{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,6]],"date-time":"2026-09-06T21:48:42Z","timestamp":1788731322053,"version":"build-2803163510"},"reference-count":99,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T00:00:00Z","timestamp":1731801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014972","name":"Agriculture and Agri-Food Canada (AAFC)","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":"Agriculture and Agri-Food Canada (AAFC)","doi-asserted-by":"publisher","award":["10022788"],"award-info":[{"award-number":["10022788"]}],"id":[{"id":"10.13039\/100014972","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AHBP project of the Higher Education Commission of Pakistan","award":["ASC-20"],"award-info":[{"award-number":["ASC-20"]}]},{"name":"AHBP project of the Higher Education Commission of Pakistan","award":["10022788"],"award-info":[{"award-number":["10022788"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Infectious bronchitis (IB) is a highly infectious avian disease caused by the infectious bronchitis virus (IBV). The disease causes lesions mainly in the respiratory, reproductive, and renal systems and has a significant economic impact on the poultry industry worldwide. Methods: We discovered two unique IBV isolates (T-62: PP737794.1 and CL-61: PP783617.1) circulating in Canada and molecularly characterized them. Results: The phylogenetic analysis revealed that the IBV isolates belong to genotype I and fall between lineages 25 and 7. Further analysis of the T-62 IBV isolate indicated that it is a potential recombinant of the Iowa state isolate (IA1162\/2020-MW) and that the CL-61 strain of the IBV is also a recombinant IBV with the Connecticut (Conn) vaccine strain as its major parent. The S1 glycoprotein of the CL-61 and T-62 strains of the IBV had 85.7% and 73.2% amino acid (aa) identities respectively compared to the Conn vaccine strain. There were 67 and 129 aa substitutions among the S1 glycoprotein of the CL-61 and T-62 strains of the IBV compared to the Conn vaccine, respectively. Importantly, two and nineteen of these aa variations were in hypervariable regions 1 (HVR1) and HVR3. Finally, the two IBV isolates possessed a higher affinity for the sialic acid ligand compared to the DMV\/1639 and Mass\/SES IBV strains. Conclusions: Genetic recombination in the IBV results in the continual emergence of new variants, posing challenges for the poultry industry. As indicated by our analyses, live attenuated vaccine strains play a role in the genetic recombination of the IBV, resulting in the emergence of variants.<\/jats:p>","DOI":"10.3390\/genes15111480","type":"journal-article","created":{"date-parts":[[2024,11,18]],"date-time":"2024-11-18T05:36:45Z","timestamp":1731908205000},"page":"1480","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Nucleotide and Amino Acid Analyses of Unique Infectious Bronchitis Virus (IBV) Variants from Canadian Poultry Flocks with Drop in Egg Production"],"prefix":"10.3390","volume":"15","author":[{"given":"Muhammad","family":"Farooq","sequence":"first","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive, NW, Calgary, AB T2N 4N1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8662-1291","authenticated-orcid":false,"given":"Ahmed","family":"Ali","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, University of Calgary, Health Research Innovation Center 2C53, 3330 Hospital Drive, NW, 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\/0000-0002-7424-5305","authenticated-orcid":false,"given":"Mohamed S. H.","family":"Hassan","sequence":"additional","affiliation":[{"name":"Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt"}],"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, Health Research Innovation Center 2C53, 3330 Hospital Drive, NW, Calgary, AB T2N 4N1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,17]]},"reference":[{"key":"ref_1","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. 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