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Phylogenetic Analysis of Infectious Bronchitis Viruses Currently Circulating in the Egyptian Field

One of the major problems of infectious bronchitis virus (IBV) is the frequent emergence of new variants in the Egyptian field. In the present study, 42 broiler chicken flocks suffered from respiratory troubles were investigated for infectious bronchitis virus in 10 Governorates in Egypt during 2016-2018. Ten out of 42 examined flocks revealed variable degrees of embryo lesions after 3-5 passages with negative heamagglutination (HA) activity. From these 10 flocks, IBV was confirmed in six flocks using reverse transcriptase polymerase chain reaction (RT-PCR) assay. Four IBV-positive isolates were selected for further sequence analysis. Partial sequencing of S1 gene revealed four IBV variant-2 isolates circulating among chickens in Egypt. These isolates are IB-Beh-Ch-F2-2016, IB-Sh-Ch-F25-2017, IB-Sh-Ch-F41-2018 and IB-Sh-Ch-F42-2018 and submitted on Gen Bank with accession numbers MH460643, MH460644, MK408615 and MK408616, respectively.  The IB-Sh-Ch-F25-2017 isolate had only one amino acid substitution while IB-Beh-Ch-F2-2016, IB-Sh-Ch-F41-2018 and IB-Sh-Ch-F42-2018 isolates had much higher genetic diversity. The similarity between classic viruses of vaccine origin used in Egypt (H120, Ma5) and our four filed isolates ranged between 75.7 and 80.4%. It could be concluded that IB variant-2 strains still circulate in the Egyptian field in spite of vaccination. Therefore we need to revise the IBV vaccines used in Egypt and try to prepare local vaccines with periodic evaluation of cross protection of such vaccines.