@article{mbs:/content/journal/jgv/10.1099/jgv.0.001474, author = "Keep, Sarah and Oade, Michael S. and Lidzbarski-Silvestre, Filip and Bentley, Kirsten and Stevenson-Leggett, Phoebe and Freimanis, Graham L. and Tennakoon, Chandana and Sanderson, Nicholas and Hammond, John A. and Jones, Richard C. and Britton, Paul and Bickerton, Erica", title = "Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus", journal= "Journal of General Virology", year = "2020", volume = "101", number = "10", pages = "1103-1118", doi = "https://doi.org/10.1099/jgv.0.001474", url = "https://www.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.001474", publisher = "Microbiology Society", issn = "1465-2099", type = "Journal Article", keywords = "transcription", keywords = "sub-genomic mRNA", keywords = "IBV", keywords = "RNA synthesis", keywords = "coronavirus", abstract = "Coronavirus sub-genomic mRNA (sgmRNA) synthesis occurs via a process of discontinuous transcription involving complementary transcription regulatory sequences (TRSs), one (TRS-L) encompassing the leader sequence of the 5′ untranslated region (UTR), and the other upstream of each structural and accessory gene (TRS-B). Several coronaviruses have an ORF located between the N gene and the 3′-UTR, an area previously thought to be non-coding in the Gammacoronavirus infectious bronchitis virus (IBV) due to a lack of a canonical TRS-B. Here, we identify a non-canonical TRS-B allowing for a novel sgmRNA relating to this ORF to be produced in several strains of IBV: Beaudette, CR88, H120, D1466, Italy-02 and QX. Interestingly, the potential protein produced by this ORF is prematurely truncated in the Beaudette strain. A single nucleotide deletion was made in the Beaudette strain allowing for the generation of a recombinant IBV (rIBV) that had the potential to express a full-length protein. Assessment of this rIBV in vitro demonstrated that restoration of the full-length potential protein had no effect on viral replication. Further assessment of the Beaudette-derived RNA identified a second non-canonically transcribed sgmRNA located within gene 2. Deep sequencing analysis of allantoic fluid from Beaudette-infected embryonated eggs confirmed the presence of both the newly identified non-canonically transcribed sgmRNAs and highlighted the potential for further yet unidentified sgmRNAs. This HiSeq data, alongside the confirmation of non-canonically transcribed sgmRNAs, indicates the potential of the coronavirus genome to encode a larger repertoire of genes than has currently been identified.", }