Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus
Abstract Background Despite numerous genetic studies on Infectious Bronchitis Virus (IBV), many strains from the Middle East remain misclassified or unclassified. Genotype 1 (GI-1) is found globally, while genotype 23 (GI-23) has emerged as the predominant genotype in the Middle East region, evolvin...
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2025-01-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-024-02614-5 |
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| author | Ali N. Alhafufi Samy Kasem Fahad N. Almajhdi Hassan A. Albaqshi Fanan A. Alaql Ehab A. Rihan Ehab M. Abd-Allah Ameen A. Alyousaf Yahya K. Aljasem Najwa D. Aljehani Mohei A. Haridy Ahmed R. Alhimaidi Ahmed S. Abdel-Moneim |
| author_facet | Ali N. Alhafufi Samy Kasem Fahad N. Almajhdi Hassan A. Albaqshi Fanan A. Alaql Ehab A. Rihan Ehab M. Abd-Allah Ameen A. Alyousaf Yahya K. Aljasem Najwa D. Aljehani Mohei A. Haridy Ahmed R. Alhimaidi Ahmed S. Abdel-Moneim |
| author_sort | Ali N. Alhafufi |
| collection | DOAJ |
| description | Abstract Background Despite numerous genetic studies on Infectious Bronchitis Virus (IBV), many strains from the Middle East remain misclassified or unclassified. Genotype 1 (GI-1) is found globally, while genotype 23 (GI-23) has emerged as the predominant genotype in the Middle East region, evolving continuously through inter- and intra-genotypic recombination. The GI-23 genotype is now enzootic in Europe and Asia. Methods Over a 24-month period from May 2022 to June 2024, 360 samples were collected from 19 layer and 3 broiler poultry farms in central Saudi Arabia. The chickens exhibited reduced laying rates and symptoms such as weakness and respiratory distress, while broilers showed respiratory issues. Samples, including tracheal swabs and various tissue specimens, were pooled, homogenized, and stored at -20 °C prior to PCR analysis. The samples underwent virus isolation in embryonated chicken eggs, RNA extraction using automated systems, and detection of IBV through real-time RT-PCR targeting a conserved 5’-UTR fragment. Full-length genome sequencing was performed, and recombination analysis was conducted using RDP 4.6. Results Saudi IBV strains were found to cluster into genotypes GI-1 and GI-23.1. The study identified critical amino acid substitutions in the hypervariable regions of the spike protein and detected recombination events in the ORF1ab, N, M, 3ab, and 5ab genes, with nsp3 of the ORF1ab showing the greatest number of recombination events. Conclusion The multiple inter- and intra-genotypic recombination events that were detected in different genes indicate that the circulating IBV strains do not share a single ancestor but have emerged through successive recombination events. |
| format | Article |
| id | doaj-art-b06db450d6c74181a4cc75cf8f36af50 |
| institution | DOAJ |
| issn | 1743-422X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj-art-b06db450d6c74181a4cc75cf8f36af502025-08-20T02:49:30ZengBMCVirology Journal1743-422X2025-01-0122111310.1186/s12985-024-02614-5Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virusAli N. Alhafufi0Samy Kasem1Fahad N. Almajhdi2Hassan A. Albaqshi3Fanan A. Alaql4Ehab A. Rihan5Ehab M. Abd-Allah6Ameen A. Alyousaf7Yahya K. Aljasem8Najwa D. Aljehani9Mohei A. Haridy10Ahmed R. Alhimaidi11Ahmed S. Abdel-Moneim12Department of Zoology, College of Science, King Saud UniversityDepartment of Virology, Faculty of Veterinary Medicine, Kafrelsheikh UniversityDepartment of Botany & Microbiology, College of Science, King Saud UniversityWEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)WEQAA Central Laboratory, National Centre for the Prevention & Control of Plant Pests & Animal Diseases (WEQAA)Department of Pathology and Clinical Pathology, Faculty of Veterinary Medicine, South Valley UniversityDepartment of Zoology, College of Science, King Saud UniversityDepartment of Microbiology, College of Medicine, Taif UniversityAbstract Background Despite numerous genetic studies on Infectious Bronchitis Virus (IBV), many strains from the Middle East remain misclassified or unclassified. Genotype 1 (GI-1) is found globally, while genotype 23 (GI-23) has emerged as the predominant genotype in the Middle East region, evolving continuously through inter- and intra-genotypic recombination. The GI-23 genotype is now enzootic in Europe and Asia. Methods Over a 24-month period from May 2022 to June 2024, 360 samples were collected from 19 layer and 3 broiler poultry farms in central Saudi Arabia. The chickens exhibited reduced laying rates and symptoms such as weakness and respiratory distress, while broilers showed respiratory issues. Samples, including tracheal swabs and various tissue specimens, were pooled, homogenized, and stored at -20 °C prior to PCR analysis. The samples underwent virus isolation in embryonated chicken eggs, RNA extraction using automated systems, and detection of IBV through real-time RT-PCR targeting a conserved 5’-UTR fragment. Full-length genome sequencing was performed, and recombination analysis was conducted using RDP 4.6. Results Saudi IBV strains were found to cluster into genotypes GI-1 and GI-23.1. The study identified critical amino acid substitutions in the hypervariable regions of the spike protein and detected recombination events in the ORF1ab, N, M, 3ab, and 5ab genes, with nsp3 of the ORF1ab showing the greatest number of recombination events. Conclusion The multiple inter- and intra-genotypic recombination events that were detected in different genes indicate that the circulating IBV strains do not share a single ancestor but have emerged through successive recombination events.https://doi.org/10.1186/s12985-024-02614-5IBVGI-1GI-23RecombinationFull-lengthCoronaviruses |
| spellingShingle | Ali N. Alhafufi Samy Kasem Fahad N. Almajhdi Hassan A. Albaqshi Fanan A. Alaql Ehab A. Rihan Ehab M. Abd-Allah Ameen A. Alyousaf Yahya K. Aljasem Najwa D. Aljehani Mohei A. Haridy Ahmed R. Alhimaidi Ahmed S. Abdel-Moneim Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus Virology Journal IBV GI-1 GI-23 Recombination Full-length Coronaviruses |
| title | Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus |
| title_full | Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus |
| title_fullStr | Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus |
| title_full_unstemmed | Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus |
| title_short | Full-length genome reveals genetic diversity and extensive recombination patterns of Saudi GI-1 and GI-23 genotypes of infectious bronchitis virus |
| title_sort | full length genome reveals genetic diversity and extensive recombination patterns of saudi gi 1 and gi 23 genotypes of infectious bronchitis virus |
| topic | IBV GI-1 GI-23 Recombination Full-length Coronaviruses |
| url | https://doi.org/10.1186/s12985-024-02614-5 |
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