Turkey coronavirus polymerase gene and genome transcription

Turkey coronavirus (TCoV) is a group 3 coronavirus in the family Coronaviridae. However, little is known about TCoV genome and genome transcription. The objectives of this study were to investigate polymerase gene and genome transcription of TCoV. Sequences of polymerase gene and full-length genome of TCoV were completed for isolates 540 and ATCC. The genome contains 27749 nucleotides (nt) for 540 and 27816-nt for ATCC, excluding poly (A) tail. Thirteen open reading frames (ORF) were predicted for TCoV genome. Polymerase gene consists of ORF1a and ORF1b. Polyprotein 1a was predicted to be produced from ORF1a and polyprotein 1ab was produced from ORF1a and ORF1b via frameshift translation. Ten and fourteen nonstructure proteins were predicted and assigned to polyprotein 1a and 1ab, respectively. Phylogenetic analysis revealed 86.3% genome sequence identity between TCoV and avian infectious bronchitis virus (IBV), another group 3 coronavirus, further supporting a close relationship between the two. Six subgenomic mRNAs (sgRNA) were transcribed by TCoV with sg3UTR as an unpredicted sgRNA for 3’ untranslated region (UTR). The discovery of sg3UTR reduced predicted 3’UTR from about 500-nt to 300-nt. Five sgRNA were detected for spike gene and all of them differentiate only at transcription-regulating sequence. The abundance of (−) sgRNA was more than that of (+) sgRNA in TCoV infected tissues. Non-structure protein 15 (nsp15) of TCoV polyprotein was a novel endoribonuclease (NendoU) preferring cleaving U-containing ssRNA. Unlike other NendoU, TCoV nsp15 did not cleave dsRNA and did not require manganese or other divalent metal ions as cofactor. The active form of TCoV nsp15 was a homohexamer in vitro. In conclusion, TCoV has its genome organization similar to that of IBV and produces six sgRNA