A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19. A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

/pdf/a-sars-cov-2-protein-interaction-map-reveals-targets-for-5d1m2n6hc1.pdf

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Alongside investigations into the virology of SARS-CoV-2, understanding the fundamental physiological and immunological processes underlying the clinical manifestations of COVID-19 is vital for the identification and rational design of effective therapies. Here, we provide an overview of the pathophysiology of SARS-CoV-2 infection. We describe the interaction of SARS-CoV-2 with the immune system and the subsequent contribution of dysfunctional immune responses to disease progression. From nascent reports describing SARS-CoV-2, we make inferences on the basis of the parallel pathophysiological and immunological features of the other human coronaviruses targeting the lower respiratory tract - severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Finally, we highlight the implications of these approaches for potential therapeutic interventions that target viral infection and/or immunoregulation.

/pdf/the-trinity-of-covid-19-immunity-inflammation-and-10rwiwjpt5.pdf

The trinity of COVID-19: immunity, inflammation and intervention.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and pathogenic coronavirus that emerged in late 2019 and has caused a pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19), which threatens human health and public safety. In this Review, we describe the basic virology of SARS-CoV-2, including genomic characteristics and receptor use, highlighting its key difference from previously known coronaviruses. We summarize current knowledge of clinical, epidemiological and pathological features of COVID-19, as well as recent progress in animal models and antiviral treatment approaches for SARS-CoV-2 infection. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail. In this Review, Shi and colleagues summarize the exceptional amount of research that has characterized acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) since this virus has swept around the globe. They discuss what we know so far about the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19.

/pdf/characteristics-of-sars-cov-2-and-covid-19-eeqnaghpho.pdf

Characteristics of SARS-CoV-2 and COVID-19

Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).

/pdf/coronaviruses-an-overview-of-their-replication-and-4lyvr9vdqs.pdf

Coronaviruses: An Overview of Their Replication and Pathogenesis

https://www.mdpi.com/2076-393X/7/4/138/pdf

Differential immune responses to hemorrhagic Fever-Causing arenaviruses

We have reported that attenuation of the virulence of a field Sendai virus (SeV) isolated by egg passage is associated with an impediment of viral genome replication in mouse respiratory cells (Kiyotani et al., Arch Virol 146, 893–908, 2001). To determine the molecular basis for the attenuation, we sequenced entire genomes of representative SeV clones isolated during egg passages and compared those with that of the parental SeV clone E0. E15cl2, a 165-fold attenuated clone in 50% mouse lethal dose (MLD50) isolated at the 15th egg passage, possessed only four mutations in the entire genome: U to A at position 20 (U20A) and U24A in the leader promoter region and A9362G and A12174U in the L gene from the 5′-end of antigenome. The former mutation in the L gene was silent and the latter changed deduced amino acid Ser at position 1207 to Cys (Ser1207Cys) in the L protein, a catalytic subunit of viral polymerase. E30cl2, a further 6-fold attenuated clone isolated at the 30th egg passage, had an additional four mutations: A8074G (Glu461Gly) and A8077G (Asp462Gly) in the hemagglutinin-neuraminidase (HN) gene and A13598C (silent) and G13927A (Ser1791Asn) in the L gene. On the other hand, a virulent revertant clone, E30M15cl5, which was obtained by 15 mouse passages of E30cl2 and had 250-fold mouse virulence compared to E30cl2, possessed eight mutaions: A24U in the leader, C1325U (silent) in the nucleocapsid gene, G8074A (Gly461Glu) in the HN gene, G10433U (Lys626Asn), C13598A (silent), A13927G (Asn1791Ser), C14626U (Thr2024Ile) and A15272C in the L gene. Among these, the mutations in the leader and the HN gene and two of the mutations in the L gene (C13598A and A13927G) were true reversions to E0. The significance of the mutations detected in the leader as well as in the L and HN genes was discussed in the context of attenuation of SeV pathogenicity by egg passage.

Identification of mutations associated with attenuation of virulence of a field Sendai virus isolate by egg passage.

Sendai virus (SeV), an enveloped virus with a single-stranded negative-sense RNA genome of 15,384 bases, belongs to the genus Respirovirus of the family Paramyxoviridae. The virus particle displays spherical morphology of relatively uniform size with a diameter of about 200 nm. The envelope comprises a lipid bilayer derived from the host plasma membrane and two inserted viral glycoproteins, fusion (F) and hemagglutinin-neuraminidase (HN) proteins. Lining beneath the envelope are the matrix or membrane (M) proteins. The nucleocapsid represents the internal structure, which comprises the genome RNA complexed with the nucleocapsid (N) protein and polymerase consisting of the L (large) protein and the P (phospho) protein (11).

There is increasing evidence suggesting that the M protein plays a key role in the assembly of paramyxoviruses and related RNA viruses. The M protein has been suggested to be essential to cross-link the external envelope proteins and the internal nucleocapsid. It also promotes the condensation of viral glycoproteins into a patch in the plasma membrane, an immediate precursor of the envelope (16, 28). The M proteins, associating with the nucleocapsid, may then provide forces from the inside for the membrane patch to bud (3, 7, 15). Bending of membranes may also be facilitated from the outside by glycoproteins (17, 18). We previously showed that the SeV M protein expressed from plasmid was released into the culture supernatant, as was seen in the case of the M protein of vesicular stomatitis virus (12, 22). Recently, the F protein as well as the M protein was shown to cause the budding of vesicles from cells (25). The SeV M protein as well as the F protein therefore has an intrinsic nature to be a driving force of virus budding.

The SeV M protein is 348 amino acids in length and contains five cysteine residues. Cysteines can form intrachain and interchain disulfide bonds and thereby contribute to the folding of polypeptides as well as homologous and heterologous protein-protein covalent interactions. Cysteines in various enzymes function as an active center, and those in various proteins sometimes form zinc finger motifs to bind metabolically important zinc ions (5, 13). The last function has recently been exemplified for a nonstructural protein of SeV, the V protein (8). Little is known, however, about the cysteine residues of the SeV M protein. It is unlikely that the cysteines in the M protein are intracellularly oxidized to form disulfide bonds because the M protein is localized in the cytosol, the reducing milieu. However, it is not known whether the cysteines of the M protein form disulfide bonds in virus particles in an oxidizing extracellular environment. Nevertheless, the fact that cysteine residues are well conserved in a wide variety of paramyxovirus M proteins suggests that the functions of the M proteins are important. We therefore focused on cysteine residues at the targets of site-directed mutagenesis and investigated the actual contribution of the M protein to SeV assembly.

Alteration of Sendai Virus Morphogenesis and Nucleocapsid Incorporation due to Mutation of Cysteine Residues of the Matrix Protein

Double-stranded (ds) RNA is produced as a replicative intermediate during RNA virus infection. Recognition of dsRNA by host pattern recognition receptors (PRRs) such as the retinoic acid (RIG-I) like receptors (RLRs) RIG-I and melanoma differentiation-associated protein 5 (MDA-5) leads to the induction of the innate immune response. The formation and intracellular distribution of dsRNA in positive-sense RNA virus infection has been well characterized by microscopy. Many negative-sense RNA viruses, including some arenaviruses, trigger the innate immune response during infection. However, negative-sense RNA viruses were thought to produce low levels of dsRNA, which hinders the imaging study of PRR recognition of viral dsRNA. Additionally, infection experiments with highly pathogenic arenaviruses must be performed in high containment biosafety level facilities (BSL-4). The interaction between viral RNA and PRRs for highly pathogenic RNA virus is largely unknown due to the additional technical challenges that researchers need to face in the BSL-4 facilities. Recently, a monoclonal antibody (Mab) (clone 9D5) originally used for pan-enterovirus detection has been found to specifically detect dsRNA with a higher sensitivity than the traditional J2 or K1 anti-dsRNA antibodies. Herein, by utilizing the 9D5 antibody, we describe a confocal microscopy protocol that has been used successfully to visualize dsRNA, viral protein and PRR simultaneously in individual cells infected by arenavirus. The protocol is also suitable for imaging studies of dsRNA and PRR distribution in pathogenic arenavirus infected cells in BSL4 facilities.

/pdf/confocal-imaging-of-double-stranded-rna-and-pattern-2x4mn7fgcl.pdf

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

Machupo virus (MACV), a New World arenavirus, is the etiological agent of Bolivian hemorrhagic fever (BHF). Junin virus (JUNV), a close relative, causes Argentine hemorrhagic fever (AHF). Previously, we reported that a recombinant, chimeric MACV (rMACV/Cd#1-GPC) expressing glycoprotein from the Candid#1 (Cd#1) vaccine strain of JUNV is completely attenuated in a murine model and protects animals from lethal challenge with MACV. A rMACV with a single F438I substitution in the transmembrane domain (TMD) of GPC, which is equivalent to the F427I attenuating mutation in Cd#1 GPC, was attenuated in a murine model but genetically unstable. In addition, the TMD mutation alone was not sufficient to fully attenuate JUNV, indicating that other domains of the GPC may also contribute to the attenuation. To investigate the requirement of different domains of Cd#1 GPC for successful attenuation of MACV, we rescued several rMACVs expressing the ectodomain of GPC from Cd#1 either alone (MCg1), along with the TMD F438I substitution (MCg2), or with the TMD of Cd#1 (MCg3). All rMACVs exhibited similar growth curves in cultured cells. In mice, the MCg1 displayed significant reduction in lethality as compared with rMACV. The MCg1 was detected in brains and spleens of MCg1-infected mice and the infection was associated with tissue inflammation. On the other hand, all animals survived MCg2 and MCg3 infection without detectable levels of virus in various organs while producing neutralizing antibody against Cd#1. Overall our data suggest the indispensable role of each GPC domain in the full attenuation and immunogenicity of rMACV/Cd#1 GPC.

/pdf/the-ectodomain-of-glycoprotein-from-the-candid-1-vaccine-4kyyl5j7o2.pdf

The Ectodomain of Glycoprotein from the Candid#1 Vaccine Strain of Junin Virus Rendered Machupo Virus Partially Attenuated in Mice Lacking IFN-αβ/γ Receptor

Cheng Huang

Papers

Differential immune responses to hemorrhagic Fever-Causing arenaviruses

Identification of mutations associated with attenuation of virulence of a field Sendai virus isolate by egg passage.

Alteration of Sendai Virus Morphogenesis and Nucleocapsid Incorporation due to Mutation of Cysteine Residues of the Matrix Protein

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

The Ectodomain of Glycoprotein from the Candid#1 Vaccine Strain of Junin Virus Rendered Machupo Virus Partially Attenuated in Mice Lacking IFN-αβ/γ Receptor