The COVID-19 (Coronavirus disease-2019) pandemic, caused by the SARS-CoV-2 coronavirus, is a significant threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and MERS-CoV. Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analysis for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b, an interaction we structurally characterized using cryo-EM. Combining genetically-validated host factors with both COVID-19 patient genetic data and medical billing records identified important molecular mechanisms and potential drug treatments that merit further molecular and clinical study.

Type I interferons (IFN-alpha/beta) are potent antiviral cytokines and modulators of the adaptive immune system. They are induced by viral infection or by double-stranded RNA (dsRNA), a by-product of viral replication, and lead to the production of a broad range of antiviral proteins and immunoactive cytokines. Viruses, in turn, have evolved multiple strategies to counter the IFN system which would otherwise stop virus growth early in infection. Here we discuss the current view on the balancing act between virus-induced IFN responses and the viral counterplayers.

The replication and pathogenicity of influenza A virus (FLUAV) are controlled in part by the alpha/beta interferon (IFN-␣/␤) system. This virus-host interplay is dependent on the production of IFN-␣/␤ and on the capacity of the viral nonstructural protein NS1 to counteract the IFN system. Two different mechanisms have been described for NS1, namely, blocking the activation of IFN regulatory factor 3 (IRF3) and blocking posttranscriptional processing of cellular mRNAs. Here we directly compare the abilities of NS1 gene products from three different human FLUAV (H1N1) strains to counteract the antiviral host response. We found that A/PR/8/34 NS1 has a strong capacity to inhibit IRF3 and activation of the IFN-␤ promoter but is unable to suppress expression of other cellular genes. In contrast, the NS1 proteins of A/Tx/36/91 and of A/BM/1/18, the virus that caused the Spanish influenza pandemic, caused suppression of additional cellular gene expression. Thus, these NS1 proteins prevented the establishment of an IFN-induced antiviral state, allowing virus replication even in the presence of IFN. Interestingly, the block in gene expression was dependent on a newly described NS1 domain that is important for interaction with the cleavage and polyadenylation specificity factor (CPSF) component of the cellular pre-mRNA processing machinery but is not functional in A/PR/8/34 NS1. We identified the Phe-103 and Met-106 residues in NS1 as being critical for CPSF binding, together with the previously described C-terminal binding domain. Our results demonstrate the capacity of FLUAV NS1 to suppress the antiviral host defense at multiple levels and the existence of strain-specific differences that may modulate virus pathogenicity.The genome of influenza A virus (FLUAV) consists of eight RNA segments that encode nine structural proteins and two nonstructural proteins, called NS1 (41) and PB1-F2 (11). NS1 is a virulence factor of FLUAV by virtue of conferring resistance to the antiviral effects of the host interferon (IFN) system (21,40,63). Previous studies with recombinant FLUAV carrying deletions in the NS1 gene (delNS1) showed a strong attenuation in IFN-competent systems, whereas the NS1-deleted virus replicated to levels similar to those of wild-type virus in cell culture and in mice with a defect in the IFN system (16,23,39).The expression of type I IFNs (IFN-␣/␤) is induced in response to viral infection. Viral single-stranded and doublestranded RNAs (dsRNAs) with phosphorylated 5Ј ends are among the viral products that induce IFN-␣/␤ (32, 42, 55). These viral RNA molecules activate a variety of cellular signaling pathways, resulting in the activation of transcription factors, such as the IFN regulatory factors (IRFs) and the stress-induced transcription factors NF-B and c-Jun/ATF2 (34, 60, 64). Upon activation, these latent transcription factors move from the cytoplasm into the nucleus and initiate the expression of type I IFNs. IFN-␣/␤ subtypes bind to a common type I IFN receptor, thus activating the JAK-STAT signaling ...

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GTPase is a key mediator of cell-autonomous innate immunityHis-tagged full-length human MxA (Fig. 1a) was recombinantly expressed in bacteria and purified to homogeneity (Methods, Supp. Fig. 1). In crystallization trials, small needle-shaped protein crystals were obtained which represented proteolytic cleavage products of the MD and GED (Supp. Fig. 2). We solved the phase problem by a single anomalous dispersion protocol and could build and refine a model containing two molecules in the asymmetric unit (Methods, Supp. Table 1 and 2). Each monomer spans nearly the complete MD and the amino(N-)-terminal part of the GED (amino acids 366-633) which together fold into an elongated anti-parallel fourhelical bundle where the MD contributes three helices and the GED one (Fig. 1b, Supp. Fig. 3). This segment corresponds to the stalk region of dynamin 7 , and we refer to it as stalk of MxA. The first visible amino acid, Glu366, is 15 amino acids downstream of the last visible residue of the corresponding G-domain structure in rat dynamin (Supp. Fig. 3) 8 . It marks the start of helix α1 in the MxA stalk which is divided in α1 N and α1 C by a 10 amino acid long loop, L1, introducing a 30° kink. A putative loop L2 (amino acids 438-447) opposite of the deduced position of the G-domain is not visible in our structure. L2 was previously demonstrated to be the target of a functionally neutralising monoclonal antibody 9,10 . Helix α2 runs anti-parallel to α1 back to the G-domain. It ends in a short loop L3 and is followed by helix α3 that extends in parallel to α1. The 40 amino acid long loop L4 (residues 532-572) is at the equivalent sequence position as the PH domain of dynamin (Fig. 1a, Supp. Fig. 3) and is absent in our model. L4 is predicted to be unstructured and was previously shown to be proteinase K sensitive 11 .At the C-terminus, the GED supplies 44 residues to helix α4 which proceeds in parallel to helix α2 back to the G-domain. It is followed by a short helix α5 which directs the polypeptide chain towards the N-terminus of the MD. The carboxy(C-)-terminal 30 highly conserved residues of the GED known to be involved in antiviral specificity 12 are missing in our model. In dynamin, the corresponding residues were shown to directly interact with the G-domain 13 . The stalk of MxA is divergent from the corresponding structures of other dynamin superfamily members, such as GBP1 14 , EHD2 15 and BDLP 16 although some features are shared (Supp. Fig. 4). 4 In the crystal lattice, each MxA stalk is assembled in a criss-cross pattern resulting in a linear oligomer, where each stalk contributes three distinct interfaces (Fig. 1c). Such an arrangement of the stalks is plausible for the Mx oligomer since all G-domains would be located at one side of the oligomer whereas the putative substrate-binding site in L2 and L4 would be located at the opposite side (Fig. 1b, c).The hydrophobic interface-1 covering 1300 Å 2 is conserved among Mx proteins and dynamins and has a two-fold symmetry between the associating monomers (Fig....

Mx proteins are interferon-induced GTPases that belong to the dynamin superfamily of large GTPases. Similarities include a high molecular weight, a propensity to self-assemble, a relatively low affinity for GTP, and a high intrinsic rate of GTP hydrolysis. A unique property of Mx GTPases is their antiviral activity against a wide range of RNA viruses, including bunyaand orthomyxoviruses. The human MxA GTPase accumulates in the cytoplasm of interferon-treated cells, partly associating with the endoplasmic reticulum. In the case of bunyaviruses, MxA interferes with transport of the viral nucleocapsid protein (N) to the Golgi compartment, the site of virus assembly. In the case of Thogoto virus (an orthomyxovirus), MxA prevents the incoming viral nucleocapsids from being transported into the nucleus, the site of viral transcription and replication. In both cases, the GTP-binding and carboxyterminal effector functions of MxA are required for target recognition. In general, Mx GTPases appear to detect viral infection by sensing nucleocapsid-like structures. As a consequence, these viral components are trapped and sorted to locations where they become unavailable for the generation of new virus particles.

Virus-infected cells secrete a broad range of interferons (IFN) which confer resistance to yet uninfected cells by triggering the synthesis of antiviral factors. The relative contributions of the various IFN subtypes to innate immunity against virus infections remain elusive. IFN-␣, IFN-␤, and other type I IFN molecules signal through a common, universally expressed cell surface receptor, whereas type III IFN (IFN-) uses a distinct cell-typespecific receptor complex for signaling. Using mice lacking functional receptors for type I IFN, type III IFN, or both, we found that IFN-plays an important role in the defense against several human pathogens that infect the respiratory tract, such as influenza A virus, influenza B virus, respiratory syncytial virus, human metapneumovirus, and severe acute respiratory syndrome (SARS) coronavirus. These viruses were more pathogenic and replicated to higher titers in the lungs of mice lacking both IFN receptors than in mice with single IFN receptor defects. In contrast, Lassa fever virus, which infects via the respiratory tract but primarily replicates in the liver, was not influenced by the IFN-receptor defect. Careful analysis revealed that expression of functional IFN-receptor complexes in the lung and intestinal tract is restricted to epithelial cells and a few other, undefined cell types. Interestingly, we found that SARS coronavirus was present in feces from infected mice lacking receptors for both type I and type III IFN but not in those from mice lacking single receptors, supporting the view that IFN-contributes to the control of viral infections in epithelial cells of both respiratory and gastrointestinal tracts.The interferon (IFN) system represents a major element of the innate immune response against viral infections (10,13,14). Virus-induced IFN is a complex mixture of biologically active molecules, which includes type I and type III IFN. Type I IFN consists of 14 different IFN-␣ subtypes in the mouse as well as IFN-␤, IFN-, IFN-ε, and limitin, which all signal through the same universally expressed cell surface receptor complex (IFNAR) (30). Type III IFN includes IFN-1, IFN-2, and IFN-3 (21, 28), of which only the latter two are encoded by genes that are expressed in the mouse (22). Type III IFN uses a distinct receptor complex (IL28R) for signaling (21, 28), which appears to be expressed on only a few cell types, including epithelial cells (29). Binding of type I IFN and type III IFN to their cognate receptor complexes triggers signaling cascades that result in the activation of a large number of genes, many of which encode antiviral proteins (10, 32). Type I IFN and type III IFN trigger highly similar gene expression profiles in responsive cells, suggesting that both IFN types might serve similar functions. However, it has to date been largely unclear to which extent IFN-might contribute to innate immunity.Using knockout mouse strains that lack receptors for type I IFN (IFNAR1 0/0 ), type III IFN (IL28R␣ 0/0 ), or both (IFNAR1 0/0 IL28R␣ 0/0 ), we have recently ...

In this study, we analyzed the replication and budding sites of severe acute respiratory syndrome coronavirus (SARS-CoV) at early time points of infection. We detected cytoplasmic accumulations containing the viral nucleocapsid protein, viral RNA and the non-structural protein nsp3. Using EM techniques, we found that these putative viral replication sites were associated with characteristic membrane tubules and double membrane vesicles that most probably originated from ER cisternae. In addition to its presence at the replication sites, N also accumulated in the Golgi region and colocalized with the viral spike protein. Immuno-EM revealed that budding occurred at membranes of the ERGIC (ER-Golgi intermediate compartment) and the Golgi region as early as 3 h post infection, demonstrating that SARS-CoV replicates surprisingly fast. Our data suggest that SARS-CoV establishes replication complexes at ER-derived membranes. Later on, viral nucleocapsids have to be transported to the budding sites in the Golgi region where the viral glycoproteins accumulate and particle formation occurs.