1. Coronaviruses Chapter 40

2. Structure and Composition Enveloped Spike proteins resemble solar corona or crown 120-160 nm Positive-strand RNA (27-32 kb) Cytoplasmic replication Budding into ER and Golgi Notoriously difficult to propagate in culture High frequency of recombination Cause colds and severe acute respiratory syndrome (SARS)

3. Classification Family Coronaviridae Genus Coronavirus Genus Torovirus Replication Details are largely unknown because viruses are difficult to grow in cell culture Mouse hepatitis virus is model for coronavirus replication Viral spike proteins mediate attachment Aminopeptidase N is a cell receptor target for many coronaviruses Endocytosis is thought to mediate infection After uncoating, the viral genome (mRNA) is translated to produce RNA polymerase Subgenomic RNAs are synthesized for each viral polypeptide Genomic RNA is cosynthesized with nucleocapsid Results in nucleocapsid binding immediately to genomic RNA Progeny virus buds from ER and Golgi and are packaged into vesicles Vesicles travel to and fuse with plasma membrane, releasing viral particles from cell

4. Coronavirus Infections Pathogenesis Limited knowledge Highly species-specific Typically mild upper respiratory infections (“colds”) that remain localized Exception: SARS Immunity is not durable Many people become resusceptible after a few years Laboratory Diagnosis ELISA - may not discriminate past infections HA PCR Virus isolation is difficult (often impossible) and requires great expertise

5. Severe Acute Respiratory Syndrome Initial outbreak in SE Asia Hong Kong and Singapore first reported Disease originated in China Originally thought to be from wild game markets Palm civet cat (which isn’t a cat) - Paradoxurus hermaphroditus Raccoon dog (which isn’t a dog) - Nyctereutes procyonoides It is a bat virus Chinese horseshoe bats (Rhinolophus sinicus) No virus isolation Amplification of coronavirus RNA from anal swabs Serology It is highly-similar, but not identical to SARS-CoV Mutations have most likely occurred in transmission from bats to civets to humans Reverse genetics of SARS-CoV and some bat viruses has been done No animal pathogenesis model

6. SARS CoV

7. Coronavirus Phylogeny Chymotrypsin-like protease (3CL pro ), RNA-dependent RNA polymerase (Pol), spike (S), and nucleocapsid (N)

8. Coronaviruses Are Bat Viruses

9. SARS Pathogenesis Virus is transmitted by respiratory and fecal routes Infection is mediated by human angiotensin-converting enzyme 2 (hACE2) receptor High expression Lung alveolar epithelial cells Intestinal enterocytes Low expression Blood vessels (virtually all organs) Pneumonia Cause of death is lung failure

10. Pulmonary Inflammation of SARS Pathologic findings of lung tissue sections. A: Pulmonary congestion and edema (H&E stain, original magnification x100). B: A mild degree of interstitial lymphocytic infiltration. Intra-alveolar organizing exudative lesion was occasionally found. Detached atypical pneumocytes indicated by arrow (H&E stain, original magnification x200). C: Atypical multinucleated pneumocytes were occasionally identified. Definite viral inclusion was not apparent (H&E stain, original magnification x400). D: Fibrin thrombi were frequently noted in small pulmonary arteries and arterioles (H&E stain, original magnification x200).

11. Is SARS an Immunopathogenesis? CriterionEvidence in SARSPrecedent in other viral infections Worse disease with decrease in viral load Controversial; viral titres, measured in nasopharyngeal-aspirate samples, decrease as clinical disease worsens; but high viral loads have been detected in lungs and immune cells after death MHV-induced demyelination increases as virus is cleared; MHV-3-induced hepatitis correlates with macrophage activation and not viral load; and IBV- induced nephritis is detected in chickens with very low viral loads Macrophage or DC infection Infection is abortive but induces expression of pro-inflammatory mediators MHV and FIPV productively infect macrophages Macrophage infiltration into sites of inflammation Macrophages are present in large numbers in infected lungs In MHV infection, macrophages infiltrate the CNS coincident with demyelination (thought to be the final effector cell); and in FIPV infection, macrophages are the main cell type in granulomas and are crucial for pathogenesis High concentration of pro-inflammatory mediators in serum or at site of infection Controversial; anti-inflammatory mediators might contribute to delayed viral clearance MHV-3-induced FGL2 expression is crucial for liver necrosis; in MHV-JHM-infected mice, IFN- is required for CD8+ T-cell-mediated responses; and in FIPV infection, increased cytokine concentrations are present in blood and tissues during exacerbation of disease Inhibition of type I IFN induction in infected cells Shown using isolated macrophages, DCs and fibroblasts MHV does not induce type I IFN expression Lymphopenia and neutrophilia Present in most severe cases; and lymphocytic infection has been detected In FIPV infection, lymphopaenia is present during clinical relapses; and in MHV-3 infection, lymphopaenia is present and lymphocytic infection has been detected HaemophagocytosisPresent in severe casesNot reported