Coronaviruses post-SARS: update on replication and pathogenesis

Abstract

Although coronaviruses were first identified nearly 60 years ago, they only received notoriety in 2003 when one of their members was identified as the aetiological agent of severe acute respiratory syndrome. Previously these viruses were known to be important agents of respiratory and enteric infections of domestic and companion animals and to cause approximately 15% of all cases of the common cold. This Review focuses on recent advances in our understanding of the mechanisms of coronavirus replication, interactions with the host immune response and disease pathogenesis. It also highlights the recent identification of numerous novel coronaviruses and the propensity of this virus family to cross species barriers.

Figure 1. The Nidoviruses.

Phylogenetic relationship of viruses in the order Nidoviruses.

Figure 2. Structure of coronavirus genome and virion.

a | Schematic diagram of representative genomes from each of the coronavirus groups. Approximately the first two-thirds of the 26–32 Kb, positive-sense RNA genome encodes a large polyprotein (ORF1a/b; green) that is proteolytically cleaved to generate 15 or 16 non-structural proteins (nsps; nsps for severe acute respiratory syndrome coronavirus (SARS-CoV) are illustrated). The 3′-end third of the genome encodes four structural proteins — spike (S), membrane (M), envelope (E) and nucleocapsid (N) (all shown in blue) — along with a set of accessory proteins that are unique to each virus species (shown in red). Some group 2 coronaviruses express an additional structural protein, haemagglutinin-esterase (not shown). b | Schematic diagram of the coronavirus virion. 2′OMT, ribose-2′-O-methyltransferase; ExoN, 3′→5′ exonuclease; Hel, helicase; IBV, infection bronchitis virus; NendoU, uridylate-specific endoribonuclease; RDRP, RNA-dependent RNA polymerase; ssRBP, single-stranded RNA binding protein; ssRNA, single-stranded RNA; TGEV, transmissible gastroenteritis virus.

Figure 3. Mechanism of coronavirus replication and transcription.

Following entry into the cell and uncoating, the positive sense RNA genome is translated to generate replicase proteins from open reading frame 1a/b (ORF1a/b). These proteins use the genome as a template to generate full-length negative sense RNAs, which subsequently serve as templates in generating additional full-length genomes (a). Coronavirus mRNAs all contain a common 5′ leader sequence fused to downstream gene sequences. These leaders are added by a discontinuous synthesis of minus sense subgenomic RNAs using genome RNA as a template (reviewed in Ref. 29). Subgenomic RNAs are initiated at the 3′ end of the genome and proceed until they encounter one of the transcriptional regulatory sequences (TRS; red) that reside upstream of most open-reading frames (b). Through base-pairing interactions, the nascent transcript is transferred to the complementary leader TRS (light red) (c) and transcription continues through the 5′ end of the genome (d). These subgenomic RNAs then serve as templates for viral mRNA production (e).

Figure 4. Coronavirus-induced membrane alterations as platforms for viral replication.

Coronavirus infection induces the formation of a reticulovesicular network of modified membranes that are thought to be the sites of virus replication. These modifications, which include double-membrane vesicles (DMVs), vesicle packets (VPs, single-membrane vesicles surrounded by a shared outer membrane) and convoluted membranes (CMs), are all interconnected and contiguous with the rough endoplasmic reticulum (RER). Viral double-stranded RNA is mostly localized to the interior of the DMVs and inner vesicles of the VPs, whereas replicase proteins (that is, nsp3, nsp5 and nsp8) are present on the surrounding CM. Some nsp8 can be detected inside the DMVs. All membranes are bound by ribosomes. (Figure based on data from Refs. , , .)

Figure 5. Cross-species transmission of coronaviruses.

a | Severe acute respiratory syndrome (SARS)-like bat coronavirus (BtCoV) spread and adapted to wild animals such as the Himalayan palm civet that was sold as food in Chinese wet markets. The virus frequently spread to animal handlers in these markets, but caused minimal or no disease. Further adaptation resulted in strains that replicated efficiently in the human host, caused disease and could spread from person to person. b | Human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV) are closely related and it is thought that the virus originated in one species and then crossed species. BCoV has also spread to numerous other animals, such as alpaca and wild ruminants. c | Feline coronavirus I (FCoV-I) and canine coronavirus I (CCoV-I) are thought to share a common ancestor. CCoV-I underwent recombination with an unknown coronavirus to give rise to canine coronavirus II (CCoV-II). CCoV-II in turn underwent recombination with FCoV-I (in an unknown host) to give rise to feline coronavirus II (FCoV-II). CCoV-II probably also spread to pigs, resulting in transmissible gastroenteritis virus (TGEV).

Figure 6. Inefficient activation of the type 1 interferon response, and immunopathological disease, in coronavirus infections.

a | Coronaviruses, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis virus (MHV), induce a type 1 interferon (IFN) response in plasmacytoid dendritic cells (pDC) and macrophages, via TLR7- and MDA5-dependent pathways, respectively. b | IFNα and/or IFNβ is not produced in either SARS-CoV fibroblasts or DCs, partly because coronavirus macromolecules appear to be invisible to immune sensors. Additionally, coronaviruses encode proteins that actively inhibit IFNα and/or IFNβ expression (such as nucleocapsid (N) protein, nsp3, ORF6 and ORF3b) or signalling through the type 1 IFN receptor (such as N, nsp1, ORF6 and ORF3b). c | Consequently, the kinetics of virus clearance is delayed, with subsequent robust T and B cell and cytokine and/or chemokine responses. d | This pro-inflammatory response results in immunopathological disease that occurs during the process of virus clearance. In MHV-infected mice, virus clearance involves recruitment of activated macrophages and microglia to sites of virus infection, leading to demyelination. Similar mechanisms with exuberant cytokine production may function in the lungs of SARS-CoV-infected humans, leading to severe pulmonary disease (adult respiratory distress syndrome, ARDS). AP1, activator protein 1; DMV, double-membrane vesicle; dsRNA, double-stranded RNA; NF-κB, nuclear factor-κB; ssRNA, single-stranded RNA.