RESULTS:

The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors leading to viral attachment. The spike protein exists in two structurally distinct conformations prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein must be triggered leading to membrane fusion. This article reviews current knowledge about the structures and functions of coronavirus spike proteins illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions. I further discuss the evolution of these two critical functions of coronavirus spike proteins receptor recognition and membrane fusion in the context of the corresponding functions from other viruses and host cells.

Infection by different coronaviruses (CoVs) causes alterations in the transcriptional and translational patterns cell cycle cytoskeleton and apoptosis pathways of the host cells. In addition CoV infection may cause inflammation alter immune and stress responses and modify the coagulation pathways. The balance between the up- and downregulated genes could explain the pathogenesis caused by these viruses. We review specific aspects of CoV-host interactions. CoV genome replication takes place in the cytoplasm in a membrane-protected microenvironment and may control the cell machinery by locating some of their proteins in the host cell nucleus. CoVs initiate translation by cap-dependent and cap-independent mechanisms. CoV transcription involves a discontinuous RNA synthesis (template switching) during the extension of a negative copy of the subgenomic mRNAs. The requirement for base-pairing during transcription has been formally demonstrated in arteriviruses and CoVs. CoV N proteins have RNA chaperone activity that may help initiate template switching. Both viral and cellular proteins are required for replication and transcription and the role of selected proteins is addressed.

In less than two decades three deadly zoonotic coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2 have emerged in humans causing SARS MERS and coronavirus disease 2019 (COVID-19) respectively. The current COVID-19 pandemic poses an unprecedented crisis in health care and social and economic development. It reinforces the cruel fact that CoVs are constantly evolving possessing the genetic malleability to become highly pathogenic in humans. In this review we start with an overview of CoV diseases and the molecular virology of CoVs focusing on similarities and differences between SARS-CoV-2 and its highly pathogenic as well as low-pathogenic counterparts. We then discuss mechanisms underlying pathogenesis and virus-host interactions of SARS-CoV-2 and other CoVs emphasizing the host immune response. Finally we summarize strategies adopted for the prevention and treatment of CoV diseases and discuss approaches to develop effective antivirals and vaccines.

Over the past three decades coronavirus (CoV) diseases have impacted humans more than any other emerging infectious disease. The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causative agent of COVID-19 (coronavirus disease 2019) has resulted in huge economic disruptions and loss of human lives. The SARS-CoV-2 genome was found to mutate more rapidly due to sustained transmission in humans and potentially animals resulting in variants of concern (VOCs) that threaten global human health. However the primary difficulties are filling in the current knowledge gaps in terms of the origin and modalities of emergence for these viruses. Because many CoVs threatening human health are suspected to have a zoonotic origin identifying the animal hosts implicated in the spillover or spillback events would be beneficial for current pandemic management and to prevent future outbreaks. In this review wesummarize the animal models zoonotic reservoirs and cross-species transmission of the emerging human CoVs. Finally we comment on potential sources of SARS-CoV-2 Omicron VOCs and the new SARS-CoV-2 recombinants currently under investigation.

Over the last two decades the world has witnessed the global spread of two genetically related highly pathogenic coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. However the impact of these outbreaks differed significantly with respect to the hospitalizations and fatalities seen worldwide. While many studies have been performed recently on SARS-CoV-2 a comparative pathogenesis analysis with SARS-CoV may further provide critical insights into the mechanisms of disease that drive coronavirus-induced respiratory disease. In this review we comprehensively describe clinical and experimental observations related to transmission and pathogenesis of SARS-CoV-2 in comparison with SARS-CoV focusing on human animal and in vitro studies. By deciphering the similarities and disparities of SARS-CoV and SARS-CoV-2 in terms of transmission and pathogenesis mechanisms we offer insights into the divergent characteristics of these two viruses. This information may also be relevant to assessing potential novel introductions of genetically related highly pathogenic coronaviruses.

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years we have witnessed the emergence of two zoonotic highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Replication of HCoV is regulated by a diversity of host factors and induces drastic alterations in cellular structure and physiology. Activation of critical signaling pathways during HCoV infection modulates the induction of antiviral immune response and contributes to the pathogenesis of HCoV. Recent studies have begun to reveal some fundamental aspects of the intricate HCoV-host interaction in mechanistic detail. In this review we summarize the current knowledge of host factors co-opted and signaling pathways activated during HCoV infection with an emphasis on HCoV-infection-induced stress response autophagy apoptosis and innate immunity. The cross talk among these pathways as well as the modulatory strategies utilized by HCoV is also discussed.

Severe acute respiratory syndrome (SARS) emerged from China as an untreatable and rapidly spreading respiratory illness of unknown etiology. Following point source exposure in February 2003 more than a dozen guests infected at a Hong Kong hotel seeded multi-country outbreaks that persisted through the spring of 2003. The World Health Organization responded by invoking traditional public health measures and advanced technologies to control the illness and contain the cause. A novel coronavirus was implicated and its entire genome was sequenced by mid-April 2003. The urgency of responding to this threat focused scientific endeavor and stimulated global collaboration. Through real-time application of accumulating knowledge the world proved capable of arresting the first pandemic threat of the twenty-first century despite early respiratory-borne spread and global susceptibility. This review synthesizes lessons learned from this remarkable achievement. These lessons can be applied to re-emergence of SARS or to the next pandemic threat to arise.

When judged by ubiquity adaptation and emergence of new diseases RNA viruses are arguably the most successful biological organisms. This success has been attributed to a defect of sorts: high mutation rates (low fidelity) resulting in mutant swarms that allow rapid selection for fitness in new environments. Studies of viruses with small RNA genomes have identified fidelity determinants in viral RNA-dependent RNA polymerases and have shown that RNA viruses likely replicate within a limited fidelity range to maintain fitness. In this review we compare the fidelity of small RNA viruses with that of the largest RNA viruses the coronaviruses. Coronaviruses encode the first known viral RNA proofreading exoribonuclease a function that likely allowed expansion of the coronavirus genome and that dramatically increases replication fidelity and the range of tolerated variation. We propose models for regulation of coronavirus fidelity and discuss the implications of altered fidelity for RNA virus replication pathogenesis and evolution.

Over the past two decades deadly coronaviruses with the most recent being the severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) 2019 pandemic have majorly challenged public health. The path for virus invasion into humans and other hosts is mediated by host–pathogen interactions specifically virus–receptor binding. An in-depth understanding of the virus–receptor binding mechanism is a prerequisite for the discovery of vaccines antibodies and small-molecule inhibitors that can interrupt this interaction and prevent or cure infection. In this review we discuss the viral entry mechanism the known structural aspects of virus–receptor interactions (SARS-CoV-2 S/humanACE2 SARS-CoV S/humanACE2 and MERS-CoV S/humanDPP4) the key protein domains and amino acid residues involved in binding and the small-molecule inhibitors and other drugs that have (as of June 2020) exhibited therapeutic potential. Specifically we review the potential clinical utility of two transmembrane serine protease 2 (TMPRSS2)-targeting protease inhibitors nafamostat mesylate and camostat mesylate as well as two novel potent fusion inhibitors and the repurposed Ebola drug remdesivir which is specific to RNA-dependent RNA polymerase against human coronaviruses including SARS-CoV-2.

Enabled by new approaches for rapid identification and selection of human monoclonal antibodies atomic-level structural information for viral surface proteins and capacity for precision engineering of protein immunogens and self-assembling nanoparticles a new era of antigen design and display options has evolved. While HIV-1 vaccine development has been a driving force behind these technologies and concepts clinical proof-of-concept for structure-based vaccine design may first be achieved for respiratory syncytial virus (RSV) where conformation-dependent access to neutralization-sensitive epitopes on the fusion glycoprotein determines the capacity to induce potent neutralizing activity. Success with RSV has motivated structure-based stabilization of other class I viral fusion proteins for use as immunogens and demonstrated the importance of structural information for developing vaccines against other viral pathogens particularly difficult targets that have resisted prior vaccine development efforts. Solving viral surface protein structures also supports rapid vaccine antigen design and application of platform manufacturing approaches for emerging pathogens.