Emergence and genetic analysis of variant pathogenic 4/91 (serotype 793/B) infectious bronchitis virus in Egypt during 2019

Abstract

Infectious bronchitis virus (IBV) affects both vaccinated and unvaccinated flocks worldwide, with a significant impact on the poultry industry. The aim of the present study is to characterize an emerging variant pathogenic IBV originating from field outbreaks in vaccinated Egyptian layer flock. Samples were collected from disease-suspected flock with a history of administration of live and inactivated IBV vaccines (Ma5 type). Virus propagation in embryonated chicken eggs (ECEs), after three successive passages, revealed typical IBV lesions such as curling and dwarfism. The reported isolate was identified by a real-time reverse transcriptase PCR assay targeting nucleocapsid (N) gene and, further characterized by full-length spike (S1) gene sequencing. Phylogenetic analysis revealed clustering of the isolated virus within 4/91 genotype of GI-13 lineage. Deduced amino acid sequences identity revealed 75-76% and 88-90% similarity with the currently used classic (H120, Ma5, and M41) and variant vaccine strains (4/91 and CR88) in Egypt, respectively. Recombination analysis gave an evidence for distinct patterns of origin for the studied isolate providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-13 lineage in the Egyptian field. The studied isolate (IBV/CK/EG/ Fadllah-10/2019) emerged as a result of recombination between the variant group (Egy/var I genotype, GI-23 lineage) as a major parent and the CR88 variant vaccine strain (4/91 genotype, GI-13 lineage) as minor parent. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants which ascertain the importance of disease monitoring in vaccinated flocks as well as re-appropriation for the current vaccine strategies.

Pathogenic characteristics of a QX-like infectious bronchitis virus strain SD in chickens exposed at different ages and protective efficacy of combining live homologous and heterologous vaccination

“…IBV exists as numerous serotypes, which causes difficulties with regard to the prevention and control of the disease [15][16][17]. IB therefore remains a serious threat to chicken production in many countries around the world [18][19][20][21][22].…”

A Recombinant La Sota Vaccine Strain Expressing Multiple Epitopes of Infectious Bronchitis Virus (IBV) Protects Specific Pathogen-Free (SPF) Chickens against IBV and NDV Challenges

“…Avian infectious bronchitis (IB) is an acute and highly contagious viral respiratory disease of chickens. IB occurs worldwide and causes substantial economic losses in the poultry industry [1][2][3][4][5]. IB is caused by the infectious bronchitis virus (IBV) which belongs to the order Nidovirales, family Coronaviridae, genus Gammacoronavirus.…”

Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events

“…Therefore, further studies are required to clearly determine the clinicopathobiological features of these viruses in a chicken model. Interestingly, the GI-23 genotype plays a two-faced role in these recombinant events in the Saudi Arabian poultry flocks, not only providing fragments for other strains but also receiving fragments during infection, which has been reported previously in neighboring countries [ 31 , 32 ].…”

“…Our results indicated that Saudi Arabian IBV viruses in this study were diversified into three distinct genotypes, i.e., GI-1, GI-13, and GI-23 ( Figure 1 and Figure 2 ) according to Valsastro et al [ 17 ]. Multiple reports have demonstrated the emergence of variant strains related to 4/91, IS/1494, and IS/885 (IS/720/99) within the Middle East [ 31 , 32 ]. A Bayesian consensus phylogenetic analysis, which was verified using the neighbor-joining method, clearly divided isolated IBV strains in this study into three lineages.…”

“…The phylogenetic analyses performed on the full-length S1 genes of nine IBV strains isolated in this study showed that they cluster into different groups, i.e., GI-1, GI-13, and GI-23 lineages. These subsequent IBV lineages could have reached to Saudi Arabian poultry because of international trade, including uncontrolled movement of animals across borders [ 39 , 40 ] or through the virus carried by wild birds from the neighboring countries including Egypt [ 32 ]. Likewise, strains similar to those circulating in Egypt, India, China, and Italy have also been previously reported in Saudi Arabia [ 34 , 35 , 36 , 37 , 38 ].…”