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1.
PLoS Biol ; 20(9): e3001787, 2022 09.
Article in English | MEDLINE | ID: covidwho-2029766

ABSTRACT

Writing in PLOS Biology, Ching and colleagues show that ACE2-decorated exosomes are deployed as natural inhibitory decoys against SARS-CoV-2. High decoy levels correlate with improved patient outcomes, suggesting they directly help COVID-19 recovery and supporting the concept of successful future decoy-based therapies.


Subject(s)
COVID-19 , Exosomes , Angiotensin-Converting Enzyme 2 , Cell Line , Humans , SARS-CoV-2
2.
PLoS Biol ; 20(7): e3001709, 2022 07.
Article in English | MEDLINE | ID: covidwho-1923649

ABSTRACT

Autoantibodies neutralizing the antiviral action of type I interferons (IFNs) have been associated with predisposition to severe Coronavirus Disease 2019 (COVID-19). Here, we screened for such autoantibodies in 103 critically ill COVID-19 patients in a tertiary intensive care unit (ICU) in Switzerland. Eleven patients (10.7%), but no healthy donors, had neutralizing anti-IFNα or anti-IFNα/anti-IFNω IgG in plasma/serum, but anti-IFN IgM or IgA was rare. One patient had non-neutralizing anti-IFNα IgG. Strikingly, all patients with plasma anti-IFNα IgG also had anti-IFNα IgG in tracheobronchial secretions, identifying these autoantibodies at anatomical sites relevant for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Longitudinal analyses revealed patient heterogeneity in terms of increasing, decreasing, or stable anti-IFN IgG levels throughout the length of hospitalization. Notably, presence of anti-IFN autoantibodies in this critically ill COVID-19 cohort appeared to predict herpesvirus disease (caused by herpes simplex viruses types 1 and 2 (HSV-1/-2) and/or cytomegalovirus (CMV)), which has been linked to worse clinical outcomes. Indeed, all 7 tested COVID-19 patients with anti-IFN IgG in our cohort (100%) suffered from one or more herpesviruses, and analysis revealed that these patients were more likely to experience CMV than COVID-19 patients without anti-IFN autoantibodies, even when adjusting for age, gender, and systemic steroid treatment (odds ratio (OR) 7.28, 95% confidence interval (CI) 1.14 to 46.31, p = 0.036). As the IFN system deficiency caused by neutralizing anti-IFN autoantibodies likely directly and indirectly exacerbates the likelihood of latent herpesvirus reactivations in critically ill patients, early diagnosis of anti-IFN IgG could be rapidly used to inform risk-group stratification and treatment options. Trial Registration: ClinicalTrials.gov Identifier: NCT04410263.


Subject(s)
COVID-19 , Cytomegalovirus Infections , Herpes Simplex , Interferon Type I , Autoantibodies , Critical Illness , Humans , Immunoglobulin G , SARS-CoV-2
3.
ACS Infect Dis ; 8(7): 1265-1279, 2022 07 08.
Article in English | MEDLINE | ID: covidwho-1908084

ABSTRACT

There is a pressing need for host-directed therapeutics that elicit broad-spectrum antiviral activities to potentially address current and future viral pandemics. Apratoxin S4 (Apra S4) is a potent Sec61 inhibitor that prevents cotranslational translocation of secretory proteins into the endoplasmic reticulum (ER), leading to anticancer and antiangiogenic activity both in vitro and in vivo. Since Sec61 has been shown to be an essential host factor for viral proteostasis, we tested Apra S4 in cellular models of viral infection, including SARS-CoV-2, influenza A virus, and flaviviruses (Zika, West Nile, and Dengue virus). Apra S4 inhibited viral replication in a concentration-dependent manner and had high potency particularly against SARS-CoV-2 and influenza A virus, with subnanomolar activity in human cells. Characterization studies focused on SARS-CoV-2 revealed that Apra S4 impacted a post-entry stage of the viral life-cycle. Transmission electron microscopy revealed that Apra S4 blocked formation of stacked double-membrane vesicles, the sites of viral replication. Apra S4 reduced dsRNA formation and prevented viral protein production and trafficking of secretory proteins, especially the spike protein. Given the potent and broad-spectrum activity of Apra S4, further preclinical evaluation of Apra S4 and other Sec61 inhibitors as antivirals is warranted.


Subject(s)
COVID-19 , Influenza A virus , Zika Virus Infection , Zika Virus , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Depsipeptides , Humans , Pandemics , SARS-CoV-2 , Zika Virus Infection/drug therapy
4.
Cell Rep ; 38(12): 110549, 2022 03 22.
Article in English | MEDLINE | ID: covidwho-1757198

ABSTRACT

Host interferons (IFNs) powerfully restrict viruses through the action of several hundred IFN-stimulated gene (ISG) products, many of which remain uncharacterized. Here, using RNAi screening, we identify several ISG restriction factors with previously undescribed contributions to IFN-mediated defense. Notably, RABGAP1L, a Tre2/Bub2/Cdc16 (TBC)-domain-containing protein involved in regulation of small membrane-bound GTPases, robustly potentiates IFN action against influenza A viruses (IAVs). Functional studies reveal that the catalytically active TBC domain of RABGAP1L promotes antiviral activity, and the RABGAP1L proximal interactome uncovered its association with proteins involved in endosomal sorting, maturation, and trafficking. In this regard, RABGAP1L overexpression is sufficient to disrupt endosomal function during IAV infection and restricts an early post-attachment, but pre-fusion, stage of IAV cell entry. Other RNA viruses that enter cells primarily via endocytosis are also impaired by RABGAP1L, while entry promiscuous SARS-CoV-2 is resistant. Our data highlight virus endocytosis as a key target for host defenses.


Subject(s)
Antiviral Agents , COVID-19 , Cell Line , Endocytosis , Humans , SARS-CoV-2
5.
Curr Opin Virol ; 52: 211-216, 2022 02.
Article in English | MEDLINE | ID: covidwho-1588013

ABSTRACT

Host silencing of transposable elements (TEs) is critical to prevent genome damage and inappropriate inflammation. However, new evidence suggests that a virus-infected host may re-activate TEs and co-opt them for antiviral defense. RNA-Seq and specialized bioinformatics have revealed the diversity of virus infections that induce TEs. Furthermore, studies with influenza virus have uncovered how infection-triggered changes to the SUMOylation of TRIM28, an epigenetic co-repressor, lead to TE de-repression. Importantly, there is a growing appreciation of how de-repressed TEs stimulate antiviral gene expression, either via cis-acting enhancer functions or via their recognition as viral mimetics by innate immune nucleic acid sensors (e.g. RIG-I, mda-5 and cGAS). Understanding how viruses trigger, and counteract, TE-based antiviral immunity should provide insights into pathogenic mechanisms.


Subject(s)
DNA Transposable Elements , Viruses , Antiviral Agents , Immunity, Innate , Viruses/genetics
6.
Elife ; 102021 05 18.
Article in English | MEDLINE | ID: covidwho-1389779

ABSTRACT

When culturing SARS-CoV-2 in the laboratory it is vital to avoid deletions in the gene for the spike protein that could affect the interpretation of experiments.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Animals , Chlorocebus aethiops , Humans , SARS-CoV-2
7.
J Gen Virol ; 102(7)2021 07.
Article in English | MEDLINE | ID: covidwho-1328965

ABSTRACT

Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3 CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel in vitro fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3 CL main protease inhibitor in vitro (IC50 value of 29 µM) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3 CL main protease inhibitor in vitro, but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , COVID-19/drug therapy , COVID-19/virology , Chymases/antagonists & inhibitors , Phenylurea Compounds/pharmacology , Quinolines/pharmacology , SARS-CoV-2/drug effects , Adenosine Monophosphate/pharmacology , Alanine/pharmacology , Animals , Antiviral Agents/pharmacology , COVID-19/enzymology , Cells, Cultured , Drug Evaluation, Preclinical , Humans , Molecular Docking Simulation , Protein Kinase Inhibitors/pharmacology , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity
8.
PLoS Pathog ; 17(6): e1009644, 2021 06.
Article in English | MEDLINE | ID: covidwho-1278205

ABSTRACT

Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and translational response to cellular infection by murine hepatitis virus (MHV), often used as a model for the Betacoronavirus genus to which the recently emerged SARS-CoV-2 also belongs. We found the UPR to be amongst the most significantly up-regulated pathways in response to MHV infection. To confirm and extend these observations, we show experimentally the induction of all three branches of the UPR in both MHV- and SARS-CoV-2-infected cells. Over-expression of the SARS-CoV-2 ORF8 or S proteins alone is itself sufficient to induce the UPR. Remarkably, pharmacological inhibition of the UPR greatly reduced the replication of both MHV and SARS-CoV-2, revealing the importance of this pathway for successful coronavirus replication. This was particularly striking when both IRE1α and ATF6 branches of the UPR were inhibited, reducing SARS-CoV-2 virion release (~1,000-fold). Together, these data highlight the UPR as a promising antiviral target to combat coronavirus infection.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/drug therapy , Murine hepatitis virus/drug effects , Unfolded Protein Response/drug effects , Activating Transcription Factor 6/metabolism , Animals , Antiviral Agents/therapeutic use , Cell Line , Chlorocebus aethiops , Drug Delivery Systems , Endoribonucleases/metabolism , HEK293 Cells , Humans , Mice , RNA-Seq , Vero Cells , Viral Proteins/metabolism , Virus Replication/drug effects
9.
Nat Nanotechnol ; 16(8): 918-925, 2021 08.
Article in English | MEDLINE | ID: covidwho-1260944

ABSTRACT

Minimizing the spread of viruses in the environment is the first defence line when fighting outbreaks and pandemics, but the current COVID-19 pandemic demonstrates how difficult this is on a global scale, particularly in a sustainable and environmentally friendly way. Here we introduce and develop a sustainable and biodegradable antiviral filtration membrane composed of amyloid nanofibrils made from food-grade milk proteins and iron oxyhydroxide nanoparticles synthesized in situ from iron salts by simple pH tuning. Thus, all the membrane components are made of environmentally friendly, non-toxic and widely available materials. The membrane has outstanding efficacy against a broad range of viruses, which include enveloped, non-enveloped, airborne and waterborne viruses, such as SARS-CoV-2, H1N1 (the influenza A virus strain responsible for the swine flu pandemic in 2009) and enterovirus 71 (a non-enveloped virus resistant to harsh conditions, such as highly acidic pH), which highlights a possible role in fighting the current and future viral outbreaks and pandemics.


Subject(s)
Amyloid/chemistry , Antiviral Agents/pharmacology , Ferric Compounds/chemistry , Micropore Filters , Nanoparticles/chemistry , Amyloid/pharmacology , Antiviral Agents/chemistry , Ferric Compounds/pharmacology , Humans , Lactoglobulins/chemistry , Micropore Filters/virology , Virus Inactivation/drug effects , Viruses/classification , Viruses/drug effects , Viruses/isolation & purification , Water Purification
10.
PLoS Biol ; 19(3): e3001006, 2021 03.
Article in English | MEDLINE | ID: covidwho-1148237

ABSTRACT

Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 [COVID-19]) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.


Subject(s)
SARS-CoV-2/physiology , Virus Replication/physiology , Amino Acid Substitution , Animals , Base Sequence , Bronchi/pathology , COVID-19/diagnosis , COVID-19/virology , Cells, Cultured , Chlorocebus aethiops , Epithelial Cells/pathology , Epithelial Cells/virology , Furin/metabolism , Host-Pathogen Interactions , Humans , SARS-CoV-2/isolation & purification , Vero Cells
11.
Trends Microbiol ; 29(11): 973-982, 2021 11.
Article in English | MEDLINE | ID: covidwho-1142259

ABSTRACT

Pandemics are caused by novel pathogens to which pre-existing antibody immunity is lacking. Under these circumstances, the body must rely on innate interferon-mediated defenses to limit pathogen replication and allow development of critical humoral protection. Here, we highlight studies on disease susceptibility during H1N1 influenza and COVID-19 (SARS-CoV-2) pandemics. An emerging concept is that genetic and non-genetic deficiencies in interferon system components lead to uncontrolled virus replication and severe illness in a subset of people. Intriguingly, new findings suggest that individuals with autoantibodies neutralizing the antiviral function of interferon are at increased risk of severe COVID-19. We discuss key questions surrounding how such autoantibodies develop and function, as well as the general implications of diagnosing interferon deficiencies for personalized therapies.


Subject(s)
Disease Resistance , Host-Pathogen Interactions , Interferons/metabolism , Virus Diseases/etiology , Virus Diseases/metabolism , Alleles , Animals , Antibodies, Neutralizing/immunology , Autoantibodies/immunology , Autoimmunity , Disease Progression , Disease Resistance/immunology , Disease Susceptibility , Genetic Predisposition to Disease , Host-Pathogen Interactions/immunology , Humans , Interferons/antagonists & inhibitors , Interferons/immunology , Loss of Function Mutation , Polymorphism, Single Nucleotide , Severity of Illness Index , Virus Diseases/diagnosis , Virus Diseases/epidemiology
12.
mBio ; 11(5)2020 09 10.
Article in English | MEDLINE | ID: covidwho-760223

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is a recently emerged respiratory coronavirus that has infected >23 million people worldwide with >800,000 deaths. Few COVID-19 therapeutics are available, and the basis for severe infections is poorly understood. Here, we investigated properties of type I (ß), II (γ), and III (λ1) interferons (IFNs), potent immune cytokines that are normally produced during infection and that upregulate IFN-stimulated gene (ISG) effectors to limit virus replication. IFNs are already in clinical trials to treat COVID-19. However, recent studies highlight the potential for IFNs to enhance expression of host angiotensin-converting enzyme 2 (ACE2), suggesting that IFN therapy or natural coinfections could exacerbate COVID-19 by upregulating this critical virus entry receptor. Using a cell line model, we found that beta interferon (IFN-ß) strongly upregulated expression of canonical antiviral ISGs, as well as ACE2 at the mRNA and cell surface protein levels. Strikingly, IFN-λ1 upregulated antiviral ISGs, but ACE2 mRNA was only marginally elevated and did not lead to detectably increased ACE2 protein at the cell surface. IFN-γ induced the weakest ISG response but clearly enhanced surface expression of ACE2. Importantly, all IFN types inhibited SARS-CoV-2 replication in a dose-dependent manner, and IFN-ß and IFN-λ1 exhibited potent antiviral activity in primary human bronchial epithelial cells. Our data imply that type-specific mechanisms or kinetics shape IFN-enhanced ACE2 transcript and cell surface levels but that the antiviral action of IFNs against SARS-CoV-2 counterbalances any proviral effects of ACE2 induction. These insights should aid in evaluating the benefits of specific IFNs, particularly IFN-λ, as repurposed therapeutics.IMPORTANCE Repurposing existing, clinically approved, antiviral drugs as COVID-19 therapeutics is a rapid way to help combat the SARS-CoV-2 pandemic. Interferons (IFNs) usually form part of the body's natural innate immune defenses against viruses, and they have been used with partial success to treat previous new viral threats, such as HIV, hepatitis C virus, and Ebola virus. Nevertheless, IFNs can have undesirable side effects, and recent reports indicate that IFNs upregulate the expression of host ACE2 (a critical entry receptor for SARS-CoV-2), raising the possibility that IFN treatments could exacerbate COVID-19. Here, we studied the antiviral- and ACE2-inducing properties of different IFN types in both a human lung cell line model and primary human bronchial epithelial cells. We observed differences between IFNs with respect to their induction of antiviral genes and abilities to enhance the cell surface expression of ACE2. Nevertheless, all the IFNs limited SARS-CoV-2 replication, suggesting that their antiviral actions can counterbalance increased ACE2.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus Infections/drug therapy , Interferon Type I/pharmacology , Interferon-gamma/pharmacology , Interferons/pharmacology , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/drug therapy , Aged , Angiotensin-Converting Enzyme 2 , Animals , Betacoronavirus/immunology , COVID-19 , Cell Line , Chlorocebus aethiops , Female , Humans , Immunotherapy/methods , Interferon Type I/adverse effects , Interferon-gamma/adverse effects , Interferons/adverse effects , Pandemics , Peptidyl-Dipeptidase A/genetics , RNA, Messenger/biosynthesis , RNA, Messenger/genetics , Receptors, Virus/metabolism , Respiratory Mucosa/cytology , Respiratory Mucosa/virology , SARS-CoV-2 , Up-Regulation/drug effects , Vero Cells , Virus Replication/drug effects
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