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An unusual pattern of mRNA synthesis occurs in cells infected with members of the families Coronaviridae and Arteriviridae, in which subgenomic mRNAs that form a 3′-coterminal nested set with the viral genome are synthesized (Fig. 6.18). These viral families were combined into the order Nidovirales to denote this shared property (nidus is Latin for “nest”).

Figure 6.17 Three RNA polymerases with distinct specificities in alphavirus-infected cells. These RdRPs contain the entire sequence of the P1234 polyprotein and differ only in the number of proteolytic cleavages in this sequence.

Figure 6.18 Nidoviral genome organization and expression. (A) Organization of open reading frames. The (+) strand viral RNA is shown at the top, with open reading frames as boxes. The genomic RNA is translated to form polyproteins 1a and 1ab, which are processed to form the RdRP. Structural proteins are encoded by nested mRNAs. (B) Model of the synthesis of nested mRNAs. Discontinuous transcription occurs during (−) strand RNA synthesis. Most of the (+) strand template is not copied, probably because it loops out as the polymerase completes synthesis of the leader RNA (orange). The resulting (−) strand RNAs, with leader sequences at the 3′ ends, are then copied to form mRNAs.

The subgenomic mRNAs of these viruses comprise a leader and a body that are synthesized from noncontiguous sequences at the 5′ and 3′ ends, respectively, of the viral (+) strand genome (Fig. 6.18A). The leader and body are separated by a conserved junction sequence encoded both at the 3′ end of the leader and at the 5′ end of the mRNA body. Subgenome-length (−) strands are produced when the template loops out as the polymerase completes synthesis of the leader RNA (Fig. 6.18B). These (−) strand subgenome-length RNAs then serve as templates for mRNA synthesis.