In Brazil, infectious bronchitis (IB) caused by infectious bronchitis virus (IBV) is endemic, despite the large use of vaccines, as a result of the continuous emergence and spread of new viral types. The structural protein S (spike) is the main target for genotyping and phylogenetic studies. However, most of the IBV genome codes for non-structural proteins, including putative proteases, but hitherto these have been poorly explored regarding the diversity of IBV lineages. The present study aims to assess the diversity of the papain-like protease (PLpro), non-structural protein 2 (nsp2) and S structural protein genes in Brazilian IBV strains. To this end, pools of organs (respiratory tract, kidneys, reproductive tract and enteric contents) from commercial breeders, broilers and layers, showing clinical signs of IBV infection, will be sampled and screened for IBV by Nested-RT-PCR targeting 3'UTR region of viral genome, followed by Nested-RT-PCR targeting S1 gene and RT-PCR targeting PLpro and nsp2 genes, and, finally, DNA sequencing and genealogic analysis. Besides, samples will be submitted to quantitative PCR targeting M gene mRNA, for viral quantification. The purpose is to analyze genealogically the genes under study; to assess molecular markers associated with different clinical signs and the association with the viral titers measured. As a result, it's expected that the data collected in this study will contribute to the knowledge on IBV evolution, tropism and pathogenic mechanisms, for the improvement of efficient preventive measures.
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