الفهرس 
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Abstract
Four Egyptian isolates of IBV were selected from the years 2010 and 2012.
We attempted in this study to monitor the evolution of the new virus in Egypt, to compare the vaccinal strains with our selected field isolates and to detect the differences and predict based on the molecular level if new vaccines are needed and to differentiate between different types of analysis based on the partial sequencing of different regions of the S1 gene.
First of all a real-time RT-PCR is done for more confirmation of the result of the IBV isolates, then a 1000 bp fragments of the S1 gene (there were two fragments involved the whole gene) was amplified by PCR thermocycler using specific primers, DNA bands of the expected sizes (1000 bp) were purified and the purified PCR products were sequenced directly. After that alignment and phylogenetic analysis of the isolates in the study is done using bio-informatics software in additional to another Egyptian strains from the Genbank and the vaccinal strains of the vaccines used in Egypt.
The phylogenetic analysis of the S1 gene, clarify that Egyptian viruses can be divided into three groups, the new Egyptian variants lied in the second and the third groups and showed high differences to the vaccinal strains, however our results showed by amino acid identity levels that D274 is the closest vaccinal strain to the Egyptian variants.
We recommended active surveillances to be carried out to confirm our grouping and to find out if more groups of variants exist in the Egyptian field.
Also comparison of the used regions in the analysis was made and we concluded that results depended on whole gene is different from both HVR 1-2 and HVR3 however, both can be used for monitoring emergence of new variants or differentiating vaccinal from field strains but not for characterization of new variants or further molecular studies or selection of vaccinal strains.
We also monitored the important mutations across the gene and predicted the most important amino acid changes in our variant isolates that may be related pathogenicity or immunogenicity especially at amino acid residues 53, 58, 132, 119 and 379.
Prediction of glycosylation and palmitoylation sites was also made to more comparison between the field isolates and the vaccinal strains.
The final conclusion of this study is that the commercially used vaccines are genotypically distant from the field strains however the need of new vaccine needs protective studies also to be carried out, The Egyptian new variant is closer to the reference strain IS/1494 more than IS/885, depending on HVRs may lead to different results from the full S1gene results and active surveillances are recommended to follow up the IBV evolution and change.