Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens

Abstract

Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.

Global Emergence of Infectious Bronchitis Virus Variants: Evolution, Immunity, and Vaccination Challenges

“…For example, the IBV GA98 was suggested to have emerged under the immune selection pressure exerted by the use of the DE072 vaccine, and showed fast evolutionary and mutation rates of 2.5% and 1.5% per year, respectively, in the HVR [116] compared to 0.3%-0.6% mutation rate per year for the 793/B genotype in the absence of vaccine use [119]. Under experimental conditions, Flageul et al [120] demonstrated that IBV D388 evolved rapidly over three passages in both unvaccinated chickens and chickens vaccinated with the heterologous vaccine strain H120. However, the viral population selection and genetic drift were completely different in both groups.…”

Diagnosis of Infectious Bronchitis Infection in Broiler Chicken Farms in Salah Al-Din Governorate

“…One of the most dangerous viruses that can infect chickens is the avian infectious bronchitis virus, or IBV. In light of this virus, the chicken industry faces difficulties in many regions of the world [1]. The prototypical coronavirus known as the infectious bronchitis virus causes millions of dollars' worth of annual losses for the poultry industry globally [2,3].…”

A pathogenic and recombinant infectious bronchitis virus variant (CK/CH/GX/202109) with multiorgan tropism

“…Thus, novel or variant IBV strains have been frequently isolated following immune failure [ 20 , 21 ]. The selection pressures introduced by the use of vaccines, in addition to those exerted by the infected host microenvironment and physical and biosecurity-associated factors, have caused IBV to evolve rapidly [ 22 ].…”