Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus

Arteri‐, corona‐, toro‐ and roniviruses are evolutionarily related positive‐strand RNA viruses, united in the order Nidovirales. The best studied nidoviruses, the corona‐ and arteriviruses, employ a unique transcription mechanism, which involves discontinuous RNA synthesis, a process resembling similarity‐assisted copy‐choice RNA recombination. During infection, multiple subgenomic (sg) mRNAs are transcribed from a mirror set of sg negative‐strand RNA templates. The sg mRNAs all possess a short 5′ common leader sequence, derived from the 5′ end of the genomic RNA. The joining of the non‐contiguous ‘leader’ and ‘body’ sequences presumably occurs during minus‐strand synthesis. To study whether toroviruses use a similar transcription mechanism, we characterized the 5′ termini of the genome and the four sg mRNAs of Berne virus (BEV). We show that BEV mRNAs 3–5 lack a leader sequence. Surprisingly, however, RNA 2 does contain a leader, identical to the 5′‐terminal 18 residues of the genome. Apparently, BEV combines discontinuous and non‐discontinous RNA synthesis to produce its sg mRNAs. Our findings have important implications for the understanding of the mechanism and evolution of nidovirus transcription.