الفهرس 
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Abstract
Avian infectious bronchitis virus (IBV), a major pathogen of commercial poultry flocks, circulates in the form of multiple ever emerging variants threatening the poultry industry. This study was conducted to survey the presence of IBV in Luxor Governorate during 2015 -2016. Examination of 43 pooled samples including trachea and kidney homogenates by real-time RT- PCR for N gene, revealed 35 (81.4%) out of 43 commercial broiler flocks were positive to IBV.
The clinical examination of the investigated flocks revealed general signs of illness, respiratory signs and renal problems in some flocks. The respiratory signs ranged from mild to severe, gasping, sneezing, rales and coughing. Mortality rates ranging from 4-12 %. At necropsy, the main lesions found were tracheitis, lung congestion, air-sacculitis. Some flocks frequently showed mucous or caseated material in trachea and bronchi. Pale or congested and enlarged kidneys with slight to moderate distention of the ureters with urates were also seen. The results of virus isolation of IBV in 9-11-day old ECE showed that the virus causes subcutaneous haemorrhage, curling and dwarfing.
The 400-bp of HVR3 of the S1 gene of ten selected samples were amplified by RT-PCR, sequenced, and aligned for phylogenetic and amino-acid similarity analyses. Analysis of the partial S1 sequences derived from the obtained samples identified that all the sequences were related (71.8%–90.1%) to the Israel variant-2 IS/1494/06 (GI-23) and (74.8%–94.7%) to Eg\12120S\2012 previously identified and reported in Egypt. The IBV identified in this study also showed similarity to IS/885/00 (71%–92.4%) The ten IBV viruses shared from 71% to 90.8% homologies between each other but are very different from the vaccinal strains used in Egypt with 62.6 to 84.7 % similarities. They shared (65.6-84.7 %) to 4/91 vaccinal strains of IBV and (62.6-79.4%) to H120 and Ma5. IBV/EG/LUXOR-38-2016 had the highest derived amino acid similarity (79.4%) to the H120 and Ma5 vaccine strains, while IBV/EG/LUXOR-24-2016 had the lowest similarity (62.6%) to these two vaccinal strains. They also shared 66.4-84% and 62.6-80.2% amino acid identities with CR88 and D274, respectively Phylogenetic analysis revealed that all the Luxor detected viruses grouped within the D1456 like Egyptian IBV viruses within the Variant 2 IBV cluster but in a different subcluster and none of them is a vaccinal strain suggesting that IBV circulating in this region can be regarded as a new genotype of IBV.In conclusion, IBVs similar to those circulating in Egypt including various governorates were identified in chickens from Luxor broiler flocks. Clinical signs and pathologic changes were mainly confined to the respiratory and urinary tracts of infected chickens. The results indicate that IBV circulating in Luxor is very different from the used vaccinal strains. Monitoring the emerging IBV variants is extremely important for establishing an effective control strategy for the disease in Luxor and surrounding area. Vaccination programs currently applied in Luxor should be assessed in future studies