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Innate Immune Sensing of Viruses and Viral Evasion
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Innate Immune Sensing of Viruses and Viral Evasion

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viral Immunology, Vaccines, and Antivirals".

Deadline for manuscript submissions: closed (15 June 2020) | Viewed by 85580

Special Issue Editors

Dr. Renate König

E-Mail Website
Guest Editor
Paul-Ehrlich-Institut, Langen, Germany
Interests: virus–host interaction; innate immune responses
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Carsten Münk

E-Mail Website
Guest Editor
Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
Interests: HIV; retroviruses; restriction factors; innate sensing; antiviral deaminases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Innate immunity represents the first line of defense against viruses. The success of the immediate response relies on the recognition of invariant features encoded by viruses termed pathogen-associated molecular patterns (PAMPs) by specialized sensors called pattern recognition receptors (PRRs). The consequence of this surveillance network and the downstream pathway activation is the secretion of cytokines, type I interferons (IFNs), and the expression of interferon-stimulated genes. Viruses have evolved multiple ways to dampen the host IFN response by interfering, disrupting, or evading specific host regulators, both up- and downstream of IFN induction. Recent discoveries have shown that the sensing pathways are highly regulated by post-translational modifications and co-regulating proteins. Moreover, emerging evidence indicates that there exists crosstalk between the sensing pathways. Furthermore, unexpected pathways seem to play important roles in detecting and responding to viral infections. This Special Issue will cover recent discoveries in the regulation of innate immune pathways during viral infections, novel mechanisms of exploitation, or the manipulation of regulators of the pathways by viruses and novel cellular network complexes that play a role in sensing viruses.

Dr. Renate König
Dr. Carsten Münk
Guest Editors

Manuscript Submission Information

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Keywords

  • innate sensing
  • viral counteraction
  • pattern-recognition receptor complex
  • regulation of innate pathways
  • innate immune response
  • virus–host interaction

Published Papers (18 papers)

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Editorial

Jump to: Research, Review

3 pages, 169 KiB  
Editorial
Special Issue: “Innate Immune Sensing of Viruses and Viral Evasion”
by Renate König and Carsten Münk
Viruses 2021, 13(4), 567; https://doi.org/10.3390/v13040567 - 26 Mar 2021
Cited by 1 | Viewed by 1457
Abstract
In this Special Issue, a wide variety of original and review articles provide a timely overview of how viruses are recognized by and evade from cellular innate immunity, which represents the first line of defense against viruses [...] Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)

Research

Jump to: Editorial, Review

20 pages, 1794 KiB  
Article
TNF Signaling Dictates Myeloid and Non-Myeloid Cell Crosstalk to Execute MCMV-Induced Extrinsic Apoptosis
by Pratyusha Mandal, A. Louise McCormick and Edward S. Mocarski
Viruses 2020, 12(11), 1221; https://doi.org/10.3390/v12111221 - 28 Oct 2020
Cited by 7 | Viewed by 3146
Abstract
Cytomegaloviruses all encode the viral inhibitor of caspase-8-induced apoptosis (vICA). After binding to this initiator caspase, vICA blocks caspase-8 proteolytic activity and ability to activate caspase-3 and/or caspase-7. In this manner, vICA has long been known to prevent apoptosis triggered via tumor necrosis [...] Read more.
Cytomegaloviruses all encode the viral inhibitor of caspase-8-induced apoptosis (vICA). After binding to this initiator caspase, vICA blocks caspase-8 proteolytic activity and ability to activate caspase-3 and/or caspase-7. In this manner, vICA has long been known to prevent apoptosis triggered via tumor necrosis factor (TNF) family death receptor-dependent extrinsic signaling. Here, we employ fully wild-type murine cytomegalovirus (MCMV) and vICA-deficient MCMV (∆M36) to investigate the contribution of TNF signaling to apoptosis during infection of different cell types. ∆M36 shows the expected ability to kill mouse splenic hematopoietic cells, bone marrow-derived macrophages (BMDM), and dendritic cells (BMDC). Antibody blockade or genetic elimination of TNF protects myeloid cells from death, and caspase-8 activation accompanies cell death. Interferons, necroptosis, and pyroptotic gasdermin D (GSDMD) do not contribute to myeloid cell death. Human and murine fibroblasts or murine endothelial cells (SVEC4-10) normally insensitive to TNF become sensitized to ∆M36-induced apoptosis when treated with TNF or TNF-containing BMDM-conditioned medium. We demonstrate that myeloid cells are the natural source of TNF that triggers apoptosis in either myeloid (autocrine) or non-myeloid cells (paracrine) during ∆M36 infection of mice. Caspase-8 suppression by vICA emerges as key to subverting innate immune elimination of a wide variety of infected cell types. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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19 pages, 2992 KiB  
Article
MAVS Genetic Variation Is Associated with Decreased HIV-1 Replication In Vitro and Reduced CD4+ T Cell Infection in HIV-1-Infected Individuals
by Melissa Stunnenberg, Lisa van Pul, Joris K. Sprokholt, Karel A. van Dort, Sonja I. Gringhuis, Teunis B. H. Geijtenbeek and Neeltje A. Kootstra
Viruses 2020, 12(7), 764; https://doi.org/10.3390/v12070764 - 16 Jul 2020
Cited by 2 | Viewed by 3176
Abstract
The mitochondrial antiviral protein MAVS is a key player in the induction of antiviral responses; however, human immunodeficiency virus 1 (HIV-1) is able to suppress these responses. Two linked single nucleotide polymorphisms (SNPs) in the MAVS gene render MAVS insensitive to HIV-1-dependent suppression, [...] Read more.
The mitochondrial antiviral protein MAVS is a key player in the induction of antiviral responses; however, human immunodeficiency virus 1 (HIV-1) is able to suppress these responses. Two linked single nucleotide polymorphisms (SNPs) in the MAVS gene render MAVS insensitive to HIV-1-dependent suppression, and have been shown to be associated with a lower viral load at set point and delayed increase of viral load during disease progression. Here, we studied the underlying mechanisms involved in the control of viral replication in individuals homozygous for this MAVS genotype. We observed that individuals with the MAVS minor genotype had more stable total CD4+ T cell counts during a 7-year follow up and had lower cell-associated proviral DNA loads. Genetic variation in MAVS did not affect immune activation levels; however, a significantly lower percentage of naïve CD4+ but not CD8+ T cells was observed in the MAVS minor genotype. In vitro HIV-1 infection of peripheral blood mononuclear cells (PBMCs) from healthy donors with the MAVS minor genotype resulted in decreased viral replication. Although the precise underlying mechanism remains unclear, our data suggest that the protective effect of the MAVS minor genotype may be exerted by the initiation of local innate responses affecting viral replication and CD4+ T cell susceptibility. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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21 pages, 4036 KiB  
Article
Persistent Innate Immune Stimulation Results in IRF3-Mediated but Caspase-Independent Cytostasis
by Christian Urban, Hendrik Welsch, Katharina Heine, Sandra Wüst, Darya A. Haas, Christopher Dächert, Aparna Pandey, Andreas Pichlmair and Marco Binder
Viruses 2020, 12(6), 635; https://doi.org/10.3390/v12060635 - 11 Jun 2020
Cited by 7 | Viewed by 4042
Abstract
Persistent virus infection continuously produces non-self nucleic acids that activate cell-intrinsic immune responses. However, the antiviral defense evolved as a transient, acute phase response and the effects of persistently ongoing stimulation onto cellular homeostasis are not well understood. To study the consequences of [...] Read more.
Persistent virus infection continuously produces non-self nucleic acids that activate cell-intrinsic immune responses. However, the antiviral defense evolved as a transient, acute phase response and the effects of persistently ongoing stimulation onto cellular homeostasis are not well understood. To study the consequences of long-term innate immune activation, we expressed the NS5B polymerase of Hepatitis C virus (HCV), which in absence of viral genomes continuously produces immune-stimulatory RNAs. Surprisingly, within 3 weeks, NS5B expression declined and the innate immune response ceased. Proteomics and functional analyses indicated a reduced proliferation of those cells most strongly stimulated, which was independent of interferon signaling but required mitochondrial antiviral signaling protein (MAVS) and interferon regulatory factor 3 (IRF3). Depletion of MAVS or IRF3, or overexpression of the MAVS-inactivating HCV NS3/4A protease not only blocked interferon responses but also restored cell growth in NS5B expressing cells. However, pan-caspase inhibition could not rescue the NS5B-induced cytostasis. Our results underline an active counter selection of cells with prolonged innate immune activation, which likely constitutes a cellular strategy to prevent persistent virus infections. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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21 pages, 2733 KiB  
Article
Hepatitis B Virus DNA is a Substrate for the cGAS/STING Pathway but is not Sensed in Infected Hepatocytes
by Lise Lauterbach-Rivière, Maïwenn Bergez, Saskia Mönch, Bingqian Qu, Maximilian Riess, Florian W. R. Vondran, Juliane Liese, Veit Hornung, Stephan Urban and Renate König
Viruses 2020, 12(6), 592; https://doi.org/10.3390/v12060592 - 29 May 2020
Cited by 39 | Viewed by 5098
Abstract
Hepatitis B virus (HBV) chronic infection is a critical risk factor for hepatocellular carcinoma. The innate immune response to HBV infection is a matter of debate. In particular, viral escape mechanisms are poorly understood. Our study reveals that HBV RNAs are not immunostimulatory [...] Read more.
Hepatitis B virus (HBV) chronic infection is a critical risk factor for hepatocellular carcinoma. The innate immune response to HBV infection is a matter of debate. In particular, viral escape mechanisms are poorly understood. Our study reveals that HBV RNAs are not immunostimulatory in immunocompetent myeloid cells. In contrast, HBV DNA from viral particles and DNA replication intermediates are immunostimulatory and sensed by cyclic GMP-AMP Synthase (cGAS) and Stimulator of Interferon Genes (STING). We show that primary human hepatocytes express DNA sensors to reduced levels compared to myeloid cells. Nevertheless, hepatocytes can respond to HBV relaxed-circular DNA (rcDNA), when transfected in sufficient amounts, but not to HBV infection. Finally, our data suggest that HBV infection does not actively inhibit the DNA-sensing pathway. In conclusion, in infected hepatocytes, HBV passively evades recognition by cellular sensors of nucleic acids by (i) producing non-immunostimulatory RNAs, (ii) avoiding sensing of its DNAs by cGAS/STING without active inhibition of the pathway. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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Graphical abstract

12 pages, 1385 KiB  
Article
IRF7 Is Required for the Second Phase Interferon Induction during Influenza Virus Infection in Human Lung Epithelia
by Wenxin Wu, Wei Zhang, Lili Tian, Brent R. Brown, Matthew S. Walters and Jordan P. Metcalf
Viruses 2020, 12(4), 377; https://doi.org/10.3390/v12040377 - 29 Mar 2020
Cited by 10 | Viewed by 3266
Abstract
Influenza A virus (IAV) infection is a major cause of morbidity and mortality. Retinoic acid-inducible protein I (RIG-I) plays an important role in the recognition of IAV in most cell types, and leads to the activation of interferon (IFN). We investigated mechanisms of [...] Read more.
Influenza A virus (IAV) infection is a major cause of morbidity and mortality. Retinoic acid-inducible protein I (RIG-I) plays an important role in the recognition of IAV in most cell types, and leads to the activation of interferon (IFN). We investigated mechanisms of RIG-I and IFN induction by IAV in the BCi-NS1.1 immortalized human airway basal cell line and in the A549 human alveolar epithelial cell line. We found that the basal expression levels of RIG-I and regulatory transcription factor (IRF) 7 were very low in BCi-NS1.1 cells. IAV infection induced robust RIG-I and IRF7, not IRF3, expression. siRNA against IRF7 and mitochondrial antiviral-signaling protein (MAVS), but not IRF3, significantly inhibited RIG-I mRNA expression and IFN induction by IAV infection. Most importantly, even without virus infection, IFN-β alone induced RIG-I, and siRNA against IRF7 did not inhibit RIG-I induction by IFN-β. Similar results were found in the alveolar basal epithelial A549 cell line. RIG-I and IRF7 expression in humans is highly inducible and greatly amplified by IFN produced from virus infected cells. IFN induction can be separated into two phases, that initially induced by the virus with basal RIG-I (the first phase), and that induced by the subsequent virus with amplified RIG-I from the first phase IFN (the second phase). The de novo synthesis of IRF7 is required for the second phase IFN induction during influenza virus infection in human lung bronchial and alveolar epithelial cells. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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15 pages, 3188 KiB  
Article
Feline Infectious Peritonitis Virus Nsp5 Inhibits Type I Interferon Production by Cleaving NEMO at Multiple Sites
by Si Chen, Jin Tian, Zhijie Li, Hongtao Kang, Jikai Zhang, Jiapei Huang, Hang Yin, Xiaoliang Hu and Liandong Qu
Viruses 2020, 12(1), 43; https://doi.org/10.3390/v12010043 - 30 Dec 2019
Cited by 36 | Viewed by 5207
Abstract
Feline infectious peritonitis (FIP), caused by virulent feline coronavirus, is the leading infectious cause of death in cats. The type I interferon (type I IFN)-mediated immune responses provide host protection from infectious diseases. Several coronaviruses have been reported to evolve diverse strategies to [...] Read more.
Feline infectious peritonitis (FIP), caused by virulent feline coronavirus, is the leading infectious cause of death in cats. The type I interferon (type I IFN)-mediated immune responses provide host protection from infectious diseases. Several coronaviruses have been reported to evolve diverse strategies to evade host IFN response. However, whether feline infectious peritonitis virus (FIPV) antagonizes the type I IFN signaling remains unclear. In this study, we demonstrated that FIPV strain DF2 infection not only failed to induce interferon-β (IFN-β) and interferon-stimulated gene (ISG) production, but also inhibited Sendai virus (SEV) or polyinosinic-polycytidylic acid (poly(I:C))-induced IFN-β production. Subsequently, we found that one of the non-structural proteins encoded by the FIPV genome, nsp5, interrupted type I IFN signaling in a protease-dependent manner by cleaving the nuclear factor κB (NF-κB) essential modulator (NEMO) at three sites—glutamine132 (Q132), Q205, and Q231. Further investigation revealed that the cleavage products of NEMO lost the ability to activate the IFN-β promoter. Mechanistically, the nsp5-mediated NEMO cleavage disrupted the recruitment of the TRAF family member-associated NF-κB activator (TANK) to NEMO, which reduced the phosphorylation of interferon regulatory factor 3 (IRF3), leading to the inhibition of type I IFN production. Our research provides new insights into the mechanism for FIPV to counteract host innate immune response. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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Review

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14 pages, 758 KiB  
Review
Intrinsic Immune Mechanisms Restricting Human Cytomegalovirus Replication
by Eva-Maria Schilling, Myriam Scherer and Thomas Stamminger
Viruses 2021, 13(2), 179; https://doi.org/10.3390/v13020179 - 26 Jan 2021
Cited by 9 | Viewed by 3176
Abstract
Cellular restriction factors (RFs) act as important constitutive innate immune barriers against viruses. In 2006, the promyelocytic leukemia protein was described as the first RF against human cytomegalovirus (HCMV) infection which is antagonized by the viral immediate early protein IE1. Since then, at [...] Read more.
Cellular restriction factors (RFs) act as important constitutive innate immune barriers against viruses. In 2006, the promyelocytic leukemia protein was described as the first RF against human cytomegalovirus (HCMV) infection which is antagonized by the viral immediate early protein IE1. Since then, at least 15 additional RFs against HCMV have been identified, including the chromatin regulatory protein SPOC1, the cytidine deaminase APOBEC3A and the dNTP triphosphohydrolase SAMHD1. These RFs affect distinct steps of the viral replication cycle such as viral entry, gene expression, the synthesis of progeny DNA or egress. This review summarizes our current knowledge on intrinsic immune mechanisms restricting HCMV replication as well as on the viral strategies to counteract the inhibitory effects of RFs. Detailed knowledge on the interplay between host RFs and antagonizing viral factors will be fundamental to develop new approaches to combat HCMV infection. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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42 pages, 5336 KiB  
Review
Innate Immune Sensing of Viruses and Its Consequences for the Central Nervous System
by Hina Singh, Jeffrey Koury and Marcus Kaul
Viruses 2021, 13(2), 170; https://doi.org/10.3390/v13020170 - 23 Jan 2021
Cited by 27 | Viewed by 7017
Abstract
Viral infections remain a global public health concern and cause a severe societal and economic burden. At the organismal level, the innate immune system is essential for the detection of viruses and constitutes the first line of defense. Viral components are sensed by [...] Read more.
Viral infections remain a global public health concern and cause a severe societal and economic burden. At the organismal level, the innate immune system is essential for the detection of viruses and constitutes the first line of defense. Viral components are sensed by host pattern recognition receptors (PRRs). PRRs can be further classified based on their localization into Toll-like receptors (TLRs), C-type lectin receptors (CLR), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), NOD-like receptors (NLRs) and cytosolic DNA sensors (CDS). TLR and RLR signaling results in production of type I interferons (IFNα and -β) and pro-inflammatory cytokines in a cell-specific manner, whereas NLR signaling leads to the production of interleukin-1 family proteins. On the other hand, CLRs are capable of sensing glycans present in viral pathogens, which can induce phagocytic, endocytic, antimicrobial, and pro- inflammatory responses. Peripheral immune sensing of viruses and the ensuing cytokine response can significantly affect the central nervous system (CNS). But viruses can also directly enter the CNS via a multitude of routes, such as the nasal epithelium, along nerve fibers connecting to the periphery and as cargo of infiltrating infected cells passing through the blood brain barrier, triggering innate immune sensing and cytokine responses directly in the CNS. Here, we review mechanisms of viral immune sensing and currently recognized consequences for the CNS of innate immune responses to viruses. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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19 pages, 2032 KiB  
Review
Recognize Yourself—Innate Sensing of Non-LTR Retrotransposons
by Justine Lagisquet, Kilian Zuber and Thomas Gramberg
Viruses 2021, 13(1), 94; https://doi.org/10.3390/v13010094 - 12 Jan 2021
Cited by 5 | Viewed by 4925
Abstract
Although mobile genetic elements, or transposons, have played an important role in genome evolution, excess activity of mobile elements can have detrimental consequences. Already, the enhanced expression of transposons-derived nucleic acids can trigger autoimmune reactions that may result in severe autoinflammatory disorders. Thus, [...] Read more.
Although mobile genetic elements, or transposons, have played an important role in genome evolution, excess activity of mobile elements can have detrimental consequences. Already, the enhanced expression of transposons-derived nucleic acids can trigger autoimmune reactions that may result in severe autoinflammatory disorders. Thus, cells contain several layers of protective measures to restrict transposons and to sense the enhanced activity of these “intragenomic pathogens”. This review focuses on our current understanding of immunogenic patterns derived from the most active elements in humans, the retrotransposons long interspersed element (LINE)-1 and Alu. We describe the role of known pattern recognition receptors in nucleic acid sensing of LINE-1 and Alu and the possible consequences for autoimmune diseases. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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22 pages, 2053 KiB  
Review
Interplay between Hepatitis D Virus and the Interferon Response
by Zhenfeng Zhang and Stephan Urban
Viruses 2020, 12(11), 1334; https://doi.org/10.3390/v12111334 - 20 Nov 2020
Cited by 22 | Viewed by 4437
Abstract
Chronic hepatitis D (CHD) is the most severe form of viral hepatitis, with rapid progression of liver-related diseases and high rates of development of hepatocellular carcinoma. The causative agent, hepatitis D virus (HDV), contains a small (approximately 1.7 kb) highly self-pairing single-strand circular [...] Read more.
Chronic hepatitis D (CHD) is the most severe form of viral hepatitis, with rapid progression of liver-related diseases and high rates of development of hepatocellular carcinoma. The causative agent, hepatitis D virus (HDV), contains a small (approximately 1.7 kb) highly self-pairing single-strand circular RNA genome that assembles with the HDV antigen to form a ribonucleoprotein (RNP) complex. HDV depends on hepatitis B virus (HBV) envelope proteins for envelopment and de novo hepatocyte entry; however, its intracellular RNA replication is autonomous. In addition, HDV can amplify HBV independently through cell division. Cellular innate immune responses, mainly interferon (IFN) response, are crucial for controlling invading viruses, while viruses counteract these responses to favor their propagation. In contrast to HBV, HDV activates profound IFN response through the melanoma differentiation antigen 5 (MDA5) pathway. This cellular response efficiently suppresses cell-division-mediated HDV spread and, to some extent, early stages of HDV de novo infection, but only marginally impairs RNA replication in resting hepatocytes. In this review, we summarize the current knowledge on HDV structure, replication, and persistence and subsequently focus on the interplay between HDV and IFN response, including IFN activation, sensing, antiviral effects, and viral countermeasures. Finally, we discuss crosstalk with HBV. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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24 pages, 1408 KiB  
Review
System-Based Approaches to Delineate the Antiviral Innate Immune Landscape
by Karsten Krey, Aleksandra W. Babnis and Andreas Pichlmair
Viruses 2020, 12(10), 1196; https://doi.org/10.3390/v12101196 - 21 Oct 2020
Cited by 5 | Viewed by 4632
Abstract
Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and [...] Read more.
Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and how infected cells react to the virus on a molecular level. Invading viruses are commonly sensed by components of the innate immune system, which is composed of a highly effective yet complex network of proteins that, in most cases, mediate efficient virus inhibition. Central to this process is the activity of interferons and other cytokines that coordinate the antiviral response. So far, numerous methods have been used to identify how viruses interact with cellular processes and revealed that the innate immune response is highly complex and involves interferon-stimulated genes and their binding partners as functional factors. Novel approaches and careful experimental design, combined with large-scale, high-throughput methods and cutting-edge analysis pipelines, have to be utilized to delineate the antiviral innate immune landscape at a global level. In this review, we describe different currently used screening approaches, how they contributed to our knowledge on virus–host interactions, and essential considerations that have to be taken into account when planning such experiments. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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17 pages, 25575 KiB  
Review
Poxviral Targeting of Interferon Regulatory Factor Activation
by Clara Lawler and Gareth Brady
Viruses 2020, 12(10), 1191; https://doi.org/10.3390/v12101191 - 20 Oct 2020
Cited by 7 | Viewed by 3440
Abstract
As viruses have a capacity to rapidly evolve and continually alter the coding of their protein repertoires, host cells have evolved pathways to sense viruses through the one invariable feature common to all these pathogens—their nucleic acids. These genomic and transcriptional pathogen-associated molecular [...] Read more.
As viruses have a capacity to rapidly evolve and continually alter the coding of their protein repertoires, host cells have evolved pathways to sense viruses through the one invariable feature common to all these pathogens—their nucleic acids. These genomic and transcriptional pathogen-associated molecular patterns (PAMPs) trigger the activation of germline-encoded anti-viral pattern recognition receptors (PRRs) that can distinguish viral nucleic acids from host forms by their localization and subtle differences in their chemistry. A wide range of transmembrane and cytosolic PRRs continually probe the intracellular environment for these viral PAMPs, activating pathways leading to the activation of anti-viral gene expression. The activation of Nuclear Factor Kappa B (NFκB) and Interferon (IFN) Regulatory Factor (IRF) family transcription factors are of central importance in driving pro-inflammatory and type-I interferon (TI-IFN) gene expression required to effectively restrict spread and trigger adaptive responses leading to clearance. Poxviruses evolve complex arrays of inhibitors which target these pathways at a variety of levels. This review will focus on how poxviruses target and inhibit PRR pathways leading to the activation of IRF family transcription factors. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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48 pages, 2540 KiB  
Review
Dance with the Devil: Stress Granules and Signaling in Antiviral Responses
by Nina Eiermann, Katharina Haneke, Zhaozhi Sun, Georg Stoecklin and Alessia Ruggieri
Viruses 2020, 12(9), 984; https://doi.org/10.3390/v12090984 - 04 Sep 2020
Cited by 72 | Viewed by 8238
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating [...] Read more.
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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19 pages, 571 KiB  
Review
Innate Immune DNA Sensing of Flaviviruses
by Tongtong Zhu and Ana Fernandez-Sesma
Viruses 2020, 12(9), 979; https://doi.org/10.3390/v12090979 - 03 Sep 2020
Cited by 10 | Viewed by 4031
Abstract
Flaviviruses are arthropod-borne RNA viruses that have been used extensively to study host antiviral responses. Often selected just to represent standard single-stranded positive-sense RNA viruses in early studies, the Flavivirus genus over time has taught us how truly unique it is in its [...] Read more.
Flaviviruses are arthropod-borne RNA viruses that have been used extensively to study host antiviral responses. Often selected just to represent standard single-stranded positive-sense RNA viruses in early studies, the Flavivirus genus over time has taught us how truly unique it is in its remarkable ability to target not just the RNA sensory pathways but also the cytosolic DNA sensing system for its successful replication inside the host cell. This review summarizes the main developments on the unexpected antagonistic strategies utilized by different flaviviruses, with RNA genomes, against the host cyclic GAMP synthase (cGAS)/stimulator of interferon genes (STING) cytosolic DNA sensing pathway in mammalian systems. On the basis of the recent advancements on this topic, we hypothesize that the mechanisms of viral sensing and innate immunity are much more fluid than what we had anticipated, and both viral and host factors will continue to be found as important factors contributing to the host innate immune system in the future. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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14 pages, 796 KiB  
Review
Insights into Sensing of Murine Retroviruses
by Eileen A. Moran and Susan R. Ross
Viruses 2020, 12(8), 836; https://doi.org/10.3390/v12080836 - 31 Jul 2020
Cited by 4 | Viewed by 3597
Abstract
Retroviruses are major causes of disease in animals and human. Better understanding of the initial host immune response to these viruses could provide insight into how to limit infection. Mouse retroviruses that are endemic in their hosts provide an important genetic tool to [...] Read more.
Retroviruses are major causes of disease in animals and human. Better understanding of the initial host immune response to these viruses could provide insight into how to limit infection. Mouse retroviruses that are endemic in their hosts provide an important genetic tool to dissect the different arms of the innate immune system that recognize retroviruses as foreign. Here, we review what is known about the major branches of the innate immune system that respond to mouse retrovirus infection, Toll-like receptors and nucleic acid sensors, and discuss the importance of these responses in activating adaptive immunity and controlling infection. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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26 pages, 2435 KiB  
Review
Innate Immune Sensing of Influenza A Virus
by Gaurav Malik and Yan Zhou
Viruses 2020, 12(7), 755; https://doi.org/10.3390/v12070755 - 14 Jul 2020
Cited by 45 | Viewed by 7992
Abstract
Influenza virus infection triggers host innate immune response by stimulating various pattern recognition receptors (PRRs). Activation of these PRRs leads to the activation of a plethora of signaling pathways, resulting in the production of interferon (IFN) and proinflammatory cytokines, followed by the expression [...] Read more.
Influenza virus infection triggers host innate immune response by stimulating various pattern recognition receptors (PRRs). Activation of these PRRs leads to the activation of a plethora of signaling pathways, resulting in the production of interferon (IFN) and proinflammatory cytokines, followed by the expression of interferon-stimulated genes (ISGs), the recruitment of innate immune cells, or the activation of programmed cell death. All these antiviral approaches collectively restrict viral replication inside the host. However, influenza virus also engages in multiple mechanisms to subvert the innate immune responses. In this review, we discuss the role of PRRs such as Toll-like receptors (TLRs), Retinoic acid-inducible gene I (RIG-I), NOD-, LRR-, pyrin domain-containing protein 3 (NLRP3), and Z-DNA binding protein 1 (ZBP1) in sensing and restricting influenza viral infection. Further, we also discuss the mechanisms influenza virus utilizes, especially the role of viral non-structure proteins NS1, PB1-F2, and PA-X, to evade the host innate immune responses. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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33 pages, 2715 KiB  
Review
Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression
by Hella Schwanke, Markus Stempel and Melanie M. Brinkmann
Viruses 2020, 12(7), 733; https://doi.org/10.3390/v12070733 - 07 Jul 2020
Cited by 23 | Viewed by 6703
Abstract
The type I interferon (IFN) response is a principal component of our immune system that allows to counter a viral attack immediately upon viral entry into host cells. Upon engagement of aberrantly localised nucleic acids, germline-encoded pattern recognition receptors convey their find via [...] Read more.
The type I interferon (IFN) response is a principal component of our immune system that allows to counter a viral attack immediately upon viral entry into host cells. Upon engagement of aberrantly localised nucleic acids, germline-encoded pattern recognition receptors convey their find via a signalling cascade to prompt kinase-mediated activation of a specific set of five transcription factors. Within the nucleus, the coordinated interaction of these dimeric transcription factors with coactivators and the basal RNA transcription machinery is required to access the gene encoding the type I IFN IFNβ (IFNB1). Virus-induced release of IFNβ then induces the antiviral state of the system and mediates further mechanisms for defence. Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. In this review, we will revisit the steps enabling the trans-activating potential of IRF3 after its activation and the subsequent assembly of the multi-protein complex at the IFNβ enhancer that controls gene expression. Further, we will inspect the regulatory mechanisms of these steps imposed by the host cell and present the manifold strategies viruses have evolved to intervene with IFNβ transcription downstream of IRF3 activation in order to secure establishment of a productive infection. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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