The members of the Order Nidovirales share a similar genome organization with the nonstructural proteins encoded at the 5ʹ end and the structural genes at the 3ʹ end and express the 3ʹ genes from a nested set of 3′ co-terminal subgenomic messenger RNAs (sg mRNAs). Some but not all of the Nidoviruses, the sg mRNAs also have a common 5ʹ leader sequence acquired by a discontinuous transcription mechanism regulated by multiple 3ʹ transcription regulatory sequences (TRS) and the 5ʹ leader TRS. Initial studies detected a single major body TRS for each 3ʹ genes with a few alternative functional TRSs reported. The recent application of advanced techniques, such as next generation sequencing and ribosomal profiling, in studies of arteriviruses and coronaviruses has revealed an expanded sg mRNA transcriptome and coding capacity.
New insights about the regulation of Nidovirus subgenomic mRNA synthesis