Molecular Characterization and Detection of Infectious Bronchitis Virus

This thesis deals with the molecular characterization and detection of infectious bronchitis virus (IBV), an important pathogen that causes heavy losses in the poultry populations worldwide. The aim of the research was to better understand the molecular characteristics of the virus and to investigate the factors behind the continuous emergence of new genetic variants and the occurrence of outbreaks. The studies showed that the viral genome is under a continuous evolution, due to mutations, strong selective pressure and recombination events. These forces lead to a wide genetic diversity and the generation of new variants of this virus. The viral genes encoding the spike, replicase and nucleocapsid proteins can be considered the main genomic regions, which are indicating the evolution processes of IBV. The various strains contain specific structural and functional motifs in their genes and the alterations in these motifs may affect the infection biology of the virus. The constant emergence of new variants in Sweden is likely due to the introduction of novel IBV strains from other European countries through the import of poultry products, or by the continuous migration of wild birds. The in silico investigations of the spike glycoprotein coding regions of the Massachusetts and QX-like genotypes demonstrated molecular differences between these genotypic variants. It is hypothesized that the genetic diversity in the spike gene of IBV and of other avian coronaviruses, as well as of human, bat, and other animal coronaviruses could be associated with the adaptation and host specificity of these infectious agents. The data obtained by molecular characterization approach was also used for the development of a new molecular method for the improved detection and genotyping of this virus. A microarray platform was developed for the simultaneous detection and rapid typing of IBV variants. This assay provides a practical tool for better diagnosis, for studying the effectiveness of vaccination and for performing large-scale epidemiological studies.