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

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.

The emergence, evolution and spread of infectious bronchitis virus genotype GI-23

“…Genotype GI has the largest number of genetic lineages (n: 29). The Massachusetts (Mass) type belongs to the GI-1 lineage, while the Egyptian variants I and II and many Middle East IBV strains belong to the GI-23 lineage, which has spread to many countries in Africa, Asia and Europe [19][20][21][22][23]. Although classification based on the full-length S1 is very efficient, it leaves a gap in which a very large number of IBV strains for which only partial S1 sequences are available, remain unclassified.…”

“…The GI-1 and GI-13 lineages represent the old Massachusetts (Mass) and 793B lineages, respectively. Both lineages are universally distributed in all endemic countries and are most commonly used as vaccine strains, while other lineages are found only in specific parts of the world [19][20][21][22][23]. The GI-23 lineage includes IBV variants circulating in the Middle East.…”

“…The GI-23 lineage includes IBV variants circulating in the Middle East. This lineage continues to spread and poses a major challenge not only in the Middle East but also in many countries in Africa, Asia and Europe [19][20][21][22][23].…”

“…The new IBV strain sequences isolated in 2018 from Lebanon were made available in the GenBank database, and our analysis based on these sequences confirmed their clustering with the GI-23 strain. In addition, recently released Syrian IBV strain HVR3 sequences have been determined to belong to the GI-23 [22,126,127] genotype. However, no associated publications have been found in either country (Table 3).…”

Drawing Comparisons between SARS-CoV-2 and the Animal Coronaviruses

“…Animal CoVs have been known to cause important diseases in livestock and companion animals [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. Although human CoVs received attention only after the SARS-CoV outbreak of 2002–2003 [ 24 ], animal CoVs have been studied extensively for many decades, providing a plethora of important information on their complex genetic diversity, transmission, tissue tropism and pathology, host immune responses, therapeutics, and prophylaxis, some of which have striking resemblance to those seen with SARS-CoV-2.…”