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Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small protein β2-microglobulin (β2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that downregulate MHC-I expression to avoid CD8+ T cell recognition. Here we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, downregulate MHC-I expression using distinct mechanisms. One, ORF3a, a viroporin, reduces global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a novel and specific mechanism that allows immune evasion by SARS-CoV-2.Significance StatementViruses may down-regulate MHC class I expression on infected cells to avoid elimination by cytotoxic T cells. We report that the accessory proteins ORF7a and ORF3a of SARS-CoV-2 mediate this function and delineate the two distinct mechanisms involved. While ORF3a inhibits global protein trafficking to the cell surface, ORF7a acts specifically on MHC-I by competing with β2m for binding to the MHC-I heavy chain. This is the first account of molecular mimicry of β2m as a viral mechanism of MHC-I down-regulation to facilitate immune evasion.

Translational regulation is a fundamental step in gene expression with critical roles in biological processes within a cell. Here, we describe a protocol to assess translation activity in mammalian cells by incorporation of O-propargyl-puromycin (OP-Puro). OP-Puro is a puromycin analog that is incorporated into newly synthesized proteins and is detected by click chemistry reaction. We use OP-Puro labeling to assess translation activity between different cell types or cells under different growth conditions by confocal microscopy and flow cytometry. For complete details on the use and execution of this protocol, please refer to Hsu et al. (2021) and Hsu et al. (2022).

Flaviviruses continue to emerge as global health threats. There are currently no Food and Drug Administration (FDA) approved antiviral treatments for flaviviral infections. Therefore, there is a pressing need to identify host and viral factors that can be targeted for effective therapeutic intervention. Type I interferon (IFN-I) production in response to microbial products is one of the host’s first line of defense against invading pathogens. Cytidine/uridine monophosphate kinase 2 (CMPK2) is a type I interferon-stimulated gene (ISG) that exerts antiviral effects. However, the molecular mechanism by which CMPK2 inhibits viral replication is unclear. Here, we report that CMPK2 expression restricts Zika virus (ZIKV) replication by specifically inhibiting viral translation and that IFN-I- induced CMPK2 contributes significantly to the overall antiviral response against ZIKV. We demonstrate that expression of CMPK2 results in a significant decrease in the replication of other pathogenic flaviviruses including dengue virus (DENV-2), Kunjin virus (KUNV) and yellow fever virus (YFV). Importantly, we determine that the N-terminal domain (NTD) of CMPK2, which lacks kinase activity, is sufficient to restrict viral translation. Thus, its kinase function is not required for CMPK2’s antiviral activity. Furthermore, we identify seven conserved cysteine residues within the NTD as critical for CMPK2 antiviral activity. Thus, these residues may form an unknown functional site in the NTD of CMPK2 contributing to its antiviral function. Finally, we show that mitochondrial localization of CMPK2 is required for its antiviral effects. Given its broad antiviral activity against flaviviruses, CMPK2 is a promising potential pan-flavivirus inhibitor.

Yellow fever virus (YFV) tropism is restricted to human and nonhuman primates. The nonstructural protein 5 (NS5) protein of YFV binds to primate signal transducer and activator of transcription 2 (STAT2) and antagonizes interferon (IFN) signaling. However, YFV NS5 is unable to bind mouse STAT2 and antagonize murine IFN signaling. A similar observation has been made with the NS5 protein of both dengue virus (DENV) and Zika virus (ZIKV). However, the key difference between the NS5 protein of YFV and those of DENV and ZIKV is that YFV NS5 binds human STAT2 in an IFN-dependent manner. In human cells, IFN-I treatment induces K63-linked ubiquitination on lysine (K) 6 of YFV NS5, which is required for binding human STAT2. This IFN-induced ubiquitination of YFV NS5 is absent in murine cells resulting in the lack of binding of YFV NS5 and human STAT2 in murine cells. This highlights the importance of YFV NS5 ubiquitination in determining the host cell range for YFV.

Background Limited therapeutic options exist for coronavirus disease 2019 (COVID-19). COVID-19 convalescent plasma (CCP) is a potential therapeutic, but there is limited data for patients with moderate-to-severe disease. Research question What are outcomes associated with administration of CCP in patients with moderate-to-severe COVID-19 infection? Study design and methods We conducted a propensity score-matched analysis of patients with moderate-to-severe COVID-19. The primary endpoints were in-hospital mortality. Secondary endpoints were number of days alive and ventilator-free at 30 days; length of hospital stay; and change in WHO scores from CCP administration (or index date) to discharge. Of 151 patients who received CCP, 132 had complete follow-up data. Patients were transfused after a median of 6 hospital days; thus, we investigated the effect of convalescent plasma before and after this timepoint with 77 early (within 6 days) and 55 late (after 6 days) recipients. Among 3,217 inpatients who did not receive CCP, 2,551 were available for matching. Results Early CCP recipients, of whom 31 (40%) were on mechanical ventilation, had lower 14-day (15% vs 23%) and 30-day (38% vs 49%) mortality compared to a matched unexposed cohort, with nearly 50% lower likelihood of in-hospital mortality (HR 0.52, [95% CI 0.28–0.96]; P = 0.036). Early plasma recipients had more days alive and ventilator-free at 30 days (+3.3 days, [95% CI 0.2 to 6.3 days]; P = 0.04) and improved WHO scores at 7 days (-0.8, [95% CI: -1.2 to -0.4]; P = 0.0003) and hospital discharge (-0.9, [95% CI: -1.5 to -0.3]; P = 0.004) compared to the matched unexposed cohort. No clinical differences were observed in late plasma recipients. Interpretation Early administration of CCP improves outcomes in patients with moderate-to-severe COVID-19, while improvement was not observed with late CCP administration. The importance of timing of administration should be addressed in specifically designed trials.

Innate immune responses induce hundreds of interferon-stimulated genes (ISGs). Viperin, a member of the radical S-adenosyl methionine (SAM) superfamily of enzymes, is the product of one such ISG that restricts the replication of a broad spectrum of viruses. Here, we report a previously unknown antiviral mechanism in which viperin activates a ribosome collision-dependent pathway that inhibits both cellular and viral RNA translation. We found that the radical SAM activity of viperin is required for translation inhibition and that this is mediated by viperin's enzymatic product, 3'-deoxy-3',4'-didehydro-CTP (ddhCTP). Viperin triggers ribosome collisions and activates the MAPKKK ZAK pathway that in turn activates the GCN2 arm of the integrated stress response pathway to inhibit translation. The study illustrates the importance of translational repression in the antiviral response and identifies viperin as a translation regulator in innate immunity.

Many viruses infect circulating mononuclear cells thereby facilitating infection of diverse organs. Blood monocytes (PBMC) are being intensively studied as immunologic and pathologic responders to the new SARS-CoV-2 virus (CoV19) but direct evidence showing CoV19 in monocytes is lacking. Circulating myeloid cells that take up residence in various organs can harbor viral genomes for many years in lymphatic tissues and brain, and act as a source for re-infection and/or post-viral organ pathology. Because nucleocapsid (NC) proteins protect the viral genome we tested PBMC from acutely ill patients for the diagnostic 72bp NC RNA plus adjacent longer (301bp) transcripts. In 2/11 patient PBMC, but no uninfected controls, long NCs were positive as early as 2-6 days after hospital admission as validated by sequencing. Pathogenic viral fragments, or the infectious virus, are probably disseminated by rare myeloid migratory cells that incorporate CoV19 by several pathways. Predictably, these cells carried CoV19 to heart and brain educing the late post-viral pathologies now evident.

Background: Coronavirus disease 2019 (COVID-19), a multi-system disorder resulting from infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected 5.0 million individuals in the United States (US) resulting in more than 160,000 deaths. There is currently no proven effective therapy for SARS-CoV-2 infection beyond supportive care. Convalescent plasma (CP), collected from individuals who have recovered from SARS-CoV-2 infection, has been safely used to transfer virus-neutralizing antibodies to patients hospitalized with COVID-19. Herein we report on the clinical course and outcomes of patients who received CP for the treatment of COVID-19 across our health system. Methods: Hospitalized patients ≥ 18 years of age at 5 hospitals in the Yale-New Haven Health System with confirmed SARS-CoV-2 infection and severe or life-threatening disease (Figure 1) were enrolled in the US COVID-19 Expanded Access Program (EAP) and transfused 1 unit of CP. Patient outcomes were assessed at 7, 14, and 28 days after CP transfusion. Furthermore, we sought to determine mortality predictors in this patient cohort. Results: 105 patients enrolled in the EAP were transfused CP from 4/12/2020 to 6/14/2020. Median age was 62 years (28-88 years). 62.9% of patients were male. Individuals of a non-white race comprised 56.2% of our cohort and 33.3% identified as Hispanic or Latinx. 47.6% of patients had a body mass index greater than 30, with 13.3% classified as extremely obese. Diabetes mellitus, hypertension, and hyperlipidemia were highly prevalent in our population. Concomitant therapy for COVID-19 included hydroxychloroquine (79.0%), tocilizumab (79.0%), and remdesivir (23.8%) (Table 1). 91 patients required the intensive care unit (ICU) during their hospital course, with 87 patients in the ICU at the time of CP transfusion. 42.9% of patients had an improvement in their World Health Organization (WHO) Ordinal Scale score by day 7 post-CP transfusion (median 4 days to improvement), while 9.5% demonstrated an increase in their WHO score indicating worsening oxygenation during the 7 days following CP (Figure 2). Mortality was 10.48% at 7 days, 20.95% at 14 days, and 28.57% at 28 days post-CP transfusion (Figure 2). Of the patients in the ICU at the time of CP, 56 (64.4%) de-escalated to non-ICU care after a median of 8 days from transfusion and 55 (63.2%) were ultimately discharged from the hospital. The median time from CP transfusion to discharge in survivors was 14 days (2-103 days), while median time from CP to death in non-survivors was 10 days (1-76 days). The mean time in days both from hospital admission to CP and from positive SARS-CoV-2 polymerase chain reaction (PCR) to CP trended slightly longer in non-survivors when compared to survivors (8.6 vs 6.9 days, p=0.218 and 9.7 vs 7.3 days, p=0.85, respectively). D-dimer levels >5 milligrams per liter fibrinogen equivalent units (mg/L FEU) were associated with increased mortality at 24 (OR 2.79, 95% CI 1.18-6.72), 48 (OR 3.64, 95% CI 1.44-9.70), and 72 hours (OR 2.99, 95% CI 1.23-7.66) post-CP transfusion (Figure 3). Twelve patients (11.4%) on prophylactic or intermediate dose anticoagulation were subsequently escalated to therapeutic dosing during the 7 days after CP transfusion. Furthermore, a ferritin level of >3000 nanograms per milliliter (ng/mL) on the day of CP was associated with increased mortality (OR 5.14, 95% CI 1.34-19.68). Conclusions: CP therapy was administered through the EAP to COVID-19 patients with severe disease and with advanced age, high frequency of obesity, and extensive co-morbidity. In this COVID-19 population with high expected mortality, 42.9% of patients improved by WHO Ordinal Scale score within 7 days of CP transfusion and 52.4% were alive and discharged at 28 days. Baseline ferritin and d-dimer levels at 24, 48, and 72 hours post-CP were predictors of mortality, the latter raising the possibility that the increased thrombotic risk associated with COVID-19 may be exacerbated by administration of blood products from donors potentially in a residual procoagulant state. Further studies by our group are underway to assess hemostatic balance in donor CP, to estimate associations with outcomes by comparing patients who received CP with a matched control cohort of COVID-19 patients who did not receive CP, and to evaluate efficacy of CP in a randomized, placebo-controlled clinical trial. Disclosures McLeod: Gilead Pharmaceuticals: Other: Medical Advisor . OffLabel Disclosure: We have described in this abstract patients across our health system who received investigational convalescent plasma therapy through enrollment in the "Expanded Access to Convalescent Plasma for the Treatment of Patients with COVID-19" protocol that is funded by BARDA and run by the Mayo Clinic, where primary IRB protocol is held. Previous guidance issued by the FDA regarding investigational use of COVID-19 convalescent plasma included recommendations for the expanded access program as a method by which to facilitate access to this blood product across the nation. Safety data reported thus far from the expanded access program has demonstrated no concerning findings, with a very low rate of serious adverse events. Therefore given the overall tolerability of convalescent plasma and the lack of other proven therapies for COVID-19, we believe it is important to report these findings even in the absence of current approval for convalescent plasma transfusion in the management of COVID-19.

The recent yellow fever virus (YFV) epidemic in Brazil in 2017 and Zika virus (ZIKV) epidemic in 2015 serve to remind us of the importance of flaviviruses as emerging human pathogens. With the current global flavivirus threat, there is an urgent need for antivirals and vaccines to curb the spread of these viruses. However, the lack of suitable animal models limits the research questions that can be answered. A common trait of all flaviviruses studied thus far is their ability to antagonize interferon (IFN) signaling so as to enhance viral replication and dissemination. Previously, we reported that YFV NS5 requires the presence of type I IFN (IFN-α/β) for its engagement with human signal transducer and activator of transcription 2 (hSTAT2). In this manuscript, we report that like the NS5 proteins of ZIKV and dengue virus (DENV), YFV NS5 protein is able to bind hSTAT2 but not murine STAT2 (mSTAT2). Contrary to what has been demonstrated with ZIKV NS5 and DENV NS5, replacing mSTAT2 with hSTAT2 cannot rescue the YFV NS5-STAT2 interaction, as YFV NS5 is also unable to interact with hSTAT2 in murine cells. We show that the IFN-α/β-dependent ubiquitination of YFV NS5 that is required for STAT2 binding in human cells is absent in murine cells. In addition, we demonstrate that mSTAT2 restricts YFV replication in vivo. These data serve as further impetus for the development of an immunocompetent mouse model that can serve as a disease model for multiple flaviviruses. IMPORTANCE Flaviviruses such as yellow fever virus (YFV), Zika virus (ZIKV), and dengue virus (DENV) are important human pathogens. A common flavivirus trait is the antagonism of interferon (IFN) signaling to enhance viral replication and spread. We report that like ZIKV NS5 and DENV NS5, YFV NS5 binds human STAT2 (hSTAT2) but not mouse STAT2 (mSTAT2), a type I IFN (IFN-α/β) pathway component. Additionally, we show that contrary to what has been demonstrated with ZIKV NS5 and DENV NS5, YFV NS5 is unable to interact with hSTAT2 in murine cells. We demonstrate that mSTAT2 restricts YFV replication in mice and that this correlates with a lack of IFN-α/β-induced YFV NS5 ubiquitination in murine cells. The lack of suitable animal models limits flavivirus pathogenesis, vaccine, and drug research. These data serve as further impetus for the development of an immunocompetent mouse model that can serve as a disease model for multiple flaviviruses.

Despite mounting evidence for SARS-CoV-2 engagement with immune cells, most express little, if any, of the canonical receptor of SARS-CoV-2, ACE2. Here, using a myeloid-cell receptor-focused ectopic expression screen, we identified several C-type lectins (DC-SIGN, L-SIGN, LSECtin, ASGR1, and CLEC10A) and Tweety family member 2 (TTYH2) as glycan-dependent binding partners of the SARS-CoV-2 spike. Except for TTYH2, these molecules primarily interacted with spike via regions outside of the receptor-binding domain. Single-cell RNA-sequencing analysis of pulmonary cells from COVID-19 patients indicated predominant expression of these molecules on myeloid cells. Although these receptors do not support active replication of SARS-CoV-2, their engagement with virus induced robust proinflammatory responses in myeloid cells that correlated with COVID-19 severity. We also generated a bispecific anti-spike nanobody that not only blocked ACE2-mediated infection but also the myeloid receptors-mediated proinflammatory responses. Our findings suggest SARS-CoV-2-myeloid receptor interactions promote immune hyper-activation, which represents potential targets for COVID-19 therapy., Graphical Abstract, Most immune cells express little, if any, of the canonical SARS-CoV-2 receptor, ACE2. Lu et al. report that C-type lectins and TTYH2 act as SARS-CoV-2 myeloid cell-interacting partners that trigger immune hyper-activation, but not infection. These findings raise the possibility that these virus-myeloid cell interactions are directly involved in COVID-19 immunopathogenesis and could be targeted for COVID-19 therapy.

SummaryType I interferons (IFN-I) are essential antiviral cytokines produced upon microbial infection. IFN-I elicits this activity through the upregulation of hundreds of IFN-I-stimulated genes (ISGs). The full breadth of ISG induction demands activation of a number of cellular factors including the IκB kinase epsilon (IKKε). However, the mechanism of IKKε activation upon IFN receptor signaling has remained elusive. Here we show that TRIM6, a member of the E3-ubiquitin ligase tripartite motif (TRIM) family of proteins, interacted with IKKε and promoted induction of IKKε-dependent ISGs. TRIM6 and the E2-ubiquitin conjugase UbE2K cooperated in the synthesis of unanchored K48-linked polyubiquitin chains, which activated IKKε for subsequent STAT1 phosphorylation. Our work attributes a previously unrecognized activating role of K48-linked unanchored polyubiquitin chains in kinase activation and identifies the UbE2K-TRIM6-ubiquitin axis as critical for IFN signaling and antiviral response.

La Piedad Michoacán Mexico Virus (LPMV) is a member of the Rubulavirus genus within the Paramyxoviridae family. LPMV is the etiologic agent of "blue eye disease", causing a significant disease burden in swine in Mexico with long-term implications for the agricultural industry. This virus mainly affects piglets and is characterized by meningoencephalitis and respiratory distress. It also affects adult pigs, causing reduced fertility and abortions in females, and orchitis and epididymitis in males. Viruses of the Paramyxoviridae family evade the innate immune response by targeting components of the interferon (IFN) signaling pathway. The V protein, expressed by most paramyxoviruses, is a well-characterized IFN signaling antagonist. Until now, there were no reports on the role of the LPMV-V protein in inhibiting the IFN response. In this study we demonstrate that LPMV-V protein antagonizes type I but not type II IFN signaling by binding STAT2, a component of the type I IFN cascade. Our results indicate that the last 18 amino acids of LPMV-V protein are required for binding to STAT2 in human and swine cells. While LPMV-V protein does not affect the protein levels of STAT1 or STAT2, it does prevent the IFN-induced phosphorylation and nuclear translocation of STAT1 and STAT2 thereby inhibiting cellular responses to IFN α/β.

The recent yellow fever virus (YFV) epidemic in Brazil in 2017 and Zika virus (ZIKV) epidemic in 2015 serve to remind us of the importance of flaviviruses as emerging human pathogens. With the current global flavivirus threat, there is an urgent need for antivirals and vaccines to curb the spread of these viruses. However, the lack of suitable small animal models limits the research questions that can be answered. A common trait of all flaviviruses studied thus far is their ability to antagonize interferon (IFN) signaling so as to establish infection and subsequent dissemination. Previously, we reported that YFV NS5 requires the presence of type I IFN (IFNα/β) for its engagement with human Signal Transducer and Activator of Transcription 2 (hSTAT2). We now report that like the NS5 proteins of ZIKV and dengue virus (DENV), YFV NS5 protein is able to bind hSTAT2 but not murine STAT2 (mSTAT2). Contrary to what has been demonstrated with ZIKV NS5 and DENV NS5, replacing mSTAT2 with hSTAT2 cannot rescue the YFV NS5-STAT2 interaction, as YFV NS5 is also unable to interact with hSTAT2 in murine cells. We show that the IFNα/β-dependent ubiquitination of YFV NS5 that is required for STAT2 binding in human cells is absent in murine cells. In addition, we demonstrate that mSTAT2 restricts YFV replication in vivo. These data serve as further impetus for the development of an immunocompetent mouse model that can serve as a disease model for multiple flaviviruses.

The innate immune response involves the induction of hundreds of interferon-stimulated genes (ISGs), many of which play a role in cancer immunosurveillance and antiviral immunity. Therefore, understanding how ISGs function and coordinate with the cellular network is of critical importance. We focus on one such ISG, viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible). Viperin has been reported to inhibit a broad spectrum of DNA and RNA viruses, including many flaviviruses, human cytomegalovirus (HCMV), Chikungunya virus, influenza A virus, Sindbis virus, vesicular stomatitis virus, tick-borne encephalitis virus, HIV-1 and more. It is highly conserved in evolution, from protozoans to humans. Viperin is a peripheral membrane protein, associating on the cytosolic face of the ER via its N-terminal amphipathic helix. The cytosolic domain contains a radical SAM domain with a [4Fe-4S] cluster coordinated by three cysteine residues in the active site. Although the enzymatic function and substrate of viperin is still under debate, a recent study reveals that viperin catalyzes the conversion of cytidine triphosphate to 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP) via its radical SAM activity. However, a general mechanism for viperin action and its potential roles within the innate immune response remain to be defined. Here, we demonstrate that viperin inhibits global protein translation via its radical SAM-dependent enzymatic activity. Using immortalized mouse macrophages from wild-type and viperin knockout mice we show that, although other ISGs are induced, type I IFN treatment of WT but not viperin KO mouse microphages leads to a global change in polysome profile with an increase in the ribosome fraction and a decrease in actively translating ribosomes. In parallel, the translational regulation function was evaluated in 293T-cells with transient transfection and doxycycline-inducible system. Despite no IFN stimulation and therefore no other ISG expression, viperin effectively represses translation. Furthermore, we find that viperin reduces global protein translation by ~30% in live cells using [35S]-methionine metabolic pulse-labeling or O-propargyl-puromycin (OPP) labelling. The radical SAM enzymatic activity is required for translational inhibition: site-directed mutagenesis of amino residues involved in iron-sulfur cluster and substrate binding abolishes the translational inhibition activity. We also demonstrate that ddhCTP, a recently identified vipern product, inhibits global protein translation in live cells. Viral replication requires the host translation machinery to make viral proteins, and our results suggest that much of its antiviral activity may be attributable to translational regulation. We show that viperin inhibits viral protein synthesis and viral replication of the Kunjin virus, a West Nile Virus variant, in tissue culture cells. Our study suggests a partially unifying mechanism for the broad antiviral function of viperin based on translational regulation. Citation Format: Chun-Chieh Hsu, Maudry Laurent-Rolle, Peter Cresswell. Regulation of translation by the interferon-induced antiviral protein viperin [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B163.

Flaviviruses transmitted by arthropods represent a tremendous disease burden for humans, causing millions of infections annually. All vector-borne flaviviruses studied to date suppress host innate responses to infection by inhibiting alpha/beta interferon (IFN-α/β)-mediated JAK-STAT signal transduction. The viral nonstructural protein NS5 of some flaviviruses functions as the major IFN antagonist, associated with inhibition of IFN-dependent STAT1 phosphorylation (pY-STAT1) or with STAT2 degradation. West Nile virus (WNV) infection prevents pY-STAT1 although a role for WNV NS5 in IFN antagonism has not been fully explored. Here, we report that NS5 from the virulent NY99 strain of WNV prevented pY-STAT1 accumulation, suppressed IFN-dependent gene expression, and rescued the growth of a highly IFN-sensitive virus (Newcastle disease virus) in the presence of IFN, suggesting that this protein can function as an efficient IFN antagonist. In contrast, NS5 from Kunjin virus (KUN), a naturally attenuated subtype of WNV, was a poor suppressor of pY-STAT1. Mutation of a single residue in KUN NS5 to the analogous residue in WNV-NY99 NS5 (S653F) rendered KUN NS5 an efficient inhibitor of pY-STAT1. Incorporation of this mutation into recombinant KUN resulted in 30-fold greater inhibition of JAK-STAT signaling than with the wild-type virus and enhanced KUN replication in the presence of IFN. Thus, a naturally occurring mutation is associated with the function of NS5 in IFN antagonism and may influence virulence of WNV field isolates.

SummaryTo successfully establish infection, flaviviruses have to overcome the antiviral state induced by type I interferon (IFN-I). The nonstructural NS5 proteins of several flaviviruses antagonize IFN-I signaling. Here we show that yellow fever virus (YFV) inhibits IFN-I signaling through a unique mechanism that involves binding of YFV NS5 to the IFN-activated transcription factor STAT2 only in cells that have been stimulated with IFN-I. This NS5-STAT2 interaction requires IFN-I-induced tyrosine phosphorylation of STAT1 and the K63-linked polyubiquitination at a lysine in the N-terminal region of YFV NS5. We identified TRIM23 as the E3 ligase that interacts with and polyubiquitinates YFV NS5 to promote its binding to STAT2 and trigger IFN-I signaling inhibition. Our results demonstrate the importance of YFV NS5 in overcoming the antiviral action of IFN-I and offer a unique example of a viral protein that is activated by the same host pathway that it inhibits.

An estimated 50 million dengue virus (DENV) infections occur annually and more than forty percent of the human population is currently at risk of developing dengue fever (DF) or dengue hemorrhagic fever (DHF). Despite the prevalence and potential severity of DF and DHF, there are no approved vaccines or antiviral therapeutics available. An improved understanding of DENV immune evasion is pivotal for the rational development of anti-DENV therapeutics. Antagonism of type I interferon (IFN-I) signaling is a crucial mechanism of DENV immune evasion. DENV NS5 protein inhibits IFN-I signaling by mediating proteasome-dependent STAT2 degradation. Only proteolytically-processed NS5 can efficiently mediate STAT2 degradation, though both unprocessed and processed NS5 bind STAT2. Here we identify UBR4, a 600-kDa member of the N-recognin family, as an interacting partner of DENV NS5 that preferentially binds to processed NS5. Our results also demonstrate that DENV NS5 bridges STAT2 and UBR4. Furthermore, we show that UBR4 promotes DENV-mediated STAT2 degradation, and most importantly, that UBR4 is necessary for efficient viral replication in IFN-I competent cells. Our data underscore the importance of NS5-mediated STAT2 degradation in DENV replication and identify UBR4 as a host protein that is specifically exploited by DENV to inhibit IFN-I signaling via STAT2 degradation., Author Summary Dengue virus (DENV) is the leading cause of mosquito-borne viral illness and death in humans. At present, there are no vaccines and no specific antiviral therapeutics to prevent or treat DENV infections. We previously described that the NS5 protein of DENV inhibits type I interferon signaling in virus-infected cells by mediating STAT2 degradation. This property allows DENV to overcome the antiviral effects of type I interferon, contributing to viral replication in the host. We have now obtained new insight into the mechanism by which DENV NS5 induces STAT2 degradation. NS5 bridges STAT2 with the cellular protein UBR4, a member of a family of predicted E3 ligases, resulting in UBR4-mediated STAT2 degradation. Elimination of UBR4 or mutations in NS5 that prevent its binding to UBR4 prevent NS5 from inducing STAT2 degradation. Importantly, UBR4 is required for optimal DENV replication in the presence of a competent type I interferon system. Our data demonstrate the requirement of a host factor, UBR4, for DENV to overcome the antiviral interferon response. This information might be important for the design of specific DENV inhibitors that prevent dengue virus from evading innate immunity.

Intracellular innate immune responses are essential to protect host cells against pathogens. Upon infection, pattern recognition receptors detect incoming microbes and trigger downstream signaling pathways leading to production of antiviral type-I interferons (IFNs).These signaling pathways are regulated by different posttranslational modifications including the ubiquitin (Ub) system. Proteins covalently attached to K48-linked polyUb are targeted for degradation by the proteasome, whereas protein modification with K63-linked polyUb may have non-proteolytic activating functions. Unanchored Ub chains that are not covalently attached to any protein are also important for kinase activation. Tripartite motif (TRIM) proteins, which function as E3-ubiquitin ligases, have been implicated in antiviral activity. We found that TRIM6 is important in the synthesis of unanchored K48-linked polyUb chains, which activate the IKKε kinase for STAT1 phosphorylation and induction of an antiviral response. These polyUb chains and IKKε interact in vivo in an IFN-I signaling dependent manner upon virus infection in mice. To better understand the physiological role of unanchored polyUb during virus infection, we developed a system to isolate ubiquitin-interacting proteins from the lungs of influenza-infected mice. Using a proteomics approach we identified new cellular factors that interact with unanchored polyUb chains in vivo and may be involved in the innate immune antiviral response.

Flaviviruses are insect-borne, positive-strand RNA viruses that have been disseminated worldwide. Their genome is translated into a polyprotein, which is subsequently cleaved by a combination of viral and host proteases to produce three structural proteins and seven nonstructural proteins. The nonstructural protein NS4B of dengue 2 virus partially blocks activation of STAT1 and interferon-stimulated response element (ISRE) promoters in cells stimulated with interferon (IFN). We have found that this function of NS4B is conserved in West Nile and yellow fever viruses. Deletion analysis shows that that the first 125 amino acids of dengue virus NS4B are sufficient for inhibition of alpha/beta IFN (IFN-α/β) signaling. The cleavable signal peptide at the N terminus of NS4B, a peptide with a molecular weight of 2,000, is required for IFN antagonism but can be replaced by an unrelated signal peptide. Coexpression of dengue virus NS4A and NS4B together results in enhanced inhibition of ISRE promoter activation in response to IFN-α/β. In contrast, expression of the precursor NS4A/B fusion protein does not cause an inhibition of IFN signaling unless this product is cleaved by the viral peptidase NS2B/NS3, indicating that proper viral polyprotein processing is required for anti-interferon function.