Abstract
In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.
Highlights
Infectious bronchitis virus (IBV) is a highly contagious and emerging viral disease-causing organism of chickens and belongs to genus Gammacoronavirus within the family Coronaviridae [1].Infectious bronchitis virus (IBV) can replicate efficiently in a wide variety of epithelial cells of respiratory, renal, reproductive, and digestive tracts [1]
We present the isolation and integrative genetic analysis that map the evolution of IBV in Saudi
Typical IBV lesions such as embryo curling and dwarfism were detected in embryonated chicken eggs (ECEs) after three successive passages
Summary
Infectious bronchitis virus (IBV) is a highly contagious and emerging viral disease-causing organism of chickens and belongs to genus Gammacoronavirus within the family Coronaviridae [1]. Infectious bronchitis virus (IBV) can replicate efficiently in a wide variety of epithelial cells of respiratory, renal, reproductive, and digestive tracts [1]. RNA virus with genome length of approximately 27.6 kb which encodes four major structural proteins, spike (S), membrane (M), envelope (E), phosphorylated nucleocapsid (N) proteins, and several accessory proteins (3a, 3b, 5a, and 5b) [2,3]. The S1 forms the extracellular part of virus and plays a major role in tissue tropism, induction of protective immunity, virus neutralization, cell attachment, and serotype specificity, whereas S2 subunit anchors the spike into the virus membrane. During IBV replication and evolution, the high mutation rate in the
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