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The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates the rapid development of new therapies against coronavirus disease 2019 (COVID-19) infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2–induced protein network, based on disease signatures defined by COVID-19 multiomics datasets, and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2–induced pathways, 40 of which are already in COVID-19 clinical trials, testifying to the validity of the approach. Using artificial neural network analysis, we classified these 200 drugs into nine distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (126) and immune response (74). Two drugs (proguanil and sulfasalazine) implicated in viral replication were shown to inhibit replication in cell assays. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials.
Namshik Han; Woochang Hwang; Konstantinos Tzelepis; Patrick Schmerer; Eliza Yankova; Méabh MacMahon; Winnie Lei; Nicholas M. Katritsis; Anika Liu; Ulrike Felgenhauer; Alison Schuldt; Rebecca Harris; Kathryn Chapman; Frank McCaughan; Friedemann Weber; Tony Kouzarides. Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies. Science Advances 2021, 7, eabh3032 .
AMA StyleNamshik Han, Woochang Hwang, Konstantinos Tzelepis, Patrick Schmerer, Eliza Yankova, Méabh MacMahon, Winnie Lei, Nicholas M. Katritsis, Anika Liu, Ulrike Felgenhauer, Alison Schuldt, Rebecca Harris, Kathryn Chapman, Frank McCaughan, Friedemann Weber, Tony Kouzarides. Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies. Science Advances. 2021; 7 (27):eabh3032.
Chicago/Turabian StyleNamshik Han; Woochang Hwang; Konstantinos Tzelepis; Patrick Schmerer; Eliza Yankova; Méabh MacMahon; Winnie Lei; Nicholas M. Katritsis; Anika Liu; Ulrike Felgenhauer; Alison Schuldt; Rebecca Harris; Kathryn Chapman; Frank McCaughan; Friedemann Weber; Tony Kouzarides. 2021. "Identification of SARS-CoV-2–induced pathways reveals drug repurposing strategies." Science Advances 7, no. 27: eabh3032.
Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated eukaryotic translation initiation factor 2 [eIF2(αP)] tightly binds to eIF2B to prevent it from exchanging guanine nucleotides on unphosphorylated eIF2. Sandfly fever Sicilian virus (SFSV) evades this cap-dependent translation suppression through the interaction between its nonstructural protein NSs and host eIF2B. Our cryo-electron microscopy (cryo-EM) analysis revealed that SFSV NSs binds to the α-subunit of eIF2B in a competitive manner with eIF2(αP). Together with SFSV NSs, eIF2B exhibits normal nucleotide exchange activity even in the presence of eIF2(αP). A genome-wide ribosome profiling analysis clarified that SFSV NSs in human cultured cells attenuates the ISR. Furthermore, SFSV NSs exhibited neuroprotective effects against the ISR-inducing stress. Since the ISR inhibition is beneficial in various neurological disease models, SFSV NSs is promising as a therapeutic ISR inhibitor.
Kazuhiro Kashiwagi; Yuichi Shichino; Tatsuya Osaki; Ayako Sakamoto; Madoka Nishimoto; Mari Takahashi; Mari Mito; Friedemann Weber; Yoshiho Ikeuchi; Shintaro Iwasaki; Takuhiro Ito. eIF2B-capturing viral protein NSs suppresses the integrated stress response. 2021, 1 .
AMA StyleKazuhiro Kashiwagi, Yuichi Shichino, Tatsuya Osaki, Ayako Sakamoto, Madoka Nishimoto, Mari Takahashi, Mari Mito, Friedemann Weber, Yoshiho Ikeuchi, Shintaro Iwasaki, Takuhiro Ito. eIF2B-capturing viral protein NSs suppresses the integrated stress response. . 2021; ():1.
Chicago/Turabian StyleKazuhiro Kashiwagi; Yuichi Shichino; Tatsuya Osaki; Ayako Sakamoto; Madoka Nishimoto; Mari Takahashi; Mari Mito; Friedemann Weber; Yoshiho Ikeuchi; Shintaro Iwasaki; Takuhiro Ito. 2021. "eIF2B-capturing viral protein NSs suppresses the integrated stress response." , no. : 1.
The pathogenesis and host-viral interactions of the Crimean–Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and is not well evaluated. To understand the host immune responses against CCHFV, we have performed a global transcriptomic analysis of peripheral blood mononuclear cells from a longitudinal cohort of CCHF patients who survived the infection and temporal untargeted proteomics analysis of CCHFV infected Huh7 cells. Our results indicate that during the acute phase of CCHFV infection, the host's metabolic reprogramming towards central carbon metabolism including glycolysis and glutaminolysis occurs that favours the virus replication as blocking these pathways in vitro inhibits CCHFV cellular replication. Furthermore, CCHFV replication was inhibited by blocking Akt with MK-2206 suggesting a regulatory role of PI3K/Akt/mTOR pathways. We also show activation of key interferon stimulating genes during infection, suggesting a role for type I and II interferon-mediated antiviral mechanisms. Targeting immune-metabolic pathways could be attractive therapeutic intervention for CCHFV.
Ujjwal Neogi; Nazif Elaldi; Sofia Appelberg; Anoop Ambikan; Emma Kennedy; Stuart Dowall; Binnur Bagci; Soham Gupta; Jimmy Rodriguez; Sara Svensson Akusjärvi; Vanessa Monteil; Akos Vegvari; Akhil Banerjea; Friedemann Weber; Roger Hewson; Ali Mirazimi. Longitudinal blood cell transcriptomic profiling and in vitro temporal proteomics provides novel insights into metabolic reprogramming and host-immune responses against Crimean-Congo Hemorrhagic Fever Virus. 2021, 1 .
AMA StyleUjjwal Neogi, Nazif Elaldi, Sofia Appelberg, Anoop Ambikan, Emma Kennedy, Stuart Dowall, Binnur Bagci, Soham Gupta, Jimmy Rodriguez, Sara Svensson Akusjärvi, Vanessa Monteil, Akos Vegvari, Akhil Banerjea, Friedemann Weber, Roger Hewson, Ali Mirazimi. Longitudinal blood cell transcriptomic profiling and in vitro temporal proteomics provides novel insights into metabolic reprogramming and host-immune responses against Crimean-Congo Hemorrhagic Fever Virus. . 2021; ():1.
Chicago/Turabian StyleUjjwal Neogi; Nazif Elaldi; Sofia Appelberg; Anoop Ambikan; Emma Kennedy; Stuart Dowall; Binnur Bagci; Soham Gupta; Jimmy Rodriguez; Sara Svensson Akusjärvi; Vanessa Monteil; Akos Vegvari; Akhil Banerjea; Friedemann Weber; Roger Hewson; Ali Mirazimi. 2021. "Longitudinal blood cell transcriptomic profiling and in vitro temporal proteomics provides novel insights into metabolic reprogramming and host-immune responses against Crimean-Congo Hemorrhagic Fever Virus." , no. : 1.
Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus that causes an important disease in ruminants, with great economic losses. The infection can be also transmitted to humans; therefore, it is considered a major threat to both human and animal health. In a previous work, we described a novel RVFV variant selected in cell culture in the presence of the antiviral agent favipiravir that was highly attenuated in vivo. This variant displayed 24 amino acid substitutions in different viral proteins when compared to its parental viral strain, two of them located in the NSs protein that is known to be the major virulence factor of RVFV. By means of a reverse genetics system, in this work we have analyzed the effect that one of these substitutions, P82L, has in viral attenuation in vivo. Rescued viruses carrying this single amino acid change were clearly attenuated in BALB/c mice while their growth in an interferon (IFN)-competent cell line as well as the production of interferon beta (IFN-β) did not seem to be affected. However, the pattern of nuclear NSs accumulation was modified in cells infected with the mutant viruses. These results highlight the key role of the NSs protein in the modulation of viral infectivity.
Belén Borrego; Sandra Moreno; Nuria de la Losa; Friedemann Weber; Alejandro Brun. The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice. Viruses 2021, 13, 542 .
AMA StyleBelén Borrego, Sandra Moreno, Nuria de la Losa, Friedemann Weber, Alejandro Brun. The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice. Viruses. 2021; 13 (4):542.
Chicago/Turabian StyleBelén Borrego; Sandra Moreno; Nuria de la Losa; Friedemann Weber; Alejandro Brun. 2021. "The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice." Viruses 13, no. 4: 542.
Helium ion microscopy (HIM) offers the opportunity to obtain direct views of biological samples such as cellular structures, virus particles, and microbial interactions. Imaging with the HIM combines sub-nanometer resolution, large depth of field, and high surface sensitivity. Due to its charge compensation capability, the HIM can image insulating biological samples without additional conductive coatings. Here, we present an exploratory HIM study of SARS-CoV-2 infected Vero E6 cells, in which several areas of interaction between cells and virus particles, as well as among virus particles, were imaged. The HIM pictures show the three-dimensional appearance of SARS-CoV-2 and the surface of Vero E6 cells at a multiplicity of infection of approximately 1 with great morphological detail. The absence of a conductive coating allows for a distinction between virus particles bound to the cell membrane and virus particles lying on top of the membrane. After prolonged imaging, it was found that ion-induced deposition of hydrocarbons from the vacuum renders the sample sufficiently conductive to allow for imaging even without charge compensation. The presented images demonstrate the potential of the HIM in bioimaging, especially for the imaging of interactions between viruses and their host organisms.
Natalie Frese; Patrick Schmerer; Martin Wortmann; Matthias Schürmann; Matthias König; Michael Westphal; Friedemann Weber; Holger Sudhoff; Armin Gölzhäuser. Imaging of SARS-CoV-2 infected Vero E6 cells by helium ion microscopy. Beilstein Journal of Nanotechnology 2021, 12, 172 -179.
AMA StyleNatalie Frese, Patrick Schmerer, Martin Wortmann, Matthias Schürmann, Matthias König, Michael Westphal, Friedemann Weber, Holger Sudhoff, Armin Gölzhäuser. Imaging of SARS-CoV-2 infected Vero E6 cells by helium ion microscopy. Beilstein Journal of Nanotechnology. 2021; 12 (1):172-179.
Chicago/Turabian StyleNatalie Frese; Patrick Schmerer; Martin Wortmann; Matthias Schürmann; Matthias König; Michael Westphal; Friedemann Weber; Holger Sudhoff; Armin Gölzhäuser. 2021. "Imaging of SARS-CoV-2 infected Vero E6 cells by helium ion microscopy." Beilstein Journal of Nanotechnology 12, no. 1: 172-179.
Rift valley fever virus (RVFV) is a mosquito-borne bunyavirus that causes an important disease in ruminants, with great economic losses. The infection can be also transmitted to humans; therefore it is considered a major threat to both human and animal health. In a previous work, we described a novel RVFV variant selected in cell culture in the presence of the antiviral agent favipiravir that was highly attenuated in vivo. This variant displayed 24 amino acid substitutions in different viral proteins when compared to its parental viral strain, two of them located in the NSs protein that is known to be the major virulence factor of RVFV. By means of a reverse genetics system, in this work we have analyzed the effect that one of these substitutions, P82L, has in viral attenuation in vivo. Rescued viruses carrying this single amino acid change were clearly attenuated in BALB/c mice while their growth in an IFN-competent cell line as well as the production of IFN-β did not seem to be affected. However, the pattern of nuclear NSs accumulation was modified in cells infected with the mutant viruses. These results unveil a new RVFV virulence marker highlighting the multiple ways of NSs protein to modulate viral infectivity.
Belén Borrego; Sandra Moreno; Nuria de la Losa; Friedemann Weber; Alejandro Brun. The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice Not Related with a Type-I IFN Antagonistic Phenotype. 2021, 1 .
AMA StyleBelén Borrego, Sandra Moreno, Nuria de la Losa, Friedemann Weber, Alejandro Brun. The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice Not Related with a Type-I IFN Antagonistic Phenotype. . 2021; ():1.
Chicago/Turabian StyleBelén Borrego; Sandra Moreno; Nuria de la Losa; Friedemann Weber; Alejandro Brun. 2021. "The Change P82L in the Rift Valley Fever Virus NSs Protein Confers Attenuation in Mice Not Related with a Type-I IFN Antagonistic Phenotype." , no. : 1.
Background Many ruminant diseases of viral aetiology can be effectively prevented using appropriate vaccination measures. For diseases such as Rift Valley fever (RVF) the long inter-epizootic periods make routine vaccination programs unfeasible. Coupling RVF prophylaxis with seasonal vaccination programmes by means of multivalent vaccine platforms would help to reduce the risk of new RVF outbreaks. Methodology/Principal findings In this work we generated recombinant attenuated Rift Valley fever viruses (RVFVs) encoding in place of the virulence factor NSs either the VP2 capsid protein or a truncated form of the non-structural NS1 protein of bluetongue virus serotype 4 (BTV-4). The recombinant viruses were able to carry and express the heterologous BTV genes upon consecutive passages in cell cultures. In murine models, a single immunization was sufficient to protect mice upon RVFV challenge and to elicit a specific immune response against BTV-4 antigens that was fully protective after a BTV-4 boost. In sheep, a natural host for RVFV and BTV, both vaccines proved immunogenic although conferred only partial protection after a virulent BTV-4 reassortant Morocco strain challenge. Conclusions/Significance Though additional optimization will be needed to improve the efficacy data against BTV in sheep, our findings warrant further developments of attenuated RVFV as a dual vaccine platform carrying heterologous immune relevant antigens for ruminant diseases in RVF risk areas.
Sandra Moreno; Eva Calvo-Pinilla; Stephanie Devignot; Friedemann Weber; Javier Ortego; Alejandro Brun. Recombinant Rift Valley fever viruses encoding bluetongue virus (BTV) antigens: Immunity and efficacy studies upon a BTV-4 challenge. PLOS Neglected Tropical Diseases 2020, 14, e0008942 .
AMA StyleSandra Moreno, Eva Calvo-Pinilla, Stephanie Devignot, Friedemann Weber, Javier Ortego, Alejandro Brun. Recombinant Rift Valley fever viruses encoding bluetongue virus (BTV) antigens: Immunity and efficacy studies upon a BTV-4 challenge. PLOS Neglected Tropical Diseases. 2020; 14 (12):e0008942.
Chicago/Turabian StyleSandra Moreno; Eva Calvo-Pinilla; Stephanie Devignot; Friedemann Weber; Javier Ortego; Alejandro Brun. 2020. "Recombinant Rift Valley fever viruses encoding bluetongue virus (BTV) antigens: Immunity and efficacy studies upon a BTV-4 challenge." PLOS Neglected Tropical Diseases 14, no. 12: e0008942.
Helium ion microscopy (HIM) offers the opportunity to obtain direct views of biological samples such as cellular structures, virus particles, and microbial interactions. Imaging with the HIM combines sub-nanometer resolution, large depth of field, and high surface sensitivity. Due to its charge compensation capability, the HIM can image insulating biological samples without additional conductive coatings. Here, we present an exploratory HIM study of SARS-CoV-2 infected Vero E6 cells, in which several areas of interactions between cells and virus particles, as well as among virus particles, were imaged. The HIM pictures show the three-dimensional appearance of SARS-CoV-2 and the surface of Vero E6 cells at a multiplicity of infection of approximately 1 with great morphological detail. The absence of a conductive coating allows a distinction between virus particles bound to the cell membrane and virus particles lying on top of the membrane. After prolonged imaging, it was found that ion-induced deposition of hydrocarbons from the vacuum renders the sample sufficiently conductive to allow imaging even without charge compensation. The presented images demonstrate the potential of the HIM in bioimaging, especially for the imaging of interactions between viruses and their host organisms.
Natalie Frese; Patrick Schmerer; Martin Wortmann; Matthias Schürmann; Matthias König; Michael Westphal; Friedemann Weber; Holger Sudhoff; Armin Gölzhäuser. Imaging of SARS-CoV-2 infected Vero E6 Cells by Helium Ion Microscopy. 2020, 2020, 136 .
AMA StyleNatalie Frese, Patrick Schmerer, Martin Wortmann, Matthias Schürmann, Matthias König, Michael Westphal, Friedemann Weber, Holger Sudhoff, Armin Gölzhäuser. Imaging of SARS-CoV-2 infected Vero E6 Cells by Helium Ion Microscopy. . 2020; 2020 (1):136.
Chicago/Turabian StyleNatalie Frese; Patrick Schmerer; Martin Wortmann; Matthias Schürmann; Matthias König; Michael Westphal; Friedemann Weber; Holger Sudhoff; Armin Gölzhäuser. 2020. "Imaging of SARS-CoV-2 infected Vero E6 Cells by Helium Ion Microscopy." 2020, no. 1: 136.
There is currently no specific prophylaxis or vaccine against Crimean-Congo haemorrhagic fever virus (CCHFV). Crimean-Congo haemorrhagic fever (CCHF) is a severe febrile illness transmitted by Hyalomma ticks in endemic areas, handling of infected livestock or care of infected patients. We report here the successful protection against CCHFV-mediated disease in a non-human primate disease model. Cynomolgus macaques were vaccinated with a DNA-based vaccine using in vivo electroporation-assisted delivery. The vaccine contained two plasmids encoding the glycoprotein precursor (GPC) and the nucleoprotein (NP) of CCHFV. Animals received three vaccinations and we recorded potent antibody and T cell responses after vaccination. While all sham-vaccinated animals developed viraemia, high tissue viral loads and CCHF-induced disease, the NP + GPC vaccinated animals were significantly protected. In conclusion, this is evidence of a vaccine that can protect against CCHFV-induced disease in a non-human primate model. This supports clinical development of the vaccine to protect groups at risk for contracting the infection. A DNA-based vaccine elicits humoral and cellular immunity and provides protection against Crimean-Congo haemorrhagic fever virus-mediated disease in a non-human primate model.
David W. Hawman; Gustaf Ahlén; K. Sofia Appelberg; Kimberly Meade-White; Patrick W. Hanley; Dana Scott; Vanessa Monteil; Stephanie Devignot; Atsushi Okumura; Friedemann Weber; Heinz Feldmann; Matti Sällberg; Ali Mirazimi. A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model. Nature Microbiology 2020, 6, 187 -195.
AMA StyleDavid W. Hawman, Gustaf Ahlén, K. Sofia Appelberg, Kimberly Meade-White, Patrick W. Hanley, Dana Scott, Vanessa Monteil, Stephanie Devignot, Atsushi Okumura, Friedemann Weber, Heinz Feldmann, Matti Sällberg, Ali Mirazimi. A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model. Nature Microbiology. 2020; 6 (2):187-195.
Chicago/Turabian StyleDavid W. Hawman; Gustaf Ahlén; K. Sofia Appelberg; Kimberly Meade-White; Patrick W. Hanley; Dana Scott; Vanessa Monteil; Stephanie Devignot; Atsushi Okumura; Friedemann Weber; Heinz Feldmann; Matti Sällberg; Ali Mirazimi. 2020. "A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model." Nature Microbiology 6, no. 2: 187-195.
The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction, the FSE-arch, that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure-based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses and will aid future efforts to develop antiviral strategies.
Omer Ziv; Jonathan Price; Lyudmila Shalamova; Tsveta Kamenova; Ian Goodfellow; Friedemann Weber; Eric A. Miska. The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. Molecular Cell 2020, 80, 1067 -1077.e5.
AMA StyleOmer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber, Eric A. Miska. The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. Molecular Cell. 2020; 80 (6):1067-1077.e5.
Chicago/Turabian StyleOmer Ziv; Jonathan Price; Lyudmila Shalamova; Tsveta Kamenova; Ian Goodfellow; Friedemann Weber; Eric A. Miska. 2020. "The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2." Molecular Cell 80, no. 6: 1067-1077.e5.
The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of the devastating COVID-19 lung disease pandemic. Here, we tested the inhibitory activities of the antiviral interferons of type I (IFN-alpha) and type III (IFN-lambda) against SARS-CoV-2 and compared them with those against SARS-CoV-1, which emerged in 2003. Using two mammalian epithelial cell lines (human Calu-3 and simian Vero E6), we found that both IFNs dose-dependently inhibit SARS-CoV-2. In contrast, SARS-CoV-1 was restricted only by IFN-alpha in these cell lines. SARS-CoV-2 generally exhibited a broader IFN sensitivity than SARS-CoV-1. Moreover, ruxolitinib, an inhibitor of IFN-triggered Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling, boosted SARS-CoV-2 replication in the IFN-competent Calu-3 cells. We conclude that SARS-CoV-2 is sensitive to exogenously added IFNs. This finding suggests that type I and especially the less adverse effect–prone type III IFN are good candidates for the management of COVID-19.
Ulrike Felgenhauer; Andreas Schoen; Hans Henrik Gad; Rune Hartmann; Andreas R. Schaubmar; Klaus Failing; Christian Drosten; Friedemann Weber. Inhibition of SARS–CoV-2 by type I and type III interferons. Journal of Biological Chemistry 2020, 295, 13958 -13964.
AMA StyleUlrike Felgenhauer, Andreas Schoen, Hans Henrik Gad, Rune Hartmann, Andreas R. Schaubmar, Klaus Failing, Christian Drosten, Friedemann Weber. Inhibition of SARS–CoV-2 by type I and type III interferons. Journal of Biological Chemistry. 2020; 295 (41):13958-13964.
Chicago/Turabian StyleUlrike Felgenhauer; Andreas Schoen; Hans Henrik Gad; Rune Hartmann; Andreas R. Schaubmar; Klaus Failing; Christian Drosten; Friedemann Weber. 2020. "Inhibition of SARS–CoV-2 by type I and type III interferons." Journal of Biological Chemistry 295, no. 41: 13958-13964.
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne orthonairovirus that has become a serious threat to the public health. CCHFV has a single-stranded, tripartite RNA genome composed of L, M, and S segments. Cleavage of the M polyprotein precursor generates the two envelope glycoproteins (GPs) as well as three secreted nonstructural proteins GP38 and GP85 or GP160, representing GP38 only or GP38 linked to a mucin-like protein (MLD), and a double-membrane-spanning protein called NSm. Here, we examined the relevance of each M-segment non-structural proteins in virus assembly, egress and infectivity using a well-established CCHFV virus-like-particle system (tc-VLP). Deletion of MLD protein had no impact on infectivity although it reduced by 60% incorporation of GPs into particles. Additional deletion of GP38 abolished production of infectious tc-VLPs. The loss of infectivity was associated with impaired Gc maturation and exclusion from the Golgi, showing that Gn is not sufficient to target CCHFV GPs to the site of assembly. Consistent with this, efficient complementation was achieved in cells expressing MLD-GP38 in trans with increased levels of preGc to Gc conversion, co-targeting to the Golgi, resulting in particle incorporation and restored infectivity. Contrastingly, a MLD-GP38 variant retained in the ER allowed preGc cleavage but failed to rescue miss-localization or infectivity. NSm deletion, conversely, did not affect trafficking of Gc but interfered with Gc processing, particle formation and secretion. NSm expression affected N-glycosylation of different viral proteins most likely due to increased speed of trafficking through the secretory pathway. This highlights a potential role of NSm in overcoming Golgi retention and facilitating CCHFV egress. Thus, deletions of GP38 or NSm demonstrate their important role on CCHFV particle production and infectivity. GP85 is an essential viral factor for preGc cleavage, trafficking and Gc incorporation into particles, whereas NSm protein is involved in CCHFV assembly and virion secretion. Orthonairoviruses, like the lethal Crimean-Congo hemorrhagic fever virus (CCHFV), encode secreted glycoproteins, such as GP38, in addition to virion envelope glycoproteins (Gn and Gc) that are processed by internal cleavage of the viral M segment encoded polyprotein. CCHFV MLD-GP38 proteins (GP160/GP85) also include an N-terminal domain encompassing a mucin-like protein that is released from GP38 by Furin. The protective effect of non-neutralizing monoclonal antibodies targeting GP38 against lethal CCHFV challenge previously highlighted the importance of GP38 in CCHFV replication. CCHFV also encodes a double-membrane-spanning protein (NSm) of unknown function, located between the Gn and Gc on the polyprotein. To investigate the roles of these so-called accessory proteins encoded by the CCHFV M-segment in virus formation and infectivity, we generated several M-segment deletion mutants and tested them in a CCHFV transcription-entry-competent virus-like particle (tc-VLP) system. Here, we demonstrate that GP38 is crucial for Gc biogenesis, interaction with Gn and trafficking to the Golgi, and that its deletion abrogates formation of infectious particles. We also show that NSm increases the rate of protein trafficking through the secretory pathway with altered N-glycosylation profiles that are advantageous for efficient virus release. These data advanced our understanding of GP38 and NSm roles and CCHFV-host interactions.
Natalia Freitas; Margot Enguehard; Solène Denolly; Camille Levy; Gregory Neveu; Solène Lerolle; Stephanie Devignot; Friedemann Weber; Eric Bergeron; Vincent Legros; François-Loïc Cosset. The interplays between Crimean-Congo hemorrhagic fever virus (CCHFV) M segment-encoded accessory proteins and structural proteins promote virus assembly and infectivity. PLOS Pathogens 2020, 16, e1008850 .
AMA StyleNatalia Freitas, Margot Enguehard, Solène Denolly, Camille Levy, Gregory Neveu, Solène Lerolle, Stephanie Devignot, Friedemann Weber, Eric Bergeron, Vincent Legros, François-Loïc Cosset. The interplays between Crimean-Congo hemorrhagic fever virus (CCHFV) M segment-encoded accessory proteins and structural proteins promote virus assembly and infectivity. PLOS Pathogens. 2020; 16 (9):e1008850.
Chicago/Turabian StyleNatalia Freitas; Margot Enguehard; Solène Denolly; Camille Levy; Gregory Neveu; Solène Lerolle; Stephanie Devignot; Friedemann Weber; Eric Bergeron; Vincent Legros; François-Loïc Cosset. 2020. "The interplays between Crimean-Congo hemorrhagic fever virus (CCHFV) M segment-encoded accessory proteins and structural proteins promote virus assembly and infectivity." PLOS Pathogens 16, no. 9: e1008850.
The RNA helicase RIG-I plays a key role in sensing pathogen-derived RNA. Double-stranded RNA structures bearing 5′-tri- or diphosphates are commonly referred to as activating RIG-I ligands. However, endogenous RNA fragments generated during viral infection via RNase L also activate RIG-I. Of note, RNase-digested RNA fragments bear a 5′-hydroxyl group and a 2′,3′-cyclic phosphate. How endogenous RNA fragments activate RIG-I despite the lack of 5′-phosphorylation has not been elucidated. Here we describe an endogenous RIG-I ligand (eRL) that is derived from the internal transcribed spacer 2 region (ITS2) of the 45S ribosomal RNA after partial RNase A digestion in vitro, RNase A protein transfection or RNase L activation. The immunostimulatory property of the eRL is dependent on 2′,3′-cyclic phosphate and its sequence is characterized by a G-quadruplex containing sequence motif mediating guanosine-5′-triphosphate (GTP) binding. In summary, RNase generated self-RNA fragments with 2′,3′-cyclic phosphate function as nucleotide-5′-triphosphate binding aptamers activating RIG-I.
Stephanie Jung; Tina Von Thülen; Ines Yang; Viktoria Laukemper; Benjamin Rupf; Harshavardhan Janga; Georgios-Dimitrios Panagiotidis; Andreas Schoen; Marina Nicolai; Leon N Schulte; Hannah-Lena Obermann; Friedemann Weber; Andreas Kaufmann; Stefan Bauer. A ribosomal RNA fragment with 2′,3′-cyclic phosphate and GTP-binding activity acts as RIG-I ligand. Nucleic Acids Research 2020, 48, 10397 -10412.
AMA StyleStephanie Jung, Tina Von Thülen, Ines Yang, Viktoria Laukemper, Benjamin Rupf, Harshavardhan Janga, Georgios-Dimitrios Panagiotidis, Andreas Schoen, Marina Nicolai, Leon N Schulte, Hannah-Lena Obermann, Friedemann Weber, Andreas Kaufmann, Stefan Bauer. A ribosomal RNA fragment with 2′,3′-cyclic phosphate and GTP-binding activity acts as RIG-I ligand. Nucleic Acids Research. 2020; 48 (18):10397-10412.
Chicago/Turabian StyleStephanie Jung; Tina Von Thülen; Ines Yang; Viktoria Laukemper; Benjamin Rupf; Harshavardhan Janga; Georgios-Dimitrios Panagiotidis; Andreas Schoen; Marina Nicolai; Leon N Schulte; Hannah-Lena Obermann; Friedemann Weber; Andreas Kaufmann; Stefan Bauer. 2020. "A ribosomal RNA fragment with 2′,3′-cyclic phosphate and GTP-binding activity acts as RIG-I ligand." Nucleic Acids Research 48, no. 18: 10397-10412.
Crimean-Congo Hemorrhagic Fever virus (CCHFV; family Nairoviridae) is an extremely pathogenic member of the Bunyavirales order. Previous studies have shown that the N-terminal domain of the CCHFV polymerase (L) contains an ovarian tumor-type protease (OTU) domain with the capability to remove both ubiquitin and ISG15 molecules from proteins. The approximately 200 amino acids-long OTU domain, if ectopically expressed, can interfere with both the induction of antiviral type I interferons (IFN) as well as the IFN-stimulated signaling. A OTU protease mutant (C40A), by contrast, was inactive in that respect. However, the effect of the OTU protease activity in the context of the full-length L protein (approximately 4000 amino acids) is only poorly characterized, and recombinant CCHFV with the C40A mutation could not be rescued. Here, we employed transcriptionally active virus-like particles (tc-VLPs) to investigate the interaction between the L-embedded OTU protease and the IFN system. Our data show a cis requirement of the OTU protease for optimal CCHFV polymerase activity in human HuH-7 cells. The L-embedded OTU did not influence IFN signaling, the sensitivity to IFN, or IFN induction. Moreover, the attenuation of OTU C40A-mutated L could not be relieved by inactivating the IFN response, but after overexpression of conjugation-competent ISG15 the polymerase activity recovered to wild-type levels. Consequently, ISG15 was used to produce OTU-deficient tc-VLPs, a potential vaccine candidate. Our data thus indicate that in the context of full-length L the OTU domain is important for the regulation of CCHFV polymerase by ISG15. Tick-transmitted Crimean-Congo Hemorrhagic Fever virus (CCHFV) causes serious and potentially fatal disease in humans. The CCHFV polymerase possesses an N-terminal ovarian tumor-type protease (OTU) domain that cleaves ubiquitin and ISG15 modifiers from target proteins. Previous studies demonstrated that the ectopically expressed OTU domain can inhibit antiviral type I interferon responses. Hence, cleavage-negative OTU mutants of virus or transcriptionally active virus-like particles (tc-VLPs) are expected to exhibit elevated immunogenicity and would be candidates for a live vaccine. For unknown reasons, however, recombinant virus with just the OTU minus mutation cannot be generated. Using tc-VLPs, we show that in human HuH-7 cells the activity of the OTU minus polymerase is reduced by more than 80%. Curiously, the attenuation could not be compensated by inactivating the interferon system or by adding the OTU domain in trans. However, a complete reversion of the OTU minus phenotype was achieved by transcomplementation with ISG15, whereas the other OTU substrate, ubiquitin, had no such positive influence. Our data thus indicate a role of cis OTU in CCHFV polymerase regulation that is independent of an anti-interferon activity but connected to ISG15. Transcomplementation with ISG15 may be a means to rescue the OTU minus CCHV vaccine candidate.
Stephanie Devignot; Thilo Kromer; Ali Mirazimi; Friedemann Weber. ISG15 overexpression compensates the defect of Crimean-Congo hemorrhagic fever virus polymerase bearing a protease-inactive ovarian tumor domain. PLOS Neglected Tropical Diseases 2020, 14, e0008610 .
AMA StyleStephanie Devignot, Thilo Kromer, Ali Mirazimi, Friedemann Weber. ISG15 overexpression compensates the defect of Crimean-Congo hemorrhagic fever virus polymerase bearing a protease-inactive ovarian tumor domain. PLOS Neglected Tropical Diseases. 2020; 14 (9):e0008610.
Chicago/Turabian StyleStephanie Devignot; Thilo Kromer; Ali Mirazimi; Friedemann Weber. 2020. "ISG15 overexpression compensates the defect of Crimean-Congo hemorrhagic fever virus polymerase bearing a protease-inactive ovarian tumor domain." PLOS Neglected Tropical Diseases 14, no. 9: e0008610.
Gustaf Ahlén; Lars Frelin; Negin Nikouyan; Friedemann Weber; Urban Höglund; Olivia Larsson; Marie Westman; Ola Tuvesson; Eva-Karin Gidlund; Matteo Cadossi; Sofia Appelberg; Ali Mirazimi; Matti Sällberg. The SARS-CoV-2 N Protein Is a Good Component in a Vaccine. Journal of Virology 2020, 94, 1 .
AMA StyleGustaf Ahlén, Lars Frelin, Negin Nikouyan, Friedemann Weber, Urban Höglund, Olivia Larsson, Marie Westman, Ola Tuvesson, Eva-Karin Gidlund, Matteo Cadossi, Sofia Appelberg, Ali Mirazimi, Matti Sällberg. The SARS-CoV-2 N Protein Is a Good Component in a Vaccine. Journal of Virology. 2020; 94 (18):1.
Chicago/Turabian StyleGustaf Ahlén; Lars Frelin; Negin Nikouyan; Friedemann Weber; Urban Höglund; Olivia Larsson; Marie Westman; Ola Tuvesson; Eva-Karin Gidlund; Matteo Cadossi; Sofia Appelberg; Ali Mirazimi; Matti Sällberg. 2020. "The SARS-CoV-2 N Protein Is a Good Component in a Vaccine." Journal of Virology 94, no. 18: 1.
RNA-activated protein kinase (PKR) is one of the most powerful antiviral defense factors of the mammalian host. PKR acts by phosphorylating mRNA translation initiation factor eIF2α, thereby converting it from a cofactor to an inhibitor of mRNA translation that strongly binds to initiation factor eIF2B. To sustain synthesis of their proteins, viruses are known to counteract this on the level of PKR or eIF2α or by circumventing initiation factor-dependent translation altogether. Here, we report a different PKR escape strategy executed by sandfly fever Sicilian virus (SFSV), a member of the increasingly important group of phleboviruses. We found that the nonstructural protein NSs of SFSV binds to eIF2B and protects it from inactivation by PKR-generated phospho-eIF2α. Protein synthesis is hence maintained and the virus can replicate despite ongoing full-fledged PKR signaling in the infected cells. Thus, SFSV has evolved a unique strategy to escape the powerful antiviral PKR.
Jennifer Deborah Wuerth; Matthias Habjan; Markus Kainulainen; Besim Berisha; Damien Bertheloot; Giulio Superti-Furga; Andreas Pichlmair; Friedemann Weber. eIF2B as a Target for Viral Evasion of PKR-Mediated Translation Inhibition. mBio 2020, 11, 1 .
AMA StyleJennifer Deborah Wuerth, Matthias Habjan, Markus Kainulainen, Besim Berisha, Damien Bertheloot, Giulio Superti-Furga, Andreas Pichlmair, Friedemann Weber. eIF2B as a Target for Viral Evasion of PKR-Mediated Translation Inhibition. mBio. 2020; 11 (4):1.
Chicago/Turabian StyleJennifer Deborah Wuerth; Matthias Habjan; Markus Kainulainen; Besim Berisha; Damien Bertheloot; Giulio Superti-Furga; Andreas Pichlmair; Friedemann Weber. 2020. "eIF2B as a Target for Viral Evasion of PKR-Mediated Translation Inhibition." mBio 11, no. 4: 1.
The global outbreak of SARS-CoV-2 necessitates the rapid development of new therapies against COVID-19 infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Using artificial neural network analysis we classified these 200 drugs into 9 distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (130) and immune response (70). A subset of drugs implicated in viral replication were tested in cellular assays and two (proguanil and sulfasalazine) were shown to inhibit replication. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials.
Namshik Han; Woochang Hwang; Kostas Tzelepis; Patrick Schmerer; Eliza Yankova; Meabh MacMahon; Winnie Lei; Nicholas M Katritsis; Anika Liu; Alison Schuldt; Rebecca Harris; Kathryn Chapman; Frank McCaughan; Friedemann Weber; Tony Kouzarides. Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies. 2020, 1 .
AMA StyleNamshik Han, Woochang Hwang, Kostas Tzelepis, Patrick Schmerer, Eliza Yankova, Meabh MacMahon, Winnie Lei, Nicholas M Katritsis, Anika Liu, Alison Schuldt, Rebecca Harris, Kathryn Chapman, Frank McCaughan, Friedemann Weber, Tony Kouzarides. Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies. . 2020; ():1.
Chicago/Turabian StyleNamshik Han; Woochang Hwang; Kostas Tzelepis; Patrick Schmerer; Eliza Yankova; Meabh MacMahon; Winnie Lei; Nicholas M Katritsis; Anika Liu; Alison Schuldt; Rebecca Harris; Kathryn Chapman; Frank McCaughan; Friedemann Weber; Tony Kouzarides. 2020. "Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies." , no. : 1.
SUMMARYThe Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies.
Omer Ziv; Jonathan Price; Lyudmila Shalamova; Tsveta Kamenova; Ian Goodfellow; Friedemann Weber; Eric A. Miska. The short- and long-range RNA-RNA Interactome of SARS-CoV-2. 2020, 1 .
AMA StyleOmer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber, Eric A. Miska. The short- and long-range RNA-RNA Interactome of SARS-CoV-2. . 2020; ():1.
Chicago/Turabian StyleOmer Ziv; Jonathan Price; Lyudmila Shalamova; Tsveta Kamenova; Ian Goodfellow; Friedemann Weber; Eric A. Miska. 2020. "The short- and long-range RNA-RNA Interactome of SARS-CoV-2." , no. : 1.
The non-structural protein NSs is the main virulence factor of Rift Valley fever virus, a major zoonotic pathogen in Africa. NSs forms large aggregates in the nucleus and impairs induction of the antiviral type I IFN system by several mechanisms, including degradation of subunit p62 of the general RNA polymerase II transcription factor TFIIH. Here, we show that depletion of the nuclear pore protein Nup98 affects the nuclear import of NSs. Nonetheless, NSs was still able to degrade TFIIH-p62 under these conditions. Depletion of Nup98, however, had a negative effect on Rift Valley fever virus multiplication. Our data thus indicate that NSs utilizes Nup98 for import into the nucleus, but also plays a general role in the viral replication cycle.
Simone Lau; Friedemann Weber. Nuclear pore protein Nup98 is involved in replication of Rift Valley fever virus and nuclear import of virulence factor NSs. Journal of General Virology 2020, 101, 712 -716.
AMA StyleSimone Lau, Friedemann Weber. Nuclear pore protein Nup98 is involved in replication of Rift Valley fever virus and nuclear import of virulence factor NSs. Journal of General Virology. 2020; 101 (7):712-716.
Chicago/Turabian StyleSimone Lau; Friedemann Weber. 2020. "Nuclear pore protein Nup98 is involved in replication of Rift Valley fever virus and nuclear import of virulence factor NSs." Journal of General Virology 101, no. 7: 712-716.
The mosquito-borne La Crosse virus (LACV; genus Orthobunyavirus , family Peribunyaviridae , order Bunyavirales ) is prevalent in the United States and can cause severe childhood meningoencephalitis. Its main virulence factor, the nonstructural protein NSs, is a strong inhibitor of the antiviral type I interferon (IFN) system. NSs acts by imposing a global host mRNA synthesis shutoff, mediated by NSs-driven proteasomal degradation of the RPB1 subunit of RNA polymerase II. Here, we show that RPB1 degradation commences as early as 1 h postinfection, and identify the E3 ubiquitin ligase subunit Elongin C (and its binding partners Elongins A and B) as an NSs cofactor involved in RPB1 degradation and in suppression of global as well as IFN-related mRNA synthesis.
Andreas Schoen; Simone Lau; Paul Verbruggen; Friedemann Weber. Elongin C Contributes to RNA Polymerase II Degradation by the Interferon Antagonist NSs of La Crosse Orthobunyavirus. Journal of Virology 2020, 94, 1 .
AMA StyleAndreas Schoen, Simone Lau, Paul Verbruggen, Friedemann Weber. Elongin C Contributes to RNA Polymerase II Degradation by the Interferon Antagonist NSs of La Crosse Orthobunyavirus. Journal of Virology. 2020; 94 (7):1.
Chicago/Turabian StyleAndreas Schoen; Simone Lau; Paul Verbruggen; Friedemann Weber. 2020. "Elongin C Contributes to RNA Polymerase II Degradation by the Interferon Antagonist NSs of La Crosse Orthobunyavirus." Journal of Virology 94, no. 7: 1.