{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T14:56:02Z","timestamp":1782226562066,"version":"3.54.5"},"reference-count":62,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T00:00:00Z","timestamp":1743724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agriculture and Agri Food Canada (AAFC) via Poultry Science Cluster funding","award":["ASC-20"],"award-info":[{"award-number":["ASC-20"]}]},{"name":"Agriculture and Agri Food Canada (AAFC) via Poultry Science Cluster funding","award":["10022788"],"award-info":[{"award-number":["10022788"]}]},{"DOI":"10.13039\/100014972","name":"Egg Farmers of Canada","doi-asserted-by":"publisher","award":["ASC-20"],"award-info":[{"award-number":["ASC-20"]}],"id":[{"id":"10.13039\/100014972","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014972","name":"Egg Farmers of Canada","doi-asserted-by":"publisher","award":["10022788"],"award-info":[{"award-number":["10022788"]}],"id":[{"id":"10.13039\/100014972","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Higher Education of the Arab Republic of Egypt","award":["ASC-20"],"award-info":[{"award-number":["ASC-20"]}]},{"name":"Ministry of Higher Education of the Arab Republic of Egypt","award":["10022788"],"award-info":[{"award-number":["10022788"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Infectious bronchitis virus (IBV) commonly produces a range of genetic sequences during replication, particularly in the spike 1 (S1)-coding portion of the S gene, leading to distinct subpopulations within the broader viral population. It has been shown that certain microenvironments exert selective pressure on the S1-coding sequences and their encoded proteins, influencing the selection of viral subpopulations in these environments. In this study, high-throughput next-generation sequencing (NGS) was used to analyze the S1-coding sequences from tissues of the respiratory, digestive, renal, and reproductive systems of specific pathogen-free (SPF) laying hens. These tissues were collected nine days after infection with the California 1737\/04 (CA1737\/04) IBV strain, which is known to cause varying degrees of pathology in these tissues. Using a specific bioinformatics pipeline, 27 single nucleotide variants (SNVs) were detected in the S1-coding sequences derived from different tissues. These SNVs shaped multiple subpopulations (SP1\u2013SP15), with SP1 being the core subpopulation present in all tissues, while others were tissue-specific. The IBV RNA loads in the tissues were negatively correlated with the number of SNVs or the Shannon entropy values, and phylogenetic analysis revealed a genetic divergence in the S1-coding sequences from certain tissues with lower viral RNA loads, particularly those from the trachea and ovary. Furthermore, the SNVs were associated with nonsynonymous mutations, primarily located in hypervariable region 2 (HVR 2) within the N-terminal domain of S1 (S1-NTD), except for those in SP7, which was exclusive to the trachea and contained changes in HVR 3 in the C-terminal domain of S1 (S1-CTD). Overall, this study adds to the existing knowledge about IBV evolution by highlighting the role of tissue-specific environments in shaping viral genetic diversity.<\/jats:p>","DOI":"10.3390\/v17040527","type":"journal-article","created":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T11:31:00Z","timestamp":1743766260000},"page":"527","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genetic and Phenotypic Investigations of Viral Subpopulations Detected in Different Tissues of Laying Hens Following Infectious Bronchitis Virus Infection"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8662-1291","authenticated-orcid":false,"given":"Ahmed","family":"Ali","sequence":"first","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada"},{"name":"Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef 62511, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3914-777X","authenticated-orcid":false,"given":"Ryan","family":"Rahimi","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0034-1043","authenticated-orcid":false,"given":"Motamed Elsayed","family":"Mahmoud","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada"},{"name":"Department of Animal Husbandry, Faculty of Veterinary Medicine, Sohag University, Sohag 84524, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adel A.","family":"Shalaby","sequence":"additional","affiliation":[{"name":"Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef 62511, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4727-8256","authenticated-orcid":false,"given":"Rodrigo A.","family":"Gallardo","sequence":"additional","affiliation":[{"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, 1089 Veterinary Medicine Dr. VM3B, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9974-7600","authenticated-orcid":false,"given":"Mohamed Faizal","family":"Abdul-Careem","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1080\/03079457.2012.680432","article-title":"The long view: 40 years of infectious bronchitis research","volume":"41","author":"Cook","year":"2012","journal-title":"Avian Pathol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1017\/S1466252317000044","article-title":"Global distributions and strain diversity of avian infectious bronchitis virus: A review","volume":"18","author":"Bande","year":"2017","journal-title":"Anim. Health Res. Rev."},{"key":"ref_3","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_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-2438-7_1","article-title":"Coronaviruses: An overview of their replication and pathogenesis","volume":"Volume 1282","author":"Fehr","year":"2015","journal-title":"Coronaviruses"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e7384","DOI":"10.1371\/journal.pone.0007384","article-title":"The replicase gene of avian coronavirus infectious bronchitis virus is a determinant of pathogenicity","volume":"4","author":"Armesto","year":"2009","journal-title":"PLoS ONE"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1080\/03079457.2015.1022857","article-title":"Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS","volume":"44","author":"Quinteros","year":"2015","journal-title":"Avian Pathol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.virusres.2014.10.009","article-title":"The avian coronavirus spike protein","volume":"194","author":"Wickramasinghe","year":"2014","journal-title":"Virus Res."},{"key":"ref_8","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_9","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_10","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_11","doi-asserted-by":"crossref","first-page":"e0184401","DOI":"10.1371\/journal.pone.0184401","article-title":"Think globally, act locally: Phylodynamic reconstruction of infectious bronchitis virus (IBV) QX genotype (GI-19 lineage) reveals different population dynamics and spreading patterns when evaluated on different epidemiological scales","volume":"12","author":"Franzo","year":"2017","journal-title":"PLoS ONE"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1002\/1521-1878(200012)22:12<1057::AID-BIES3>3.0.CO;2-W","article-title":"The evolution of mutation rates: Separating causes from consequences","volume":"22","author":"Sniegowski","year":"2000","journal-title":"Bioessays"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e3000003","DOI":"10.1371\/journal.pbio.3000003","article-title":"Why are RNA virus mutation rates so damn high?","volume":"16","author":"Duffy","year":"2018","journal-title":"PLoS Biol."},{"key":"ref_14","first-page":"51","article-title":"Viruses as quasispecies: Biological implications","volume":"Volume 299","author":"Domingo","year":"2006","journal-title":"Quasispecies: Concept and Implications for Virology"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/scientificamerican0481-88","article-title":"The origin of genetic information","volume":"244","author":"Eigen","year":"1981","journal-title":"Sci. Am."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e1007009","DOI":"10.1371\/journal.ppat.1007009","article-title":"Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins","volume":"14","author":"Shang","year":"2018","journal-title":"PLoS Pathog."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1007\/978-1-4615-5331-1_94","article-title":"Does IBV change slowly despite the capacity of the spike protein to vary greatly?","volume":"440","author":"Cavanagh","year":"1998","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1099\/0022-1317-71-9-1929","article-title":"Antigenic domains on the peplomer protein of avian infectious bronchitis virus: Correlation with biological functions","volume":"71","author":"Koch","year":"1990","journal-title":"J. Gen. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1099\/0022-1317-73-3-591","article-title":"Location of antigenic sites defined by neutralizing monoclonal antibodies on the S1 avian infectious bronchitis virus glycopolypeptide","volume":"73","author":"Kant","year":"1992","journal-title":"J. Gen. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1080\/03079459208418816","article-title":"Location of the amino acid differences in the S1 spike glycoprotein subunit of closely related serotypes of infectious bronchitis virus","volume":"21","author":"Cavanagh","year":"1992","journal-title":"Avian Pathol."},{"key":"ref_21","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_22","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1637\/10108-022912-Reg.1","article-title":"The proportion of specific viral subpopulations in attenuated Arkansas Delmarva poultry industry infectious bronchitis vaccines influences vaccination outcome","volume":"56","author":"Ndegwa","year":"2012","journal-title":"Avian Dis."},{"key":"ref_23","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_24","doi-asserted-by":"crossref","first-page":"8903","DOI":"10.1128\/JVI.05112-11","article-title":"Binding of avian coronavirus spike proteins to host factors reflects virus tropism and pathogenicity","volume":"85","author":"Wickramasinghe","year":"2011","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1637\/9054-090809-Reg.1","article-title":"Host intraspatial selection of infectious bronchitis virus populations","volume":"54","author":"Gallardo","year":"2010","journal-title":"Avian Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1338563","DOI":"10.3389\/fvets.2024.1338563","article-title":"Comparative pathogenicity of CA1737\/04 and Mass infectious bronchitis virus genotypes in laying chickens","volume":"11","author":"Ali","year":"2024","journal-title":"Front. Vet. Sci."},{"key":"ref_27","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_28","doi-asserted-by":"crossref","first-page":"114859","DOI":"10.1016\/j.jviromet.2023.114859","article-title":"Comparison of quantitative PCR and digital PCR assays for quantitative detection of infectious bronchitis virus (IBV) genome","volume":"324","author":"Isham","year":"2024","journal-title":"J. Virol. Methods"},{"key":"ref_29","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_30","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst. Tech. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: A unified platform for automated protein structure and function prediction","volume":"5","author":"Roy","year":"2010","journal-title":"Nat. Protoc."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1637\/6075","article-title":"Detection of infectious bronchitis virus by real-time reverse transcriptase-polymerase chain reaction and identification of a quasispecies in the Beaudette strain","volume":"47","author":"Jackwood","year":"2003","journal-title":"Avian Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2007.03.018","article-title":"Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation","volume":"363","author":"Zhang","year":"2007","journal-title":"Virology"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Ali, A., Ojkic, D., Elshafiee, E.A., Shany, S., El-Safty, M.M., Shalaby, A.A., and Abdul-Careem, M.F. (2022). Genotyping and In Silico Analysis of Delmarva (DMV\/1639) Infectious Bronchitis Virus (IBV) Spike 1 (S1) Glycoprotein. Genes, 13.","DOI":"10.3390\/genes13091617"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Farooq, M., Ali, A., Hassan, M.S.H., and Abdul-Careem, M.F. (2024). Nucleotide and Amino Acid Analyses of Unique Infectious Bronchitis Virus (IBV) Variants from Canadian Poultry Flocks with Drop in Egg Production. Genes, 15.","DOI":"10.3390\/genes15111480"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1080\/03079450601110015","article-title":"Sequence changes of infectious bronchitis virus isolates in the 3\u2032 7.3 kb of the genome after attenuating passage in embryonated eggs","volume":"36","author":"Huang","year":"2007","journal-title":"Avian Pathol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1080\/03079450400025414","article-title":"Variation in the spike protein of the 793\/B type of infectious bronchitis virus, in the field and during alternate passage in chickens and embryonated eggs","volume":"34","author":"Cavanagh","year":"2005","journal-title":"Avian Pathol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1080\/03079450701338730","article-title":"S1 gene sequence heterogeneity of a pathogenic infectious bronchitis virus strain and its embryo-passaged, attenuated derivatives","volume":"36","author":"Liu","year":"2007","journal-title":"Avian Pathol."},{"key":"ref_40","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":"ref_41","doi-asserted-by":"crossref","first-page":"veac026","DOI":"10.1093\/ve\/veac026","article-title":"Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution","volume":"8","author":"Ramazzotti","year":"2022","journal-title":"Virus Evol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"6835","DOI":"10.1021\/acs.jpcb.2c04225","article-title":"Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule","volume":"126","author":"Giron","year":"2022","journal-title":"J. Phys. Chem. B"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e202100681","DOI":"10.1002\/cbic.202100681","article-title":"Charge Matters: Mutations in Omicron Variant Favor Binding to Cells","volume":"23","author":"Nie","year":"2022","journal-title":"Chembiochem"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"101346","DOI":"10.1016\/j.xcrp.2023.101346","article-title":"SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx","volume":"4","author":"Kim","year":"2023","journal-title":"Cell Rep. Phys. Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"8660","DOI":"10.1128\/jvi.70.12.8660-8668.1996","article-title":"Replication and packaging of coronavirus infectious bronchitis virus defective RNAs lacking a long open reading frame","volume":"70","author":"Wroe","year":"1996","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"8783","DOI":"10.1073\/pnas.1609057113","article-title":"Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy","volume":"113","author":"Imamichi","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.cell.2013.09.020","article-title":"Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure","volume":"155","author":"Ho","year":"2013","journal-title":"Cell"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1007\/s00705-009-0325-9","article-title":"Identification of sequence changes responsible for the attenuation of avian infectious bronchitis virus strain Arkansas DPI","volume":"154","author":"Ammayappan","year":"2009","journal-title":"Arch. Virol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.bbrc.2005.08.105","article-title":"Selection of and recombination between minor variants lead to the adaptation of an avian coronavirus to primate cells","volume":"336","author":"Fang","year":"2005","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1007\/s007050050239","article-title":"Identification of amino acids involved in a serotype and neutralization specific epitope within the s1 subunit of avian infectious bronchitis virus","volume":"142","author":"Moore","year":"1997","journal-title":"Arch. Virol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/0042-6822(87)90145-0","article-title":"Epitopes on the peplomer protein of infectious bronchitis virus strain M41 as defined by monoclonal antibodies","volume":"161","author":"Niesters","year":"1987","journal-title":"Virology"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1099\/jgv.0.000893","article-title":"Assessment of molecular and genetic evolution, antigenicity and virulence properties during the persistence of the infectious bronchitis virus in broiler breeders","volume":"98","author":"Pavani","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.virusres.2018.04.013","article-title":"Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus","volume":"250","author":"Shan","year":"2018","journal-title":"Virus Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1007\/s00705-005-0541-x","article-title":"Identification of previously unknown antigenic epitopes on the S and N proteins of avian infectious bronchitis virus","volume":"150","author":"Ignjatovic","year":"2005","journal-title":"Arch. Virol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.4049\/jimmunol.143.8.2692","article-title":"Analysis of an immunodominant region of infectious bronchitis virus","volume":"143","author":"Kusters","year":"1989","journal-title":"J. Immunol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e1002529","DOI":"10.1371\/journal.ppat.1002529","article-title":"Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection","volume":"8","author":"Henn","year":"2012","journal-title":"PLoS Pathog."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1101\/gr.6468307","article-title":"Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance","volume":"17","author":"Wang","year":"2007","journal-title":"Genome Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1086\/595703","article-title":"Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients","volume":"48","author":"Metzner","year":"2009","journal-title":"Clin. Infect. Dis."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nmeth.1527","article-title":"Limitations of next-generation genome sequence assembly","volume":"8","author":"Alkan","year":"2011","journal-title":"Nat. Methods"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1080\/03079450094108","article-title":"Detection of infectious bronchitis virus","volume":"29","year":"2000","journal-title":"Avian Pathol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Hassan, M.S.H., Ali, A., Buharideen, S.M., Goldsmith, D., Coffin, C.S., Cork, S.C., van der Meer, F., Boulianne, M., and Abdul-Careem, M.F. (2021). Pathogenicity of the Canadian Delmarva (DMV\/1639) Infectious Bronchitis Virus (IBV) on Female Reproductive Tract of Chickens. Viruses, 13.","DOI":"10.3390\/v13122488"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"105513","DOI":"10.1016\/j.micpath.2022.105513","article-title":"Immunopathogenesis of the Canadian Delmarva (DMV\/1639) infectious bronchitis virus (IBV): Impact on the reproductive tract in layers","volume":"166","author":"Hassan","year":"2022","journal-title":"Microb. Pathog."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/4\/527\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:10:18Z","timestamp":1760029818000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/4\/527"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,4]]},"references-count":62,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["v17040527"],"URL":"https:\/\/doi.org\/10.3390\/v17040527","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,4]]}}}