{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T17:54:32Z","timestamp":1790272472406,"version":"4.1.0"},"reference-count":106,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T00:00:00Z","timestamp":1755043200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ANILLO","award":["ATE220062"],"award-info":[{"award-number":["ATE220062"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4\/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile\u2014GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31. The latter, identified in isolates from 1986 to 1988, is highly divergent (22\u201324%) from other known lineages, representing a previously unreported South American IBV variant. Despite widespread Mass vaccination, genetically distinct field strains circulated during the 1980s, facilitating potential recombination with GI-1 vaccine-derived strains, including evidence of shared ancestry with GI-11, an endemic lineage from Brazil. Non-recombinant GI-16, likely introduced from Asia, was detected in isolates from 2009. Notably, a recombinant strain emerged in 2015, four years after 4\/91 vaccine introduction, indicating vaccine\u2013field-strain genetic exchange. By 2017, isolates with &gt;99% identity to the 4\/91 strain were recovered, suggesting vaccine-derived variants. In 2021, GI-1 re-emerged, showing recombination signatures between GI-1 and GI-13 (4\/91-derived) strains, likely reflecting suboptimal or inconsistent vaccination strategies. Selection analyses showed strong purifying selection across most of the S1 gene, with limited sites under positive selection in the receptor-binding domain. Phylodynamic reconstruction revealed time-structured evolution and multiple introduction events over 35 years, with lineage-specific tMRCA estimates. Collectively, these findings highlight the emergence of a novel lineage in South America and demonstrate that vaccine use, while mitigating disease, has significantly shaped the evolution of IBV in Chile. Our results underscore the importance of continuous genomic surveillance to inform vaccine strategies and limit recombinant emergence.<\/jats:p>","DOI":"10.3390\/v17081111","type":"journal-article","created":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T09:43:01Z","timestamp":1755078181000},"page":"1111","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Thirty-Five Years of IBV Evolution in Chile Reveals a Novel Lineage and Evidence of Vaccine-Driven Recombination"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2264-4128","authenticated-orcid":false,"given":"Miguel","family":"Guzm\u00e1n","sequence":"first","affiliation":[{"name":"Laboratorio de Patolog\u00eda Aviaria, Departamento de Patolog\u00eda Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8820808, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8098-4796","authenticated-orcid":false,"given":"Leandro","family":"C\u00e1diz","sequence":"additional","affiliation":[{"name":"N\u00facleo de Investigaci\u00f3n en One Health (NIOH), Facultad de Medicina Veterinaria y Agronom\u00eda, Universidad de las Am\u00e9ricas, Campus Maip\u00fa, 5 de Abril 620, Santiago 9250000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7647-9714","authenticated-orcid":false,"given":"Leonardo","family":"S\u00e1enz","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8820808, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor","family":"Hidalgo","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda Aviaria, Departamento de Patolog\u00eda Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8820808, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2866-260X","authenticated-orcid":false,"given":"Claudio","family":"Verdugo","sequence":"additional","affiliation":[{"name":"Instituto de Patolog\u00eda Animal, Universidad Austral de Chile, Campus Isla Teja, Edificio BID C 3\u00b0 Piso, Valdivia 5090000, Chile"},{"name":"Center for Surveillance and Evolution of Infectious Diseases, Universidad Austral de Chile, Valdivia 5090000, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,13]]},"reference":[{"key":"ref_1","unstructured":"Swayne, D., Boulianne, M., Logue, C., McDougald, L., and Suarez, D. (2020). Turkey Coronavirus Enteritis, Wiley-Blackwell. [14th ed.]."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"101210","DOI":"10.1016\/j.psj.2021.101210","article-title":"Genetic and Pathogenic Characterization of a Novel Recombinant Avian Infectious Bronchitis Virus Derived from GI-1, GI-13, GI-28, and GI-19 Strains in Southwestern China","volume":"100","author":"Yan","year":"2021","journal-title":"Poult. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.vetmic.2016.08.017","article-title":"Pathogenicity of Virulent Infectious Bronchitis Virus Isolate YN on Hen Ovary and Oviduct","volume":"193","author":"Zhong","year":"2016","journal-title":"Vet. Microbiol."},{"key":"ref_4","first-page":"345","article-title":"Clinicopathology of Gout in Growing Layers Induced by Avian Nephrotrophic Strains of Infectious Bronchitis Virus","volume":"35","author":"Liu","year":"2015","journal-title":"Pak. Vet. J."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.rvsc.2017.06.024","article-title":"Experimental Co-Infection of Infectious Bronchitis and Low Pathogenic Avian Influenza H9N2 Viruses in Commercial Broiler Chickens","volume":"115","author":"Hassan","year":"2017","journal-title":"Res. Vet. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1080\/03079457.2011.566260","article-title":"Infectious Bronchitis Virus Variants: A Review of the History, Current Situation and Control Measures","volume":"40","author":"Cook","year":"2011","journal-title":"Avian Pathol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.virusres.2011.04.006","article-title":"Attenuated Live Vaccine Usage Affects Accurate Measures of Virus Diversity and Mutation Rates in Avian Coronavirus Infectious Bronchitis Virus","volume":"158","author":"McKinley","year":"2011","journal-title":"Virus Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nrmicro2614","article-title":"Why Do RNA Viruses Recombine?","volume":"9","author":"Holmes","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.vetmic.2011.09.022","article-title":"Emergence of Novel Strains of Avian Infectious Bronchitis Virus in Sweden","volume":"155","author":"Abro","year":"2012","journal-title":"Vet. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/s12985-015-0347-8","article-title":"Phylogenetic Analysis of Avian Infectious Bronchitis Virus S1 Glycoprotein Regions Reveals Emergence of a New Genotype in Moroccan Broiler Chicken Flocks","volume":"12","author":"Fellahi","year":"2015","journal-title":"Virol. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.14202\/vetworld.2019.1797-1805","article-title":"Isolation and Characterization of Avian Coronavirus from Healthy Eclectus Parrots (Eclectus roratus) from Indonesia","volume":"12","author":"Suryaman","year":"2019","journal-title":"Vet. World"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.meegid.2012.09.016","article-title":"Comparative Analysis of Four Massachusetts Type Infectious Bronchitis Coronavirus Genomes Reveals a Novel Massachusetts Type Strain and Evidence of Natural Recombination in the Genome","volume":"14","author":"Liu","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11262-007-0165-1","article-title":"Creation of Diversity in the Animal Virus World by Inter-Species and Intra-Species Recombinations: Lessons Learned from Poultry Viruses","volume":"36","author":"Davidson","year":"2008","journal-title":"Virus Genes"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.meegid.2017.05.006","article-title":"Complete Genome Sequences of Two Avian Infectious Bronchitis Viruses Isolated in Egypt: Evidence for Genetic Drift and Genetic Recombination in the Circulating Viruses","volume":"53","author":"Abozeid","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/S0168-1702(01)00345-8","article-title":"Origin and Evolution of Georgia 98 (GA98), a New Serotype of Avian Infectious Bronchitis Virus","volume":"80","author":"Lee","year":"2001","journal-title":"Virus Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.vetmic.2012.10.027","article-title":"Characterization of a Recombinant Coronavirus Infectious Bronchitis Virus with Distinct S1 Subunits of Spike and Nucleocapsid Genes and a 3\u2032 Untranslated Region","volume":"162","author":"Liu","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1080\/03079457.2016.1200011","article-title":"A Novel Variant of the Infectious Bronchitis Virus Resulting from Recombination Events in Italy and Spain","volume":"46","author":"Moreno","year":"2017","journal-title":"Avian Pathol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1006\/viro.1993.1093","article-title":"Evidence of Natural Recombination within the S1 Gens of Infectious Bronchitis Virus","volume":"192","author":"Wang","year":"1993","journal-title":"Virology"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/j.meegid.2015.03.034","article-title":"Serotype Shift of a 793\/B Genotype Infectious Bronchitis Coronavirus by Natural Recombination","volume":"32","author":"Zhang","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/j.meegid.2011.01.007","article-title":"An Emerging Recombinant Cluster of Nephropathogenic Strains of Avian Infectious Bronchitis Virus in Korea","volume":"11","author":"Lim","year":"2011","journal-title":"Infect. Genet. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1080\/03079459208418816","article-title":"Location of the Amino Acid Differences in the SI Spike Glycoprotein Subunit of Closely Related Serotypes of Infectious Bronchitis Virus","volume":"21","author":"Cavanagh","year":"1992","journal-title":"Avian Pathol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.3390\/v3091777","article-title":"Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus","volume":"3","author":"Thor","year":"2011","journal-title":"Viruses"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S0065-3527(06)66005-3","article-title":"The Molecular Biology of Coronaviruses","volume":"65","author":"Masters","year":"2006","journal-title":"Adv. Virus Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1637\/10241-1007212-DIGEST.1","article-title":"Genetic Diversity and Selection Regulates Evolution of Infectious Bronchitis Virus","volume":"7","author":"Toro","year":"2012","journal-title":"Avian Dis. Dig."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"416","DOI":"10.2307\/1592981","article-title":"Characterization of Three Infectious Bronchitis Virus Isolates from China Associated with Proventriculus in Vaccinated Chickens","volume":"45","author":"Yu","year":"2001","journal-title":"Avian Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1637\/7192-040808R1","article-title":"Avian Infectious Bronchitis Virus: A Possible Cause of Reduced Fertility in the Rooster","volume":"48","author":"Boltz","year":"2004","journal-title":"Avian Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.virusres.2008.11.012","article-title":"Identification of Taiwan and China-like Recombinant Avian Infectious Bronchitis Viruses in Taiwan","volume":"140","author":"Chen","year":"2009","journal-title":"Virus Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1080\/03079450220136530","article-title":"Molecular Epizootiology of Infectious Bronchitis Virus in Sweden Indicating the Involvement of a Vaccine Strain","volume":"31","author":"Farsang","year":"2002","journal-title":"Avian Pathol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"219","DOI":"10.4142\/jvs.2009.10.3.219","article-title":"Detection and Molecular Characterization of Infectious Bronchitis Virus Isolated from Recent Outbreaks in Broiler Flocks in Thailand","volume":"10","author":"Pohuang","year":"2009","journal-title":"J. Vet. Sci."},{"key":"ref_30","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_31","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.vetmic.2019.01.020","article-title":"Novel Genotype of Infectious Bronchitis Virus Isolated in China","volume":"230","author":"Ma","year":"2019","journal-title":"Vet. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"102076","DOI":"10.1016\/j.psj.2022.102076","article-title":"Research Note: High Genetic Diversity of Infectious Bronchitis Virus from Mexico","volume":"101","author":"Marandino","year":"2022","journal-title":"Poult. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1080\/03079457.2020.1754332","article-title":"New PA\/1220\/98-like Variant of Infectious Bronchitis Virus in Poland","volume":"49","author":"Lisowska","year":"2020","journal-title":"Avian Pathol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.vetmic.2016.12.017","article-title":"Identification and Molecular Characterization of a Novel Serotype Infectious Bronchitis Virus (GI-28) in China","volume":"198","author":"Chen","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.meegid.2017.08.006","article-title":"Genome Characterization, Antigenicity and Pathogenicity of a Novel Infectious Bronchitis Virus Type Isolated from South China","volume":"54","author":"Jiang","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2775","DOI":"10.1111\/tbed.13637","article-title":"Characterization of Novel, Pathogenic Field Strains of Infectious Bronchitis Virus (IBV) in Poultry in Trinidad and Tobago","volume":"67","author":"Fusaro","year":"2020","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1099\/vir.0.000077","article-title":"Phylodynamic Analysis of Avian Infectious Bronchitis Virus in South America","volume":"96","author":"Marandino","year":"2015","journal-title":"J. Gen. Virol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1080\/03079450902737821","article-title":"Molecular Characterization of Avian Infectious Bronchitis Virus Strains from Outbreaks in Argentina (2001\u20132008)","volume":"38","author":"Rimondi","year":"2009","journal-title":"Avian Pathol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1007\/s42770-020-00394-y","article-title":"Emergence of Avian Coronavirus Genotype GI-11 in Colombia","volume":"52","year":"2021","journal-title":"Braz. J. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1080\/03079459708419246","article-title":"Infectious Bronchitis Virus: Immunopathogenesis of Infection in the Chicken","volume":"26","author":"Raj","year":"1997","journal-title":"Avian Pathol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1637\/7983-041307.1","article-title":"Molecular Characterization of Infectious Bronchitis Virus Strains Isolated from the Enteric Contents of Brazilian Laying Hens and Broilers","volume":"51","author":"Villarreal","year":"2007","journal-title":"Avian Dis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1080\/03079457.2017.1346782","article-title":"Variability in Biological Behaviour, Pathogenicity, Protectotype and Induction of Virus Neutralizing Antibodies by Different Vaccination Programmes to Infectious Bronchitis Virus Genotype Q1 Strains from Chile","volume":"46","author":"Dijkman","year":"2017","journal-title":"Avian Pathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e01555-18","DOI":"10.1128\/MRA.01555-18","article-title":"Near-Complete Genome Sequence of Infectious Bronchitis Virus Strain VFAR-047 (GI-16 Lineage), Isolated in Peru","volume":"8","year":"2019","journal-title":"Microbiolgy Resour. Announc."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Ramirez-Nieto, G., Mir, D., Almansa-Villa, D., Cordoba-Argotti, G., Beltran-Leon, M., Rodriguez-Osorio, N., Garai, J., Zabaleta, J., and Gomez, A.P. (2022). New Insights into Avian Infectious Bronchitis Virus in Colombia from Whole-Genome Analysis. Viruses, 14.","DOI":"10.3390\/v14112562"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1080\/03079457.2019.1583315","article-title":"Genetic and Antigenic Heterogeneity of Infectious Bronchitis Virus in South America: Implications for Control Programmes","volume":"48","author":"Marandino","year":"2019","journal-title":"Avian Pathol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3167","DOI":"10.1111\/tbed.14724","article-title":"Emergence and Molecular Characterization of the Avian Infectious Bronchitis Virus GI-23 in Commercial Broiler Farms from South America","volume":"69","author":"Ikuta","year":"2022","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"601","DOI":"10.2307\/1589395","article-title":"Isolation of Infectious Bronchitis Virus from Broiler Chickens in Chile","volume":"20","author":"Hidalgo","year":"1976","journal-title":"Avian Dis."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Guzm\u00e1n, M., S\u00e1enz, L., and Hidalgo, H. (2019). Molecular and Antigenic Characterization of GI-13 and GI-16 Avian Infectious Bronchitis Virus Isolated in Chile from 2009 to 2017 Regarding 4\/91 Vaccine Introduction. Animals, 9.","DOI":"10.3390\/ani9090656"},{"key":"ref_49","unstructured":"Aguirre, R. (2024, July 08). Bolet\u00edn Carne Bovina: Tendencias de Producci\u00f3n, Precios y Comercio Exterior. Available online: https:\/\/bibliotecadigital.odepa.gob.cl\/bitstream\/handle\/20.500.12650\/72073\/BCarne012023.pdf."},{"key":"ref_50","first-page":"27","article-title":"Diagnostico Preliminar de La Bronquitis Infecciosa En Chile","volume":"19","author":"Garcia","year":"1969","journal-title":"Rev. Soc. Med. Vet. Chile."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1080\/03079459108418744","article-title":"Characterisation of Strains of Infectious Bronchitis Virus Isolated in Chile","volume":"20","author":"Cubillos","year":"1991","journal-title":"Avian Pathol."},{"key":"ref_52","first-page":"175","article-title":"Detection and Characterization of Infectious Bronchitis Virus in Chile by RT-PCR and Sequence Analysis","volume":"38","author":"Lopez","year":"2006","journal-title":"Arch. Med. Vet."},{"key":"ref_53","unstructured":"(2023, July 03). SAG Lista De Enfermedades De Denuncia Obligatoria (EDO) Al Sag. Available online: https:\/\/www.sag.cl\/sites\/default\/files\/enfermedades_denuncia_obligatoria_sag_9-10-2019.pdf."},{"key":"ref_54","unstructured":"(2024, July 08). SAG Situaci\u00f3n Sanitaria De Chile A\u00f1o 2011. Available online: https:\/\/www.sag.gob.cl\/sites\/default\/files\/situacion_sanitaria_animal_2011_1.pdf."},{"key":"ref_55","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_56","unstructured":"(2024, July 08). SAG Informe Sanidad Animal A\u00f1o 2012. Available online: https:\/\/www.sag.gob.cl\/sites\/default\/files\/situacion_sanitaria_animal_2012_0.pdf."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.virusres.2015.10.015","article-title":"Molecular Detection and Smoothing Spline Clustering of the IBV Strains Detected in China during 2011\u20132012","volume":"211","author":"Zhang","year":"2016","journal-title":"Virus Res."},{"key":"ref_58","unstructured":"Guzm\u00e1n, M. (2017). Evaluaci\u00f3n de la Introducci\u00f3n de una Vacuna Viva Atenuada Sobre las Cepas de Campo del Virus del Virus Bronquitis Infecciosa (IBV) en Planteles de Producci\u00f3n Av\u00edcola, Universidad de Chile."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Guindon, S., and Gascuel, O. (2003). A Simple, Fast and Accurate Method to Estimate Large Phylogenies by Maximum-Likelihood. Syst. Biol., 52.","DOI":"10.1080\/10635150390235520"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New Algorithms and Methods to Estimate Maximim-Likelihood Phylogenies Assessing the Performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/s41586-018-0043-0","article-title":"Renewing Felsenstein\u2019s Phylogenetic Bootstrap in the Era of Big Data","volume":"556","author":"Lemoine","year":"2018","journal-title":"Nature"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Bouckaert, R., Heled, J., K\u00fchnert, D., Vaughan, T., Wu, C.H., Xie, D., Suchard, M.A., Rambaut, A., and Drummond, A.J. (2014). BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput. Biol., 10.","DOI":"10.1371\/journal.pcbi.1003537"},{"key":"ref_64","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":"ref_65","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: A Suite of Phylogenetic Analysis Tools for Evolutionary Biology","volume":"26","author":"Delport","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so Different after All: A Comparison of Methods for Detecting Amino Acid Sites under Selection","volume":"22","author":"Frost","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: Rapid Detection of Selective Pressure on Individual Sites of Codon Alignments","volume":"21","author":"Frost","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Murrell, B., Wertheim, J.O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S.L. (2012). Detecting Individual Sites Subject to Episodic Diversifying Selection. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002764"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the Temporal Structure of Heterochronous Sequences Using TempEst (Formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Rafique, S., Jabeen, Z., Pervaiz, T., Rashid, F., Luo, S., Xie, L., and Xie, Z. (2024). Avian Infectious Bronchitis Virus (AIBV) Review by Continent. Front. Cell. Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1325346"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Bali, K., Kaszab, E., Marton, S., Hamdiou, S.H., Bentaleb, R.K., Kiss, I., Palya, V., and B\u00e1nyai, K. (2022). Novel Lineage of Infectious Bronchitis Virus from Sub-Saharan Africa Identified by Random Amplification and Next-Generation Sequencing of Viral Genome. Life, 12.","DOI":"10.3390\/life12040475"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Franzo, G., Cecchinato, M., Tosi, G., Fiorentini, L., Faccin, F., Tucciarone, C.M., Trogu, T., Barbieri, I., Massi, P., and Moreno, A. (2018). GI-16 Lineage (624\/I or Q1), There and Back Again: The History of One of the Major Threats for Poultry Farming of Our Era. PLoS ONE, 13.","DOI":"10.1101\/402800"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.meegid.2018.03.014","article-title":"Phylodynamic Analysis and Molecular Diversity of the Avian Infectious Bronchitis Virus of Chickens in Brazil","volume":"61","author":"Pereira","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1080\/03079457.2010.544641","article-title":"Epidemiological Survey and Molecular Characterization of Avian Infectious Bronchitis Virus in Brazil between 2003 and 2009","volume":"40","author":"Rodrigues","year":"2011","journal-title":"Avian Pathol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.meegid.2017.07.009","article-title":"Whole-Genome Characterization of Uruguayan Strains of Avian Infectious Bronchitis Virus Reveals Extensive Recombination Between the Two Major South American Lineages","volume":"54","author":"Marandino","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1637\/aviandiseases-D-21-00103","article-title":"Genetic and Antigenic Diversity of Infectious Bronchitis Virus in South America","volume":"65","author":"Marandino","year":"2021","journal-title":"Avian Dis."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"e000292","DOI":"10.1136\/vetreccr-2016-000292","article-title":"First Evidence of Detection of Asia\/South America II (A\/SAII) Infectious Bronchitis Virus in a Commercial Broiler Flock in Peru","volume":"4","author":"Bueno","year":"2016","journal-title":"Vet. Rec. Case Rep."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1080\/03079459994506","article-title":"Breadth of Protection of the Respiratory Tract Provided by Different Live-Attenuated Infectious Bronchitis Vaccines Against Challenge with Infectious Bronchitis Viruses of Heter","volume":"28","author":"Taylor","year":"1999","journal-title":"Avian Pathol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1080\/03079457.2022.2040731","article-title":"The Inactivated Infectious Bronchitis Virus (IBV) Vaccine Used as Booster in Layer Hens Influences the Breadth of Protection against Challenge with IBV Variants","volume":"51","author":"Cook","year":"2022","journal-title":"Avian Pathol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.virol.2007.09.038","article-title":"Identification of a Natural Multi-Recombinant of Newcastle Disease Virus","volume":"371","author":"Han","year":"2008","journal-title":"Virology"},{"key":"ref_82","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":"ref_83","doi-asserted-by":"crossref","unstructured":"Murahwa, A.T., Nindo, F., Onywera, H., Meiring, T.L., Martin, D.P., and Williamson, A.L. (2019). Evolutionary Dynamics of Ten Novel Gamma-PVs: Insights from Phylogenetic Incongruence, Recombination and Phylodynamic Analyses. BMC Genom., 20.","DOI":"10.1186\/s12864-019-5735-9"},{"key":"ref_84","unstructured":"Palevitz, B.A. (2000). Evolutionary Genomics, University of Leeds."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Marandino, A., Mendoza-Gonz\u00e1lez, L., Panzera, Y., Tom\u00e1s, G., Williman, J., Techera, C., Gayosso-V\u00e1zquez, A., Ram\u00edrez-Andoney, V., Alonso-Morales, R., and Realpe-Quintero, M. (2023). Genome Variability of Infectious Bronchitis Virus in Mexico: High Lineage Diversity and Recurrent Recombination. Viruses, 15.","DOI":"10.3390\/v15071581"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/bib\/bbu015","article-title":"Causes, Consequences and Solutions of Phylogenetic Incongruence","volume":"16","author":"Som","year":"2014","journal-title":"Brief. Bioinform."},{"key":"ref_87","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":"ref_88","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.vaccine.2021.11.072","article-title":"Molecular Characterization of Infectious Bronchitis Virus in Southwestern China for the Protective Efficacy Evaluation of Four Live Vaccine Strains","volume":"40","author":"Li","year":"2022","journal-title":"Vaccine"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"104256","DOI":"10.1016\/j.psj.2024.104256","article-title":"Molecular Characteristic, Evolution, and Pathogenicity Analysis of Avian Infectious Bronchitis Virus Isolates Associated with QX Type in China","volume":"103","author":"Lu","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1080\/03079457.2011.605782","article-title":"Molecular Characterization of Infectious Bronchitis Virus Isolates from Russia and Neighbouring Countries: Identification of Intertypic Recombination in the S1 Gene","volume":"40","author":"Ovchinnikova","year":"2011","journal-title":"Avian Pathol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1016\/j.psj.2019.11.056","article-title":"Multiple Recombination Events between Field and Vaccine Strains Resulted in the Emergence of a Novel Infectious Bronchitis Virus with Decreased Pathogenicity and Altered Replication Capacity","volume":"99","author":"Ren","year":"2020","journal-title":"Poult. Sci."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"105437","DOI":"10.1016\/j.micpath.2022.105437","article-title":"Evaluation of a Novel Recombinant Strain of Infectious Bronchitis Virus Emerged from Three Attenuated Live Vaccine Strains","volume":"164","author":"Gong","year":"2022","journal-title":"Microb. Pathog."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1007\/s13337-021-00667-6","article-title":"Molecular Characterization of an Avian GA13-like Infectious Bronchitis Virus Full-Length Genome from Costa Rica","volume":"32","year":"2021","journal-title":"Virusdisease"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"3583","DOI":"10.1007\/s00705-016-3042-1","article-title":"The Sequence of the Full Spike S1 Glycoprotein of Infectious Bronchitis Virus Circulating in Egypt Reveals Evidence of Intra-Genotypic Recombination","volume":"161","author":"Zanaty","year":"2016","journal-title":"Arch. Virol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.meegid.2018.09.018","article-title":"Genetic Diversity of Avian Infectious Bronchitis Virus in China in Recent Years","volume":"66","author":"Xu","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/s11262-006-0037-0","article-title":"Phylogenetic Analysis of Partial S1 and N Gene Sequences of Infectious Bronchitis Virus Isolates from Italy Revealed Genetic Diversity and Recombination","volume":"35","author":"Bochkov","year":"2007","journal-title":"Virus Genes"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Fan, W., Tang, N., Dong, Z., Chen, J., Zhang, W., Zhao, C., He, Y., Li, M., Wu, C., and Wei, T. (2019). Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure. Viruses, 11.","DOI":"10.3390\/v11100898"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.tim.2016.09.010","article-title":"Does Sequence Conservation Provide Evidence for Biological Function?","volume":"25","author":"Omer","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/0168-1702(88)90039-1","article-title":"Amino Acids Within Hypervariable Region 1 of Avian Coronavirus IBV (Massachusetts Serotype) Spike Glycoprotein Are Associated with Neutralization Epitopes","volume":"11","author":"Cavanagh","year":"1988","journal-title":"Virus Res."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.virol.2013.09.018","article-title":"Mapping of the Receptor-Binding Domain and Amino Acids Critical for Attachment in the Spike Protein of Avian Coronavirus Infectious Bronchitis Virus","volume":"448","author":"Promkuntod","year":"2014","journal-title":"Virology"},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Gao, Z., Hu, J., Cai, Y., Liu, Y., Yin, G., Guo, X., Wang, R., Zhong, M., Liu, Q., and Feng, X. (2025). Identification of B-Cell Epitopes Located on the Surface of the S1 Protein of Infectious Bronchitis Virus M41 Strains. Viruses, 17.","DOI":"10.3390\/v17040464"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1146\/annurev-virology-110615-042301","article-title":"Structure, Function, and Evolution of Coronavirus Spike Proteins","volume":"3","author":"Li","year":"2016","journal-title":"Annu. Rev. Virol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"648","DOI":"10.2307\/1592697","article-title":"The Early History of Infectious Bronchitis","volume":"42","author":"Fabricant","year":"1998","journal-title":"Avian Dis."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"9520616","DOI":"10.1155\/2023\/9520616","article-title":"Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus","volume":"2023","author":"Chen","year":"2023","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Houta, M.H., Hassan, K.E., Legnardi, M., Tucciarone, C.M., Abdel-Moneim, A.S., Cecchinato, M., El-Sawah, A.A., Ali, A., and Franzo, G. (2021). Phylodynamic and Recombination Analyses of Avian Infectious Bronchitis Gi-23 Reveal a Widespread Recombinant Cluster and New among-Countries Linkages. Animals, 11.","DOI":"10.3390\/ani11113182"},{"key":"ref_106","first-page":"131","article-title":"Isolamento e Identifica\u00e7\u00e3o Do V\u00edrus Da Bronquite Infecciosa Das Galinhas No Brasil","volume":"10","year":"1957","journal-title":"Arquivo Escuela Veterinaria, Universidade Rural. do Estado de Minas Gerais"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/8\/1111\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:26:14Z","timestamp":1760034374000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/8\/1111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,13]]},"references-count":106,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["v17081111"],"URL":"https:\/\/doi.org\/10.3390\/v17081111","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,13]]}}}