge with infectious bronchitis virus serotype D388 (genotype QX) by maternally derived antibodies and by early vaccination","volume":"40","author":"Hoogkamer","year":"2011","journal-title":"Avian Pathol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-4939-2438-7_9","article-title":"Quantification of infectious bronchitis coronavirus by titration in vitro and in ovo","volume":"1282","author":"Kint","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/oxfordjournals.aje.a118408","article-title":"A Simple Method of Estimating Fifty Per Cent Endpoints","volume":"27","author":"Reed","year":"1938","journal-title":"Am. J. Epidemiol."},{"key":"ref_13","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":"ref_14","first-page":"167","article-title":"Infectious Bronchitis","volume":"Volume 1","author":"Swayne","year":"2020","journal-title":"Diseases of Poultry"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1007\/978-1-4939-2438-7_11","article-title":"Partial purification of IBV and subsequent isolation of viral RNA for next-generation sequencing","volume":"1282","author":"Keep","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_16","unstructured":"Aier, H.J., Bickerton, E., and Britton, P. (2015). Isolation and Propagation of Coronaviruses in Embryonated Eggs. MCoronaviruses: Methods and Protocols, Springer."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"198201","DOI":"10.1016\/j.virusres.2020.198201","article-title":"Viral variant visualizer (VVV): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity","volume":"291","author":"Flageul","year":"2021","journal-title":"Virus Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: A new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1093\/nar\/29.14.2994","article-title":"Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements","volume":"29","author":"Aravind","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1016\/j.vaccine.2008.01.006","article-title":"Avian coronavirus infectious bronchitis attenuated live vaccines undergo selection of subpopulations and mutations following vaccination","volume":"26","author":"McKinley","year":"2008","journal-title":"Vaccine"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1080\/03079450802043783","article-title":"Rapid selection in chickens of subpopulations within ArkDPI-derived infectious bronchitis virus vaccines","volume":"37","author":"Toro","year":"2008","journal-title":"Avian Pathol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1038\/emboj.2013.41","article-title":"Rules for the recognition of dilysine retrieval motifs by coatomer","volume":"32","author":"Ma","year":"2013","journal-title":"EMBO J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5913","DOI":"10.1128\/JVI.78.11.5913-5922.2004","article-title":"Intracellular Targeting Signals Contribute to Localization of Coronavirus Spike Proteins near the Virus Assembly Site","volume":"78","author":"Lontok","year":"2004","journal-title":"J. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/7\/1392\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:38:31Z","timestamp":1760139511000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/7\/1392"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,25]]},"references-count":23,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["v14071392"],"URL":"https:\/\/doi.org\/10.3390\/v14071392","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,25]]}}}