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Article ; Online: Move and countermove: the integrated stress response in picorna- and coronavirus-infected cells.

Aloise, Chiara / Schipper, Jelle G / de Groot, Raoul J / van Kuppeveld, Frank Jm

2022 Volume 79, Page(s) 102254

Abstract: Viruses, when entering their host cells, are met by a fierce intracellular immune defense. One prominent antiviral pathway is the integrated stress response (ISR). Upon activation of the ISR - typically though not exclusively upon detection of dsRNA - ... ...

Abstract	Viruses, when entering their host cells, are met by a fierce intracellular immune defense. One prominent antiviral pathway is the integrated stress response (ISR). Upon activation of the ISR - typically though not exclusively upon detection of dsRNA - translation-initiation factor eukaryotic initiation factor 2 (eIF2) becomes phosphorylated to act as an inhibitor of guanine nucleotide-exchange factor eIF2B. Thus, with the production of ternary complex blocked, a global translational arrest ensues. Successful virus replication hinges on effective countermeasures. Here, we review ISR antagonists and antagonistic mechanisms employed by picorna- and coronaviruses. Special attention will be given to a recently discovered class of viral antagonists that inhibit the ISR by targeting eIF2B, thereby allowing unabated translation initiation even at exceedingly high levels of phosphorylated eIF2.
MeSH term(s)	Humans ; Coronavirus/metabolism ; Phosphorylation ; Eukaryotic Initiation Factor-2B/metabolism ; Eukaryotic Initiation Factor-2/metabolism
Chemical Substances	Eukaryotic Initiation Factor-2B ; Eukaryotic Initiation Factor-2
Language	English
Publishing date	2022-09-28
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2022.102254
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Article ; Online: Thrombosis and Bleeding in Patients with Vaccine-Induced Immune Thrombotic Thrombocytopenia: A Systematic Review of Published Cases.

Clerici, Bianca / Pontisso, Eleonora / Aloise, Chiara / Peroni, Benedetta / Perricone, Rosaria / Pisetta, Chiara / Scavone, Mariangela / Birocchi, Simone / Podda, Gian Marco

Thrombosis and haemostasis

2023 Volume 124, Issue 5, Page(s) 423–431

Abstract: Introduction: Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a highly prothrombotic reaction to COVID-19 (coronavirus disease 2019) adenoviral vector vaccines. Its distinct bleeding and thrombotic patterns compared with other platelet ... ...

Abstract	Introduction: Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a highly prothrombotic reaction to COVID-19 (coronavirus disease 2019) adenoviral vector vaccines. Its distinct bleeding and thrombotic patterns compared with other platelet consumptive disorders remain unclear. Methods: We performed a systematic review of the literature (PubMed and Embase) up to July 31, 2022, including case reports and case series providing nonaggregate data of VITT patients. Accurate VITT diagnosis required fulfillment of the following criteria: (1) endorsement by the authors, (2) consistent vaccine type and timing, (3) presence of thrombocytopenia and thrombosis, (4) detection of anti-platelet factor 4 antibodies. Data are presented as frequencies with 95% confidence intervals (CIs) calculated with the exact binomial method. Results: We retrieved 143 eligible studies, describing 366 patients. Of 647 thrombotic events, 53% (95% CI: 49-56) were venous thromboses at unusual sites and 30% (95% CI: 27-34) were cerebral venous sinus thromboses (CVSTs). The ratio of venous-to-arterial events was 4.1. Thromboses in most sites were associated with at least another thrombotic event, with the exception of CVST and CNS arterial thrombosis (isolated in 49 and 39% of cases, respectively). Bleeding occurred in 36% (95% CI: 31-41) of patients; 68% (95% CI: 59-75) of bleeding events were intracranial hemorrhages (ICHs). Overall mortality was 24% (95% CI: 19-29), and 77% (95% CI: 58-90) in patients with isolated CVST complicated by ICH. Conclusion: VITT displays a venous-to-arterial thrombosis ratio comparable to heparin-induced thrombocytopenia. However, VITT is characterized by a higher prevalence of CVST and ICH, which contribute to the increased bleeding frequency and mortality.
MeSH term(s)	Humans ; Anticoagulants/adverse effects ; Case Reports as Topic ; COVID-19/complications ; COVID-19 Vaccines/adverse effects ; Hemorrhage ; Platelet Factor 4/immunology ; Risk Factors ; SARS-CoV-2/immunology ; Sinus Thrombosis, Intracranial/etiology ; Thrombosis/etiology ; Venous Thrombosis
Chemical Substances	Anticoagulants ; COVID-19 Vaccines ; Platelet Factor 4 (37270-94-3)
Language	English
Publishing date	2023-12-18
Publishing country	Germany
Document type	Systematic Review ; Journal Article
ZDB-ID	518294-3
ISSN	2567-689X ; 0340-6245
ISSN (online)	2567-689X
ISSN	0340-6245
DOI	10.1055/s-0043-1777134
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Article ; Online: Prevalence of anti-platelet factor 4 antibodies in healthy vaccinees with adenoviral vector vaccines-A systematic review and meta-analysis.

Clerici, Bianca / Scavone, Mariangela / Birocchi, Simone / Aloise, Chiara / Peroni, Benedetta / Negrini, Alessandra / Ghali, Claudia / Casazza, Giovanni / Podda, Gian Marco

British journal of haematology

2023 Volume 200, Issue 6, Page(s) 821–823

MeSH term(s)	Humans ; Prevalence ; Vaccines ; Genetic Vectors ; Immunologic Factors
Chemical Substances	Vaccines ; Immunologic Factors
Language	English
Publishing date	2023-01-17
Publishing country	England
Document type	Meta-Analysis ; Systematic Review ; Letter
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.18635
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Article ; Online: Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3.

Yang, Xiaoyao / Aloise, Chiara / van Vliet, Arno L W / Zwaagstra, Marleen / Lyoo, Heyrhyoung / Cheng, Anchun / van Kuppeveld, Frank J M

Viruses

2022 Volume 14, Issue 7

Abstract: Enterovirus ... ...

Abstract	Enterovirus 2A
MeSH term(s)	Antigens, Viral/metabolism ; Encephalomyocarditis virus/genetics ; Enterovirus/genetics ; Enterovirus Infections ; HeLa Cells ; Histone Methyltransferases/metabolism ; Humans ; Peptide Hydrolases/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Antigens, Viral ; Viral Proteins ; Histone Methyltransferases (EC 2.1.1.-) ; SETD3 protein, human (EC 2.1.1.43) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2022-06-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071360
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Article: Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3

Yang, Xiaoyao / Aloise, Chiara / van Vliet, Arno L. W. / Zwaagstra, Marleen / Lyoo, Heyrhyoung / Cheng, Anchun / van Kuppeveld, Frank J. M.

Viruses. 2022 June 22, v. 14, no. 7

2022

Abstract: Enterovirus 2Aᵖʳᵒ is a protease that proteolytically processes the viral polyprotein and cleaves several host proteins to antagonize host responses during enteroviral infection. Recently, the host protein actin histidine methyltransferase SET domain ... ...

Abstract	Enterovirus 2Aᵖʳᵒ is a protease that proteolytically processes the viral polyprotein and cleaves several host proteins to antagonize host responses during enteroviral infection. Recently, the host protein actin histidine methyltransferase SET domain containing 3 (SETD3) was identified to interact with 2Aᵖʳᵒ and to be essential for virus replication. The role of SETD3 and its interaction with 2Aᵖʳᵒ remain unclear. In this study, we investigated the potential involvement of SETD3 in several functions of 2Aᵖʳᵒ. For this, we introduced the 2Aᵖʳᵒ from coxsackievirus B3 (CVB3) in a mutant of encephalomyocarditis virus (EMCV) containing an inactivated Leader protein (EMCV-Lᶻⁿ) that is unable to shut down host mRNA translation, to trigger nucleocytoplasmic transport disorder (NCTD), and to suppress stress granule (SG) formation and type I interferon (IFN) induction. Both in wt HeLa cells and in HeLa SETD3 knockout (SETD3ᴷᴼ) cells, the virus containing active 2Aᵖʳᵒ (EMCV-2Aᵖʳᵒ) efficiently cleaved eukaryotic translation initiation factor 4 gamma (eIF4G) to shut off host mRNA translation, cleaved nucleoporins to trigger NCTD, and actively suppressed SG formation and IFN gene transcription, arguing against a role of SETD3 in these 2Aᵖʳᵒ-mediated functions. Surprisingly, we observed that the catalytic activity of enteroviral 2A is not crucial for triggering NCTD, as a virus containing an inactive 2Aᵖʳᵒ (EMCV-2Aᵐ) induced NCTD in both wt and SETD3ᴷᴼ cells, albeit delayed, challenging the idea that the NCTD critically depends on nucleoporin cleavage by this protease. Taken together, our results do not support a role of SETD3 in the proteolytic activities of enterovirus 2Aᵖʳᵒ.
Keywords	Cardiovirus A ; Enterovirus ; actin ; catalytic activity ; histidine ; interferons ; methyltransferases ; mutants ; nucleocytoplasmic transport ; nucleoporins ; polyproteins ; proteinases ; proteolysis ; transcription (genetics) ; virus replication ; viruses
Language	English
Dates of publication	2022-0622
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14071360
Database	NAL-Catalogue (AGRICOLA)

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Article: Thrombosis and Bleeding in Patients with Vaccine-Induced Immune Thrombotic Thrombocytopenia: A Systematic Review of Published Cases

Clerici, Bianca / Pontisso, Eleonora / Aloise, Chiara / Peroni, Benedetta / Perricone, Rosaria / Pisetta, Chiara / Scavone, Mariangela / Birocchi, Simone / Podda, Gian Marco

Thrombosis and Haemostasis

2023 Volume 124, Issue 05, Page(s) 423–431

Abstract	Introduction: Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a highly prothrombotic reaction to COVID-19 (coronavirus disease 2019) adenoviral vector vaccines. Its distinct bleeding and thrombotic patterns compared with other platelet consumptive disorders remain unclear. Methods: We performed a systematic review of the literature (PubMed and Embase) up to July 31, 2022, including case reports and case series providing nonaggregate data of VITT patients. Accurate VITT diagnosis required fulfillment of the following criteria: (1) endorsement by the authors, (2) consistent vaccine type and timing, (3) presence of thrombocytopenia and thrombosis, (4) detection of anti-platelet factor 4 antibodies. Data are presented as frequencies with 95% confidence intervals (CIs) calculated with the exact binomial method. Results: We retrieved 143 eligible studies, describing 366 patients. Of 647 thrombotic events, 53% (95% CI: 49–56) were venous thromboses at unusual sites and 30% (95% CI: 27–34) were cerebral venous sinus thromboses (CVSTs). The ratio of venous-to-arterial events was 4.1. Thromboses in most sites were associated with at least another thrombotic event, with the exception of CVST and CNS arterial thrombosis (isolated in 49 and 39% of cases, respectively). Bleeding occurred in 36% (95% CI: 31–41) of patients; 68% (95% CI: 59–75) of bleeding events were intracranial hemorrhages (ICHs). Overall mortality was 24% (95% CI: 19–29), and 77% (95% CI: 58–90) in patients with isolated CVST complicated by ICH. Conclusion: VITT displays a venous-to-arterial thrombosis ratio comparable to heparin-induced thrombocytopenia. However, VITT is characterized by a higher prevalence of CVST and ICH, which contribute to the increased bleeding frequency and mortality.
Keywords	adenovirus ; platelet ; hemorrhage ; thrombocytopenia ; thrombosis
Language	English
Publishing date	2023-12-18
Publisher	Georg Thieme Verlag KG
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	518294-3
ISSN	2567-689X ; 0340-6245
ISSN (online)	2567-689X
ISSN	0340-6245
DOI	10.1055/s-0043-1777134
Database	Thieme publisher's database

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Article ; Online: SARS-CoV-2 nucleocapsid protein inhibits the PKR-mediated integrated stress response through RNA-binding domain N2b.

Aloise, Chiara / Schipper, Jelle G / van Vliet, Arno / Oymans, Judith / Donselaar, Tim / Hurdiss, Daniel L / de Groot, Raoul J / van Kuppeveld, Frank J M

PLoS pathogens

2023 Volume 19, Issue 8, Page(s) e1011582

Abstract: The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), ...

Abstract	The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding-prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Similar observations were made for the N protein of human coronavirus 229E, suggesting that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; DNA Helicases ; COVID-19 ; Poly-ADP-Ribose Binding Proteins ; RNA Helicases ; RNA Recognition Motif Proteins/genetics ; RNA-Binding Motifs ; Encephalomyocarditis virus
Chemical Substances	DNA Helicases (EC 3.6.4.-) ; Poly-ADP-Ribose Binding Proteins ; RNA Helicases (EC 3.6.4.13) ; RNA Recognition Motif Proteins ; G3BP1 protein, human (EC 3.6.4.12)
Language	English
Publishing date	2023-08-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011582
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Article ; Online: SARS-CoV-2 nucleocapsid protein inhibits the stress response through RNA-binding domain N2b

Aloise, Chiara / Schipper, Jelle G. / Donselaar, Tim / Hurdiss, Daniel L. / de Groot, Raoul J. / van Kuppeveld, Frank J.M.

bioRxiv

Abstract	The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding - prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Observations made for the N protein of human coronavirus 229E suggests that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
Keywords	covid19
Language	English
Publishing date	2022-09-02
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.09.02.506332
Database	COVID19

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Article ; Online: Stability of an aggregation-prone partially folded state of human profilin-1 correlates with aggregation propensity.

Del Poggetto, Edoardo / Toto, Angelo / Aloise, Chiara / Di Piro, Francesco / Gori, Ludovica / Malatesta, Francesco / Gianni, Stefano / Chiti, Fabrizio / Bemporad, Francesco

The Journal of biological chemistry

2018 Volume 293, Issue 26, Page(s) 10303–10313

Abstract: A set of missense mutations in the gene encoding profilin-1 has been linked to the onset of familial forms of ALS (fALS), also known as Lou Gehrig's disease. The pathogenic potential of these mutations is linked to the formation of intracellular ... ...

Abstract	A set of missense mutations in the gene encoding profilin-1 has been linked to the onset of familial forms of ALS (fALS), also known as Lou Gehrig's disease. The pathogenic potential of these mutations is linked to the formation of intracellular inclusions of the mutant proteins and correlates with the mutation-induced destabilization of its native, fully folded state. However, the mechanism by which these mutations promote misfolding and self-assembly is yet unclear. Here, using temperature-jump and stopped-flow kinetic measurements, we show that, during refolding, WT profilin-1 transiently populates a partially folded (PF) state endowed with hydrophobic clusters exposed to the solvent and with no detectable secondary structure. We observed that this conformational state is marginally stable at neutral pH but becomes significantly populated at mildly acidic pH. Interestingly, the fALS-associated mutations did not cause a change in the refolding mechanism of profilin-1, but induced a stabilization of the PF state. In the presence of preformed profilin-1 aggregates, the PF state, unlike the unfolded and folded states, could interact with these aggregates via nonspecific hydrophobic interactions and also increase thioflavin-T fluorescence, revealing its amyloidogenic potential. Moreover, in the variants tested, we found a correlation between conformational stability of PF and aggregation propensity, defining this conformational state as an aggregation-prone folding intermediate. In conclusion, our findings indicate that mutation-induced stabilization of a partially folded state can enhance profilin-1 aggregation and thereby contribute to the pathogenicity of the mutations.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Humans ; Hydrogen-Ion Concentration ; Mutation ; Profilins/chemistry ; Profilins/genetics ; Profilins/metabolism ; Protein Aggregates ; Protein Folding ; Protein Refolding ; Protein Stability
Chemical Substances	PFN1 protein, human ; Profilins ; Protein Aggregates
Language	English
Publishing date	2018-05-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.002087
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Article ; Online: Comprehensive response to Usutu virus following first isolation in blood donors in the Friuli Venezia Giulia region of Italy: Development of recombinant NS1-based serology and sensitivity to antiviral drugs.

Caracciolo, Ilaria / Mora-Cardenas, Erick / Aloise, Chiara / Carletti, Tea / Segat, Ludovica / Burali, Maria Sole / Chiarvesio, Alexsia / Totis, Vivianna / Avšič-Županc, Tatjana / Mastrangelo, Eloise / Manfroni, Giuseppe / D'Agaro, Pierlanfranco / Marcello, Alessandro

PLoS neglected tropical diseases

2020 Volume 14, Issue 3, Page(s) e0008156

Abstract: Surveillance of Usutu virus is crucial to prevent future outbreaks both in Europe and in other countries currently naïve to the infection, such as the Americas. This goal remains difficult to achieve, notably because of the lack of large-scale cohort ... ...

Abstract	Surveillance of Usutu virus is crucial to prevent future outbreaks both in Europe and in other countries currently naïve to the infection, such as the Americas. This goal remains difficult to achieve, notably because of the lack of large-scale cohort studies and the absence of commercially available diagnostic reagents for USUV. This work started with the first identification of USUV in a blood donor in the Friuli Venezia Giulia (FVG) Region in Northern-Eastern Italy, which is endemic for West Nile virus. Considering that only one IgG ELISA is commercially available, but none for IgM, a novel NS1 antigen based IgG/M ELISA has been developed. This assay tested successfully for the detection of Usutu virus in blood donors with the identification of a second case of transmission and high levels of exposure. Furthermore, two pan-flavivirus antiviral drugs, that we previously characterized to be inhibitors of other flavivirus infectivity, were successfully tested for inhibition of Usutu virus with inhibitory concentrations in the low micromolar range. To conclude, this work identifies North-Eastern Italy as endemic for Usutu virus with implications for the screening of transfusion blood. A novel NS1-based ELISA test has been implemented for the detection of IgM/G that will be of importance as a tool for the diagnosis and surveillance of Usutu virus infection. Finally, Usutu virus is shown to be sensitive to a class of promising pan-flavivirus drugs.
MeSH term(s)	Antibodies, Viral/blood ; Antiviral Agents/pharmacology ; Blood/virology ; Blood Donors ; Enzyme-Linked Immunosorbent Assay/methods ; Female ; Flavivirus/drug effects ; Flavivirus/isolation & purification ; Flavivirus Infections/diagnosis ; Humans ; Immunoglobulin G/blood ; Immunoglobulin M/blood ; Italy ; Microbial Sensitivity Tests ; Neutralization Tests/methods ; Serologic Tests/methods ; Viral Nonstructural Proteins/immunology
Chemical Substances	Antibodies, Viral ; Antiviral Agents ; Immunoglobulin G ; Immunoglobulin M ; NS1 protein, Flavivirus ; Viral Nonstructural Proteins
Language	English
Publishing date	2020-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2727
ISSN (online)	1935-2735
ISSN	1935-2727
DOI	10.1371/journal.pntd.0008156
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