Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome.
The hallmark of coronavirus transcription is the production of multiple subgenomic mRNAs that contain sequences corresponding to both ends of the genome. (Transcription is defined as the process whereby subgenome-sized mRNAs are produced, and coronavirus replication is the process whereby genome-sized RNA, which also functions as mRNA, is produced.) Thus, the generation of subgenomic mRNAs involves a process of discontinuous transcription.
The coronavirus genomic RNA of approximately 30,000 nucleotides encodes structural proteins of the virus, nonstructural proteins that have a critical role in viral RNA synthesis (which we will refer to as replicase-transcriptase proteins), and nonstructural proteins that are nonessential for virus replication in cell culture but appear to confer a selective advantage in vivo (which we will refer to as niche-specific proteins). At least one niche-specific protein, nonstructural protein 2 (nsp2), and one structural protein, the nucleocapsid protein (N), are involved in viral RNA synthesis.
The expression of the coronavirus replicase-transcriptase protein genes is mediated by the translation of the genomic RNA. The replicase-transcriptase proteins are encoded in open-reading frame 1a (ORF1a) and ORF1b and are synthesized initially as two large polyproteins, pp1a and pp1ab. The synthesis of pp1ab involves programmed ribosomal frame shifting during translation of ORF1a. During or after synthesis, these polyproteins are cleaved by virus-encoded proteinases with papain-like (PLpro) and chymotrypsin-like folds into 16 proteins; nsp1 to nsp11 are encoded in ORF1a, and nsp12 to nsp16 are encoded in ORF1b. The replicase-transcriptase proteins, together with other viral proteins and, possibly, cellular proteins, assemble into membrane-bound replication-transcription complexes (RTC). (We will use the term RTC to describe complexes copying or producing genome- or subgenome-length RNA.) These complexes accumulate at perinuclear regions and are associated with double-membrane vesicles. Hydrophobic transmembrane domains are present in nsp3, nsp4, and nsp6 and likely serve to anchor the nascent pp1a/pp1ab polyproteins to membranes during the first step of RTC formation.3
The mechanism of coronavirus replication hereby will take the coronavirus replication of MHV (mouse hepatitis virus) for example. (Fig.1)
Fig. 1 Summary of mouse hepatitis virus (MHV) replication. MHV binds to the host-cell receptor CEACAM-1 through interaction of the spike (S) glycoprotein. Virus entry into the host cell can occur through fusion with the surface of the host cell, with the subsequent release of the genomic RNA into the cytoplasm. Alternatively, MHV can enter the host cell through the formation of endocytic vesicles, and genomic RNA is released into the cytoplasm following fusion with the vesicle membrane (not shown). Translation of the positive-strand genomic RNA gives rise to a large polyprotein that undergoes proteolytic processing to generate an RNA-dependent RNA polymerase. Through the action of the RNA polymerase, a full-length, antisense negative-strand template is generated. Subgenomic mRNAs are synthesized, presumably from subgenomic negative-strand templates. Translation of subgenomic mRNAs gives rise to structural viral proteins. S glycoprotein is expressed on the surface of the host cell and this might contribute to fusion with neighbouring uninfected cells by binding to CEACAM-1. Virus assembly occurs within vesicles, followed by virus release by fusion of virion-containing vesicles with the plasma membrane. Released virus can infect other cells and can replicate within the parent cell through binding to CEACAM-1. E, envelope protein; ER, endoplasmic reticulum; M, membrane protein; N, nucleocapsid protein; ORF, open reading frame.
Credit: Cornelia C. Bergmann, et al / Nature Reviews Microbiology.