{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T01:06:16Z","timestamp":1789088776526,"version":"build-2803163510"},"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T00:00:00Z","timestamp":1721865600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00001424"],"award-info":[{"award-number":["BBS\/E\/I\/00001424"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007031"],"award-info":[{"award-number":["BBS\/E\/I\/00007031"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007034"],"award-info":[{"award-number":["BBS\/E\/I\/00007034"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007035"],"award-info":[{"award-number":["BBS\/E\/I\/00007035"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007037"],"award-info":[{"award-number":["BBS\/E\/I\/00007037"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007038"],"award-info":[{"award-number":["BBS\/E\/I\/00007038"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/I\/00007039"],"award-info":[{"award-number":["BBS\/E\/I\/00007039"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/PI\/230001B"],"award-info":[{"award-number":["BBS\/E\/PI\/230001B"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/PI\/230002A"],"award-info":[{"award-number":["BBS\/E\/PI\/230002A"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/PI\/23NB0004"],"award-info":[{"award-number":["BBS\/E\/PI\/23NB0004"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/PI\/23NB0003"],"award-info":[{"award-number":["BBS\/E\/PI\/23NB0003"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    Avian infectious bronchitis is an acute respiratory disease of poultry of particular concern for global food security. Investigation of infectious bronchitis virus (IBV), the causative agent of avian infectious bronchitis, via reverse genetics enables deeper understanding of virus biology and a rapid response to emerging variants. Classic methods of reverse genetics for IBV can be time consuming, rely on recombination for the introduction of mutations, and, depending on the system, can be subject to genome instability and unreliable success rates. In this study, we have applied data-optimized Golden Gate Assembly design to create a rapidly executable, flexible, and faithful reverse genetics system for IBV. The IBV genome was divided into 12 fragments at high-fidelity fusion site breakpoints. All fragments were synthetically produced and propagated in\n                    <jats:italic>E<\/jats:italic>\n                    .\n                    <jats:italic>coli<\/jats:italic>\n                    plasmids, amenable to standard molecular biology techniques for DNA manipulation. The assembly can be carried out in a single reaction, with the products used directly in subsequent viral rescue steps. We demonstrate the use of this system for generation of point mutants and gene replacements. This Golden Gate Assembly-based reverse genetics system will enable rapid response to emerging variants of IBV, particularly important to vaccine development for controlling spread within poultry populations.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0307655","type":"journal-article","created":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T13:42:10Z","timestamp":1721914930000},"page":"e0307655","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["One-pot Golden Gate Assembly of an avian infectious bronchitis virus reverse genetics system"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2391-9645","authenticated-orcid":true,"given":"Katharina","family":"Bilotti","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Keep","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P.","family":"Sikkema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Pryor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Kirk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katalin","family":"Foldes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6016-5830","authenticated-orcid":true,"given":"Nicole","family":"Doyle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ge","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham","family":"Freimanis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Dowgier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0848-5917","authenticated-orcid":true,"given":"Oluwapelumi","family":"Adeyemi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. Kasra","family":"Tabatabaei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0638-7555","authenticated-orcid":true,"given":"Gregory J. S.","family":"Lohman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica","family":"Bickerton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,7,25]]},"reference":[{"key":"pone.0307655.ref001","first-page":"51","article-title":"Cultivation of the virus of infectious bronchitis","volume":"90","author":"F. Beaudette","year":"1937","journal-title":"J Am Vet Med Assoc"},{"issue":"3","key":"pone.0307655.ref002","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2.","volume":"19","author":"P V\u2019kovski","year":"2021","journal-title":"Nature Reviews Microbiology."},{"key":"pone.0307655.ref003","first-page":"413","article-title":"An apparently new respiratory disease of baby chicks","volume":"78","author":"AF Schalk","year":"1931","journal-title":"Journal of the American Veterinary Medical Association"},{"key":"pone.0307655.ref004","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.vetmic.2017.01.002","article-title":"Vaccination against infectious bronchitis virus: A continuous challenge","volume":"206","author":"B. Jordan","year":"2017","journal-title":"Veterinary Microbiology"},{"issue":"3","key":"pone.0307655.ref005","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":"J De Wit","year":"2011","journal-title":"Avian pathology"},{"key":"pone.0307655.ref006","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":"V Valastro","year":"2016","journal-title":"Infection, Genetics and Evolution"},{"issue":"3","key":"pone.0307655.ref007","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1080\/0307945042000220697","article-title":"A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China","volume":"33","author":"S Liu","year":"2004","journal-title":"Avian Pathology"},{"issue":"5","key":"pone.0307655.ref008","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":"J De Wit","year":"2011","journal-title":"Avian Pathology"},{"issue":"1","key":"pone.0307655.ref009","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1080\/03079457.2010.542742","article-title":"Efficacy and safety of an attenuated live QX-like infectious bronchitis virus strain as a vaccine for chickens","volume":"40","author":"H Geerligs","year":"2011","journal-title":"Avian Pathology"},{"issue":"6","key":"pone.0307655.ref010","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":"G Bijlenga","year":"2004","journal-title":"Avian Pathology"},{"key":"pone.0307655.ref011","doi-asserted-by":"crossref","first-page":"221","DOI":"10.2307\/1590639","article-title":"Reversion to virulence of chicken-passaged infectious bronchitis vaccine virus","author":"S Hopkins","year":"1986","journal-title":"Avian Diseases"},{"issue":"14","key":"pone.0307655.ref012","article-title":"Attenuation of infectious bronchitis virus in eggs results in different patterns of genomic variation across multiple replicates","volume":"93","author":"MS Oade","year":"2019","journal-title":"Journal of virology"},{"key":"pone.0307655.ref013","first-page":"2015","article-title":"Progress and challenges toward the development of vaccines against avian infectious bronchitis","author":"F Bande","year":"2015","journal-title":"Journal of immunology research"},{"key":"pone.0307655.ref014","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.vetmic.2017.09.020","article-title":"Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China.","volume":"211","author":"Y Pan","year":"2017","journal-title":"Veterinary microbiology"},{"key":"pone.0307655.ref015","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.coviro.2018.12.001","article-title":"Emerging and re-emerging coronaviruses in pigs","volume":"34","author":"Q Wang","year":"2019","journal-title":"Current opinion in virology"},{"issue":"7700","key":"pone.0307655.ref016","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/s41586-018-0010-9","article-title":"Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin","volume":"556","author":"P Zhou","year":"2018","journal-title":"Nature"},{"issue":"3","key":"pone.0307655.ref017","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1007\/s12250-020-00321-3","article-title":"Broad Cell Tropism of SADS-CoV In Vitro Implies Its Potential Cross-Species Infection Risk.","volume":"36","author":"Y Luo","year":"2021","journal-title":"Virologica Sinica"},{"issue":"22","key":"pone.0307655.ref018","first-page":"E5135","article-title":"Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility","volume":"115","author":"W Li","year":"2018","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"7","key":"pone.0307655.ref019","doi-asserted-by":"crossref","first-page":"3995","DOI":"10.1128\/JVI.06540-11","article-title":"Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus","volume":"86","author":"PC Woo","year":"2012","journal-title":"Journal of virology"},{"issue":"7887","key":"pone.0307655.ref020","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41586-021-04111-z","article-title":"Independent infections of porcine deltacoronavirus among Haitian children","volume":"600","author":"JA Lednicky","year":"2021","journal-title":"Nature"},{"issue":"5624","key":"pone.0307655.ref021","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1126\/science.1085952","article-title":"Characterization of a novel coronavirus associated with severe acute respiratory syndrome","volume":"300","author":"PA Rota","year":"2003","journal-title":"science"},{"issue":"19","key":"pone.0307655.ref022","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":"AM Zaki","year":"2012","journal-title":"New England Journal of Medicine"},{"issue":"8","key":"pone.0307655.ref023","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019","volume":"382","author":"N Zhu","year":"2020","journal-title":"New England journal of medicine"},{"issue":"1","key":"pone.0307655.ref024","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/s41392-022-00996-y","article-title":"COVID-19 vaccine development: milestones, lessons and prospects.","volume":"7","author":"M Li","year":"2022","journal-title":"Signal transduction and targeted therapy."},{"key":"pone.0307655.ref025","first-page":"1","article-title":"Porcine coronaviruses: overview of the state of the art.","author":"H Turlewicz-Podbielska","year":"2021","journal-title":"Virologica Sinica."},{"key":"pone.0307655.ref026","first-page":"383","volume-title":"Advances in virus research","author":"Z Ma","year":"2020"},{"key":"pone.0307655.ref027","first-page":"27","volume-title":"Reverse genetics of RNA viruses: applications and perspectives","author":"M Armesto","year":"2012"},{"key":"pone.0307655.ref028","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.virusres.2014.05.026","article-title":"Coronavirus reverse genetic systems: infectious clones and replicons","volume":"189","author":"F Almaz\u00e1n","year":"2014","journal-title":"Virus research"},{"issue":"10","key":"pone.0307655.ref029","doi-asserted-by":"crossref","first-page":"5516","DOI":"10.1073\/pnas.97.10.5516","article-title":"Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome","volume":"97","author":"F Almaz\u00e1n","year":"2000","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7813","key":"pone.0307655.ref030","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1038\/s41586-020-2294-9","article-title":"Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform","volume":"582","author":"T Thi Nhu Thao","year":"2020","journal-title":"Nature"},{"issue":"1","key":"pone.0307655.ref031","doi-asserted-by":"crossref","first-page":"3431","DOI":"10.1038\/s41467-021-23779-5","article-title":"A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses.","volume":"12","author":"AA Amarilla","year":"2021","journal-title":"Nature Communications."},{"issue":"19","key":"pone.0307655.ref032","doi-asserted-by":"crossref","first-page":"10188","DOI":"10.3390\/ijms221910188","article-title":"Cloning of a passage-free SARS-CoV-2 genome and mutagenesis using red recombination","volume":"22","author":"A Herrmann","year":"2021","journal-title":"International journal of molecular sciences"},{"issue":"5","key":"pone.0307655.ref033","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1016\/j.chom.2020.04.004","article-title":"An Infectious cDNA Clone of SARS-CoV-2","volume":"27","author":"X Xie","year":"2020","journal-title":"Cell Host & Microbe."},{"key":"pone.0307655.ref034","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1007\/3-540-26765-4_5","article-title":"Coronavirus reverse genetics by targeted RNA recombination","author":"P Masters","year":"2005","journal-title":"Coronavirus Replication and Reverse Genetics"},{"issue":"1","key":"pone.0307655.ref035","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12985-017-0775-8","article-title":"A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination","volume":"14","author":"SJ van Beurden","year":"2017","journal-title":"Virology journal"},{"issue":"24","key":"pone.0307655.ref036","doi-asserted-by":"crossref","first-page":"12359","DOI":"10.1128\/JVI.75.24.12359-12369.2001","article-title":"Reverse genetics system for the avian coronavirus infectious bronchitis virus","volume":"75","author":"R Casais","year":"2001","journal-title":"Journal of virology"},{"key":"pone.0307655.ref037","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-1-4939-6964-7_6","article-title":"Reverse genetics system for the avian coronavirus infectious bronchitis virus","author":"E Bickerton","year":"2017","journal-title":"Reverse Genetics of RNA Viruses: Methods and Protocols"},{"key":"pone.0307655.ref038","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.virol.2019.04.014","article-title":"S gene and 5a accessory gene are responsible for the attenuation of virulent infectious bronchitis coronavirus","volume":"533","author":"Y Zhao","year":"2019","journal-title":"Virology"},{"issue":"1","key":"pone.0307655.ref039","doi-asserted-by":"crossref","first-page":"2308","DOI":"10.1038\/s41467-023-37787-0","article-title":"Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6","volume":"14","author":"TY Taha","year":"2023","journal-title":"Nature Communications"},{"issue":"11","key":"pone.0307655.ref040","doi-asserted-by":"crossref","first-page":"e3647","DOI":"10.1371\/journal.pone.0003647","article-title":"A One Pot, One Step, Precision Cloning Method with High Throughput Capability.","volume":"3","author":"C Engler","year":"2008","journal-title":"PLOS ONE."},{"issue":"13","key":"pone.0307655.ref041","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1093\/nar\/gky303","article-title":"A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining","volume":"46","author":"V Potapov","year":"2018","journal-title":"Nucleic Acids Research"},{"issue":"11","key":"pone.0307655.ref042","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1021\/acssynbio.8b00333","article-title":"Comprehensive profiling of four base overhang ligation fidelity by T4 DNA ligase and application to DNA assembly","volume":"7","author":"V Potapov","year":"2018","journal-title":"ACS synthetic biology"},{"issue":"9","key":"pone.0307655.ref043","doi-asserted-by":"crossref","first-page":"e0238592","DOI":"10.1371\/journal.pone.0238592","article-title":"Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design.","volume":"15","author":"JM Pryor","year":"2020","journal-title":"PLoS One."},{"issue":"9","key":"pone.0307655.ref044","doi-asserted-by":"crossref","first-page":"e882","DOI":"10.1002\/cpz1.882","article-title":"High-Complexity One-Pot Golden Gate Assembly.","volume":"3","author":"AP Sikkema","year":"2023","journal-title":"Current protocols."},{"issue":"6","key":"pone.0307655.ref045","doi-asserted-by":"crossref","first-page":"2036","DOI":"10.1021\/acssynbio.1c00525","article-title":"Rapid 40 kb genome construction from 52 parts through data-optimized assembly design.","volume":"11","author":"JM Pryor","year":"2022","journal-title":"ACS Synthetic Biology."},{"key":"pone.0307655.ref046","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/978-1-0716-0900-2_5","article-title":"Whole-genome sequencing protocols for IBV and other coronaviruses using high-throughput sequencing.","author":"GL Freimanis","year":"2020","journal-title":"Coronaviruses: Methods and Protocols."},{"key":"pone.0307655.ref047","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/978-1-0716-0900-2_12","volume-title":"Coronaviruses: Methods and Protocols","author":"S Keep","year":"2020"},{"issue":"1","key":"pone.0307655.ref048","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1080\/03079459708419194","article-title":"Relationship between sequence variation in the S1 spike protein of infectious bronchitis virus and the extent of cross\u2010protection in vivo","volume":"26","author":"D Cavanagh","year":"1997","journal-title":"Avian Pathology"},{"issue":"2","key":"pone.0307655.ref049","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1051\/vetres:2006055","article-title":"Coronavirus avian infectious bronchitis virus","volume":"38","author":"D. Cavanagh","year":"2007","journal-title":"Vet Res"},{"issue":"9","key":"pone.0307655.ref050","doi-asserted-by":"crossref","first-page":"e226","DOI":"10.1371\/journal.pbio.0060226","article-title":"SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum","volume":"6","author":"K Knoops","year":"2008","journal-title":"PLoS biology"},{"issue":"5","key":"pone.0307655.ref051","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00801-13","article-title":"Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes.","volume":"4","author":"HJ Maier","year":"2013","journal-title":"MBio"},{"issue":"7","key":"pone.0307655.ref052","doi-asserted-by":"crossref","first-page":"754","DOI":"10.3390\/v12070754","article-title":"Temperature sensitivity: A potential method for the generation of vaccines against the avian coronavirus infectious bronchitis virus.","volume":"12","author":"S Keep","year":"2020","journal-title":"Viruses"},{"issue":"6","key":"pone.0307655.ref053","doi-asserted-by":"crossref","first-page":"e02059","DOI":"10.1128\/jvi.02059-21","article-title":"Identification of amino acids within nonstructural proteins 10 and 14 of the avian coronavirus infectious bronchitis virus that result in attenuation In Vivo and In Ovo","volume":"96","author":"S Keep","year":"2022","journal-title":"Journal of virology"},{"issue":"17","key":"pone.0307655.ref054","doi-asserted-by":"crossref","first-page":"e01100","DOI":"10.1128\/jvi.01100-22","article-title":"A Temperature-Sensitive Recombinant of Avian Coronavirus Infectious Bronchitis Virus Provides Complete Protection against Homologous Challenge","volume":"96","author":"S Keep","year":"2022","journal-title":"Journal of Virology"},{"issue":"16","key":"pone.0307655.ref055","doi-asserted-by":"crossref","first-page":"9084","DOI":"10.1128\/JVI.77.16.9084-9089.2003","article-title":"Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism","volume":"77","author":"R Casais","year":"2003","journal-title":"Journal of virology"},{"issue":"8","key":"pone.0307655.ref056","doi-asserted-by":"crossref","first-page":"e24352","DOI":"10.1371\/journal.pone.0024352","article-title":"A recombinant avian infectious bronchitis virus expressing a heterologous spike gene belonging to the 4\/91 serotype.","volume":"6","author":"M Armesto","year":"2011","journal-title":"PLoS One."},{"issue":"6","key":"pone.0307655.ref057","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.3390\/v4061011","article-title":"Mechanisms of coronavirus cell entry mediated by the viral spike protein","volume":"4","author":"S Belouzard","year":"2012","journal-title":"Viruses"},{"issue":"5","key":"pone.0307655.ref058","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1007\/s15010-021-01677-8","article-title":"SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies.","volume":"49","author":"AM Almehdi","year":"2021","journal-title":"Infection"},{"issue":"3","key":"pone.0307655.ref059","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/S0378-1135(96)01258-8","article-title":"Protectotypic differentiation of avian infectious bronchitis viruses using an in vitro challenge model","volume":"53","author":"G Dhinakar Raj","year":"1996","journal-title":"Veterinary Microbiology"},{"issue":"19","key":"pone.0307655.ref060","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01044-18","article-title":"The S2 subunit of infectious bronchitis virus Beaudette is a determinant of cellular tropism","volume":"92","author":"E Bickerton","year":"2018","journal-title":"Journal of Virology"},{"issue":"1","key":"pone.0307655.ref061","doi-asserted-by":"crossref","first-page":"e0297516","DOI":"10.1371\/journal.pone.0297516","article-title":"The spike protein of the apathogenic Beaudette strain of avian coronavirus can elicit a protective immune response against a virulent M41 challenge.","volume":"19","author":"S Keep","year":"2024","journal-title":"PLOS ONE"},{"issue":"7","key":"pone.0307655.ref062","doi-asserted-by":"crossref","first-page":"3017","DOI":"10.1002\/jmv.27738","article-title":"Reverse genetics systems for SARS-CoV-2","volume":"94","author":"W Wang","year":"2022","journal-title":"Journal of medical virology"},{"key":"pone.0307655.ref063","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/978-1-0716-0900-2_13","article-title":"In-Yeast Assembly of Coronavirus Infectious cDNA Clones Using a Synthetic Genomics Pipeline.","volume":"2203","author":"TTN Thao","year":"2020","journal-title":"Methods in molecular biology (Clifton, NJ)."},{"issue":"10","key":"pone.0307655.ref064","doi-asserted-by":"crossref","first-page":"e1008271","DOI":"10.1371\/journal.pgen.1008271","article-title":"Viral quasispecies.","volume":"15","author":"E Domingo","year":"2019","journal-title":"PLoS genetics"},{"issue":"5","key":"pone.0307655.ref065","doi-asserted-by":"crossref","first-page":"3097","DOI":"10.1128\/JVI.79.5.3097-3106.2005","article-title":"Recombinant mouse hepatitis virus strain A59 from cloned, full-length cDNA replicates to high titers in vitro and is fully pathogenic in vivo","volume":"79","author":"SE Coley","year":"2005","journal-title":"Journal of virology"},{"issue":"23","key":"pone.0307655.ref066","doi-asserted-by":"crossref","first-page":"11948","DOI":"10.1128\/JVI.01804-08","article-title":"Systematic assembly of a full-length infectious clone of human coronavirus NL63","volume":"82","author":"EF Donaldson","year":"2008","journal-title":"Journal of virology"},{"issue":"1","key":"pone.0307655.ref067","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.virol.2006.08.020","article-title":"An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells.","volume":"358","author":"S Fang","year":"2007","journal-title":"Virology"},{"issue":"22","key":"pone.0307655.ref068","doi-asserted-by":"crossref","first-page":"10600","DOI":"10.1128\/JVI.74.22.10600-10611.2000","article-title":"Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model","volume":"74","author":"B Yount","year":"2000","journal-title":"Journal of Virology"},{"issue":"6","key":"pone.0307655.ref069","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1016\/j.drudis.2020.03.010","article-title":"Viral replicons as valuable tools for drug discovery","volume":"25","author":"H. Hannemann","year":"2020","journal-title":"Drug discovery today"},{"issue":"18","key":"pone.0307655.ref070","doi-asserted-by":"crossref","first-page":"e0068721","DOI":"10.1128\/JVI.00687-21","article-title":"Construction of a Noninfectious SARS-CoV-2 Replicon for Antiviral-Drug Testing and Gene Function Studies","volume":"95","author":"HT Nguyen","year":"2021","journal-title":"J Virol"},{"issue":"6","key":"pone.0307655.ref071","doi-asserted-by":"crossref","first-page":"2438","DOI":"10.1002\/jmv.27650","article-title":"Construction and characterization of two SARS-CoV-2 minigenome replicon systems","volume":"94","author":"H Zhang","year":"2022","journal-title":"Journal of medical virology"},{"issue":"3","key":"pone.0307655.ref072","first-page":"162","article-title":"SARS-CoV-2 variant biology: immune escape, transmission and fitness.","volume":"21","author":"AM Carabelli","year":"2023","journal-title":"Nature reviews Microbiology."},{"key":"pone.0307655.ref073","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-0716-0900-2_7","article-title":"The preparation of chicken kidney cell cultures for virus propagation","author":"E Lokhman","year":"2020","journal-title":"Coronaviruses: Methods and Protocols"},{"key":"pone.0307655.ref074","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/978-1-0716-0900-2_11","article-title":"Quantification of coronaviruses by titration In vitro and Ex vivo.","author":"G Dowgier","year":"2020","journal-title":"Coronaviruses: Methods and Protocols."},{"key":"pone.0307655.ref075","first-page":"1209","article-title":"A line of cells derived from African green monkey kidney","volume":"21","author":"Y Yasumura","year":"1963","journal-title":"Nippon Rinsho"},{"issue":"24","key":"pone.0307655.ref076","doi-asserted-by":"crossref","first-page":"13804","DOI":"10.1128\/JVI.78.24.13804-13811.2004","article-title":"Recombinant infectious bronchitis coronavirus Beaudette with the spike protein gene of the pathogenic M41 strain remains attenuated but induces protective immunity","volume":"78","author":"T Hodgson","year":"2004","journal-title":"J Virol"},{"key":"pone.0307655.ref077","doi-asserted-by":"crossref","DOI":"10.1109\/IPDPS.2019.00041","article-title":"Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.","volume":"2019","author":"M Vasimuddin","year":"2019","journal-title":"2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS)"},{"issue":"1","key":"pone.0307655.ref078","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler.","volume":"70","author":"A Prjibelski","year":"2020","journal-title":"Current protocols in bioinformatics"},{"issue":"10","key":"pone.0307655.ref079","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1099\/jgv.0.001474","article-title":"Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus","volume":"101","author":"S Keep","year":"2020","journal-title":"The Journal of general virology"},{"key":"pone.0307655.ref080","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/978-1-4939-2438-7_12","article-title":"Transient dominant selection for the modification and generation of recombinant infectious bronchitis coronaviruses.","author":"SM Keep","year":"2015","journal-title":"Coronaviruses: Methods and Protocols."},{"issue":"5","key":"pone.0307655.ref081","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1099\/0022-1317-77-5-963","article-title":"Expression of bacteriophage T7 RNA polymerase in avian and mammalian cells by a recombinant fowlpox virus","volume":"77","author":"P Britton","year":"1996","journal-title":"Journal of General Virology"},{"issue":"4","key":"pone.0307655.ref082","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1080\/03079450120066421","article-title":"Protection of chickens against renal damage caused by a nephropathogenic infectious bronchitis virus","volume":"30","author":"JKA Cook","year":"2001","journal-title":"Avian Pathology"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0307655","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T13:43:09Z","timestamp":1721914989000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0307655"}},"subtitle":[],"editor":[{"given":"Haitham Mohamed","family":"Amer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,25]]},"references-count":82,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0307655","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.21.566883","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,25]]}}}