title: Genotyping and pathotyping of diversified strains of infectious bronchitis viruses circulating in Egypt.
abstract: OBJECTIVE
  To characterize the circulating infectious bronchitis virus (IBV) strains in Egypt depending on the sequence of the spike-1 (S1) gene [hypervariable region-3 (HVR-3)] and to study the pathotypic features of these strains.
  
  
  METHODS
  In this work, twenty flocks were sampled for IBV detection using RRT-PCR and isolation of IBV in specific pathogen free (SPF) chicks during the period from 2010 to 2015. Partial sequencing and phylogenetic analysis of 400 bp representing the HVR-3 of the S1 gene was conducted. Pathotypic characterization of one selected virus from each group (Egy/Var-I, Egy/Var-II and classic) was evaluated in one day old SPF chicks. The chicks were divided into 4 groups 10 birds each including the negative control group. Birds were inoculated at one day by intranasal instillation of 10(5)EID50/100 μL of IBV viruses [IBV-EG/1212B-2012 (Egy/Var-II), IBV/EG/IBV1-2011 (Egy/Var-I) and IBV-EG/11539F-2011 (classic)], while the remaining negative control group was kept uninfected. The birds were observed for clinical signs, gross lesions and virus pathogenicity. The real-time rRT-PCR test was performed for virus detection in the tissues. Histopathological examinations were evaluated in both trachea and kidneys.
  
  
  RESULTS
  The results revealed that these viruses were separated into two distinct groups; variant (GI-23) and classic (GI-1), where 16 viruses belonged to a variant group, including 2 subdivisions [Egy/Var-I (6 isolates) and Egy/Var-II (10 isolates)] and 4 viruses clustered to the classic group (Mass-like). IBV isolates in the variant group were grouped with other IBV strains from the Middle East. The variant subgroup (Egy/Var-I) was likely resembling the original Egyptian variant strain (Egypt/Beni-Suif/01) and the Israeli strain (IS/1494/2006). The second subgroup (Egy/Var-II) included the viruses circulating in the Middle East (Ck/EG/BSU-2 and Ck/EG/BSU-3/2011) and the Israeli strain (IS/885/00). The two variant subgroups (Egy/Var-I and Egy/Var-II) found to be highly pathogenic to SPF chicks with mortalities up to 50% than those of the classic group which was of low virulence (10% mortality). Pathogenicity indices were 25 (Egy/Var-II), 24 (Egy/Var-I) and 8 (classic); with clinical scores 3, 2 and 1 respectively.
  
  
  CONCLUSIONS
  These findings indicated that the recent circulating Egyptian IBVs have multiple heterogeneous origins in marked diversifying nature of their spread, with high pathotype in specific pathogen free chicks.
authors: Ali Zanaty, Abdel-Satar Arafa, Naglaa Hagag, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Ali
authors: A
authors: Zanaty
authors: Ali Zanaty, Abdel-Satar Arafa, Naglaa Hagag, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Abdel-Satar
authors: AS
authors: Arafa
authors: Ali Zanaty, Abdel-Satar Arafa, Naglaa Hagag, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Naglaa
authors: N
authors: Hagag
authors: Ali Zanaty, Abdel-Satar Arafa, Naglaa Hagag, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza 12618, Egypt.
authors: Magdy
authors: M
authors: El-Kady
keywords: Egypt; HVR-3 Sequencing; Infectious bronchitis virus; Phylogenetic analysis; S1 gene; Variant infectious bronchitis virus