Expression Study of Subgenomic mRNAs of Avian Infectious Bronchitis, Variant 2, (GI-23), using RNA-Seq Analysis

Infectious bronchitis virus (IBV), a member of the genus Gamma coronavirus under the Coronaviridae family, is one of the leading causes of persistent economic and financial burdens poultry industry of Iran. This family of viruses possesses a ~27 kb positive-sense RNA genome that produces a nested set of subgenomic mRNAs during replication.

This study investigated tissue tropism of virulent IBV variant 2, GI-23, by comparing viral gene expression differences between kidney and trachea tissue samples of 20 intranasal infected SPF chickens. At 2 and 6 days post-infection, extracted genomic RNA was subjected to RNAseq, and high-throughput analyses studied the obtained data.

Among the genomic UTRs of IBV, the highest expression was obtained for the 3'UTR (7.15E+05) in the renal samples. Nucleoprotein (N) had the 2nd highest gene expression in both tissues (4.52E+05 in the trachea and 4.13E+05 in the kidney). The lowest expression (2.34E+03 in the trachea and 2.69E+02 in the kidney) belonged to the polymerase genes. 5'UTR expression was not detected in any of the tissue samples.Furthermore, six non-structural genes (NSP4, 7, 8, 9, 11, and 15) had no detectable expression in the kidney samples. NSP11 was shared in both tissues in this case, while NSP16 had the highest expression at 1.62E+05 in tracheal samples and NSP13 at 2.88E+5 in renal samples.

We concluded that except for the 3’ UTR, a slightly higher expression was observed in tracheal samples.