الفهرس 
IntroductionOnly 14 pages are availabe for public view
 |  | from | 212 |  |  |
| | | from | 212 | | |
Abstract
Infectious bronchitis (IB) is caused by a virus of the genus Gammacoronavirus, which belongs to the family Coronaviridae. The disease is a contagious chicken illness that causes severe respiratory, reproductive, and urinary lesions, with a higher mortality rate depending on the virus strain, bird age, and immune state. IBV is a severe respiratory health concern in all endemic countries because of its virulence, the existence of many serotypes that are not protective to each other, signs of recombination, and co-circulation with other infectious respiratory viruses.
The isolation of new IBV variants continues, and despite several genetic studies on IBV, many strains from the Middle East region have been misclassified or remain unclassified. The genotype-23 (GI-23) variant emerged and dominated in the Middle East by continuously evolving either by inter- and/or intra-genotypic recombination and is currently enzootic throughout Europe and Asia. The current study provides an overview of the evolution and genetic diversity of IBV genotypes with a special focus on the GI-23 genotype. Additionally, a vaccination challenge study was conducted to evaluate the efficacy of GI-23 based Vaccines within prime-boost vaccination strategies in commercial broiler chickens.
The increase in diversity of GI-23 raised the necessity of differentiating the new isolates within the GI-23 into subclades to determine the possible evolutionary linkages. Therefore, we collected available complete S1 sequences of the GI-23 from the Middle East, and partial sequences were used to study the intragenotype diversity using MEGA X software. Results showed that lineage to be classified into 3 clades (1, 2 and 3). Also, the GI-23.2 is sub classified into three subclades (1, 2 and 3). After that, the validity of HVR3 sequencing is also examined using the same datasets to compare the phylogenetic analysis results of full and partial datasets, and their results showed its reliability in rapid diagnostics of GI-23.
In our experimental study on commercial chicks, different vaccination strategies dependent mainly on GI-23 based vaccination showed variable results due to changes in the vaccination program even though using the same vaccinal strains. The vaccination strategies were challenged with wild Isolate of GI-23 and assessed using clinical signs, ciliostasis, viral tracheal shedding quantification using qRT-PCR, and different histopathological techniques including histopathological scoring and histomorphometry. The results were variable in ciliostasis as follows; H120+VAR2 at one-day old and VAR2 at 14-days-old, VAR2 at one-day-old and H120 at 14-days old, H120 at one-day-old and VAR2 at 14-days old, H120+VAR2 at 14-days-old and H120+VAR2 at one-day-old showed 89.5, 85.5, 77, 69, 54% respectively. The other tests results were consistant with the ciliostasis findings.
In conclusion, the GI-23 (Variant 2) is the most dominant lineage of IBV in the Middle East region. In addition, it shows higher intra-genotype diversity, which reached nearly 19%. For diagnostic purposes, we confirmed the validity of HVR3 sequencing compared to the full S1 as a reliable tool for rapid diagnosis and classification of IBV strains. Moreover, the recombination analysis for GI-23 revealed a recombination breakpoint at 780 bp. The theoretical model for the GI-23 origin based on datasets of the full S1, N-terminal, C-Terminal, HVR1/2, and HVR3 proposed an ancient emergence of GI-23 back to 1950s in the Middle East region (mainly in Palestine). The phylogeographic analysis for the same datasets showed that dispersal between countries is more likely to be through certain bridges (Turkey, Iran, and Egypt).
Additionally, an experimental vaccination challenge study involving the GI-23 based vaccine in different vaccination regimes revealed that the GI-23 based vaccinations effectively reduce clinical symptoms, ciliostasis scores, quantification of tracheal viral shedding, and histological degeneration of the tracheal and renal tissues in broiler chickens. however, the study’s findings also emphasize that adopting a suitable vaccination schedule plays an important role in the efficacy of the same genetic lineages’ strains to proetct against IBV challenge.