{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:45:34Z","timestamp":1790646334805,"version":"4.1.0"},"reference-count":44,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,5,29]],"date-time":"2020-05-29T00:00:00Z","timestamp":1590710400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000308","name":"British Council","doi-asserted-by":"publisher","award":["332228521"],"award-info":[{"award-number":["332228521"]}],"id":[{"id":"10.13039\/501100000308","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000308","name":"British Council","doi-asserted-by":"publisher","award":["172710323"],"award-info":[{"award-number":["172710323"]}],"id":[{"id":"10.13039\/501100000308","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9\/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4\/91 genotype, two isolates within IS\/885 genotype, one isolate was closely related to IS\/1494\/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.<\/jats:p>","DOI":"10.3390\/genes11060605","type":"journal-article","created":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T09:19:27Z","timestamp":1591089567000},"page":"605","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6941-9294","authenticated-orcid":false,"given":"Mohammed A.","family":"Rohaim","sequence":"first","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt"},{"name":"Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3648-847X","authenticated-orcid":false,"given":"Rania F.","family":"El Naggar","sequence":"additional","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat 32897, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed A.","family":"Abdelsabour","sequence":"additional","affiliation":[{"name":"Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo 11381, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahmoud H. A.","family":"Mohamed","sequence":"additional","affiliation":[{"name":"Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia"},{"name":"Department of Avian and Rabbit Medicine, College of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim M.","family":"El-Sabagh","sequence":"additional","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt"},{"name":"Central Biotechnology Laboratory, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Munir","sequence":"additional","affiliation":[{"name":"Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,5,29]]},"reference":[{"key":"ref_1","unstructured":"King, A.M.Q., Adams, M.J., Carstens, E.B., and Lefkowitz, E.J. (2012). Family Coronaviridae. Virus Taxonomy, 9th Report of the International Committee on Taxonomy of Viruses, Elsevier Academic Press."},{"key":"ref_2","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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