The order Nidovirales consists of viruses which have positive-sense, single-stranded RNA genomes. The viruses belong to Group IV of the Baltimore classification system. As positive-sense genomes, the viruses can use some host cell proteins during replication and gene expression which occurs in the cytoplasm of the host cell. This group of viruses expresses structural proteins separately from the nonstructural ones. The structural proteins are encoded at the 3’ region of the genome and are expressed from a set of subgenomic mRNAs. These viruses encode one main proteinase and between one and three accessory proteinases which are mainly involved in expressing the replicase gene. These proteinases are also responsible for activating or inactivating specific proteins at the correct time in the virus life cycle, ensuring replication occurs at the right time. Many proteins have been identified on the genomes of Nidovirales, but their function has not yet been determined. Other enzymes that may be present in the genome include papain-like proteases, ADP-ribose/poly-binding or ADP-ribose 1''-phosphate phosphatase activities and cyclic nucleotide phosphodiesterase. Most, but not all, nidovirus subgenomic RNAs contain a 5′ leader sequence derived from the 5′ end of the genomic RNA. The frameshift that generates ORF1b frameshift occurs at a UUUAAAC heptanucleotide 'slippery' sequence located upstream of the ORF1a stop codon and a putative RNA pseudoknot structure.
Genome
This order of viruses can be distinguished from other RNA viruses by a constellation of seven conserved domains—5'-TM2-3CLpro-TM3-RdRp-Zm-HEL1-NendoU-3'—with the first three being encoded in ORF1a and the remaining four in ORF1b. TM2 and TM3 and transmembrane domains; RdRp is the RNA polymerase; Zm is a Zn-cluster binding domain fused with a helicase ; 3CLpro is a 3C-like protease; and NendoU is an uridylate-specific endonuclease. The 3CLpro has a catalytic His-Cys dyad, and is also known as the SARS coronavirus main proteinase.
Taxonomy
The order Nidovirales can be divided into two clades depending on the size of the genome: those with large genomes which included the Coronaviridae and Roniviridae and those with small genomes —a clade that includes the distantly related Arteriviridae. The large nidoviruses encode both a 2'-O-methyltransferase and a 3'–5' exoribonuclease —the latter being very unusual for an RNA virus. They also encode a superfamily 1 helicase, uridylate-specific endonuclease and several proteases. The following subfamilies and families are recognized :
