1
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Huston NC, Tsao LH, Brackney DE, Pyle AM. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proc Natl Acad Sci U S A 2024; 121:e2312080121. [PMID: 38985757 PMCID: PMC11260092 DOI: 10.1073/pnas.2312080121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 05/25/2024] [Indexed: 07/12/2024] Open
Abstract
West Nile virus (WNV) is an arthropod-borne, positive-sense RNA virus that poses an increasing global threat due to warming climates and lack of effective therapeutics. Like other enzootic viruses, little is known about how host context affects the structure of the full-length RNA genome. Here, we report a complete secondary structure of the entire WNV genome within infected mammalian and arthropod cell lines. Our analysis affords structural insights into multiple, conserved aspects of flaviviral biology. We show that the WNV genome folds with minimal host dependence, and we prioritize well-folded regions for functional validation using structural homology between hosts as a guide. Using structure-disrupting, antisense locked nucleic acids, we then demonstrate that the WNV genome contains riboregulatory structures with conserved and host-specific functional roles. These results reveal promising RNA drug targets within flaviviral genomes, and they highlight the therapeutic potential of ASO-LNAs as both WNV-specific and pan-flaviviral therapeutic agents.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Lucille H. Tsao
- Department of Chemistry, Yale University, New Haven, CT06511
| | - Doug E. Brackney
- Department of Entomology, Connecticut Agricultural Experimental Station, New Haven, CT06511
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- HHMI, Chevy Chase, MD20815
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2
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VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics 2020; 21:211. [PMID: 32448124 PMCID: PMC7245624 DOI: 10.1186/s12859-020-3537-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Background GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Since March 2020, VADR has also been used to check SARS-CoV-2 sequence submissions. Other viruses with high numbers of submissions will be added incrementally. Conclusion VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.
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3
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Faggioni G, De Santis R, Pomponi A, Grottola A, Serpini GF, Meacci M, Gennari W, Tagliazucchi S, Pecorari M, Monaco F, Savini G, Benedetti E, Remoli ME, Fortuna C, Venturi G, Rezza G, Lista F. Prevalence of Usutu and West Nile virus antibodies in human sera, Modena, Italy, 2012. J Med Virol 2018; 90:1666-1668. [PMID: 29797606 DOI: 10.1002/jmv.25230] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/16/2018] [Indexed: 12/12/2022]
Abstract
A collection of 3069 human sera collected in the area of the municipality of Modena, Emilia Romagna, Italy, was retrospectively investigated for specific antibodies against Usutu (USUV) and West Nile viruses (WNV). All the samples resulting positive using a preliminary screening test were analyzed with the plaque reduction neutralization test. Overall, 24 sera were confirmed as positive for USUV (0.78%) and 13 for WNV (0.42%). The results suggest that in 2012, USUV was circulating more than WNV in North-eastern Italy.
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Affiliation(s)
| | | | - Alice Pomponi
- Scientific Department, Army Medical Center, Roma, Italy
| | - Antonella Grottola
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | | | - Marisa Meacci
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - William Gennari
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Sara Tagliazucchi
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Monica Pecorari
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Federica Monaco
- OIE Reference Laboratory for West Nile Fever, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Giovanni Savini
- OIE Reference Laboratory for West Nile Fever, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Teramo, Italy
| | - Eleonora Benedetti
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Roma, ltaly
| | - Maria Elena Remoli
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Roma, ltaly
| | - Claudia Fortuna
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Roma, ltaly
| | - Giulietta Venturi
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Roma, ltaly
| | - Giovanni Rezza
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Roma, ltaly
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4
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Barrows NJ, Campos RK, Liao KC, Prasanth KR, Soto-Acosta R, Yeh SC, Schott-Lerner G, Pompon J, Sessions OM, Bradrick SS, Garcia-Blanco MA. Biochemistry and Molecular Biology of Flaviviruses. Chem Rev 2018; 118:4448-4482. [PMID: 29652486 DOI: 10.1021/acs.chemrev.7b00719] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.
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Affiliation(s)
- Nicholas J Barrows
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Rafael K Campos
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Department of Molecular Genetics and Microbiology , Duke University , Durham , North Carolina 27710 , United States
| | - Kuo-Chieh Liao
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Ruben Soto-Acosta
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Shih-Chia Yeh
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Julien Pompon
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore.,MIVEGEC, IRD, CNRS, Université de Montpellier , Montpellier 34090 , France
| | - October M Sessions
- Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , Galveston , Texas 77555 , United States.,Programme in Emerging Infectious Diseases , Duke-NUS Medical School , Singapore 169857 , Singapore
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5
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Delcourt V, Staskevicius A, Salzet M, Fournier I, Roucou X. Small Proteins Encoded by Unannotated ORFs are Rising Stars of the Proteome, Confirming Shortcomings in Genome Annotations and Current Vision of an mRNA. Proteomics 2017. [DOI: 10.1002/pmic.201700058] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vivian Delcourt
- Department of Biochemistry; Université de Sherbrooke; Quebec Canada
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
- PROTEO, Quebec Network for Research on Protein Function; Structure, and Engineering; Quebec Canada
| | | | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique; Réponse Inflammatoire & Spectrométrie de Masse (PRISM); Lille France
| | - Xavier Roucou
- Department of Biochemistry; Université de Sherbrooke; Quebec Canada
- PROTEO, Quebec Network for Research on Protein Function; Structure, and Engineering; Quebec Canada
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6
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Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schäffer AA, Brister JR. Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res 2016; 45:D482-D490. [PMID: 27899678 PMCID: PMC5210549 DOI: 10.1093/nar/gkw1065] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023] Open
Abstract
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can select sequences based on standardized gene, protein and metadata terms. Once sequences are selected, a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety of user directed activities. This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource.
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Affiliation(s)
- Eneida L Hatcher
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sergey A Zhdanov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri Ostapchuck
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Frajese GV, Benvenuto M, Fantini M, Ambrosin E, Sacchetti P, Masuelli L, Giganti MG, Modesti A, Bei R. Potassium increases the antitumor effects of ascorbic acid in breast cancer cell lines in vitro. Oncol Lett 2016; 11:4224-4234. [PMID: 27313770 DOI: 10.3892/ol.2016.4506] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 02/08/2016] [Indexed: 12/17/2022] Open
Abstract
Ascorbic acid (A) has been demonstrated to exhibit anti-cancer activity in association with chemotherapeutic agents. Potassium (K) is a regulator of cellular proliferation. In the present study, the biological effects of A and K bicarbonate, alone or in combination (A+K), on breast cancer cell lines were evaluated. The survival of cancer cells was determined by sulforhodamine B cell proliferation assay, while analysis of the cell cycle distribution was conducted via fluorescence-activated cell sorting. In addition, the expression of signaling proteins was analyzed upon treatment. The results indicated that there was a heterogeneous response of the different cell lines to A and K, and the best effects were achieved by A+K and A treatment. The interaction between A+K indicated an additive or synergistic effect. In addition, A+K increased the percentage of cells in the sub-G1 phase of the cell cycle, and was the most effective treatment in activating the degradation of poly(adenosine diphosphate-ribose) polymerase-1. In the breast cancer cell line MCF-7, A+K induced the appearance of the 18 kDa isoform of B-cell lymphoma-2-associated X protein (Bax), which is a more potent inducer of apoptosis than the full-length Bax-p21. The effects of A and K on the phosphorylation of extracellular signal-regulated kinase (ERK)1 and ERK2 were heterogeneous. In addition, treatment with K, A and A+K inhibited the expression of nuclear factor-κB. Overall, the results of the present study indicated that K potentiated the anti-tumoral effects of A in breast cancer cells in vitro.
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Affiliation(s)
- Giovanni Vanni Frajese
- Department of Sports Science, Human and Health, University of Rome 'Foro Italico', Rome I-00135, Italy
| | - Monica Benvenuto
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome I-00133, Italy
| | - Massimo Fantini
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome I-00133, Italy
| | - Elena Ambrosin
- Department of Sports Science, Human and Health, University of Rome 'Foro Italico', Rome I-00135, Italy
| | - Pamela Sacchetti
- Department of Experimental Medicine, University of Rome 'Sapienza', Rome I-00185, Italy
| | - Laura Masuelli
- Department of Experimental Medicine, University of Rome 'Sapienza', Rome I-00185, Italy
| | - Maria Gabriella Giganti
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome I-00133, Italy
| | - Andrea Modesti
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome I-00133, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome I-00133, Italy
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8
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Černý J, Selinger M, Palus M, Vavrušková Z, Tykalová H, Bell-Sakyi L, Štěrba J, Grubhoffer L, Růžek D. Expression of a second open reading frame present in the genome of tick-borne encephalitis virus strain Neudoerfl is not detectable in infected cells. Virus Genes 2016; 52:309-16. [PMID: 26924586 DOI: 10.1007/s11262-015-1273-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 12/10/2015] [Indexed: 12/30/2022]
Abstract
A short upstream open reading frame (uORF) was recently identified in the 5' untranslated region of some tick-borne encephalitis virus (TBEV) strains. However, it is not known if the peptide encoded by TBEV uORF (TuORF) is expressed in infected cells. Here we show that TuORF forms three phylogenetically separated clades which are typical of European, Siberian, and Far-Eastern TBEV subtypes. Analysis of selection pressure acting on the TuORF area showed that it is under positive selection pressure. Theoretically, TuORF may code for a short hydrophobic peptide embedded in a biological membrane. However, expression of TuORF was detectable neither by immunoblotting in tick and mammalian cell lines infected with TBEV nor by immunofluorescence in TBEV-infected mammalian cell lines. These results support the idea that TuORF is not expressed in TBEV-infected cell or expressed in undetectably low concentrations. Therefore we can assume that TuORF has either minor or no biological role in the TBEV life cycle.
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Affiliation(s)
- Jiří Černý
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic. .,Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic.
| | - Martin Selinger
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Zuzana Vavrušková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Tykalová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Lesley Bell-Sakyi
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Ján Štěrba
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
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9
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Rapid molecular detection and genotyping of West Nile Virus lineages 1 and 2 by real time PCR and melting curve analysis. J Virol Methods 2014; 207:54-9. [PMID: 24992671 DOI: 10.1016/j.jviromet.2014.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/26/2014] [Accepted: 06/24/2014] [Indexed: 11/20/2022]
Abstract
Following its spread in the USA, West Nile Virus (WNV) has reemerged in the Mediterranean basin with a renewed pathogenicity. The introduction of WNV lineage 2 in Europe and its co-circulation with lineage 1 has resulted in a continuously changing epidemiological scenario, highlighting the importance of differential detection of the two lineages. The paper describes a new real-time PCR method for the detection and genotyping of the two main lineages of WNV. The method requires a single pair of primers and probes and is based on the analysis of highly conserved consensus sequences detected in the 5' terminus of the viral genome.
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10
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Chabierski S, Barzon L, Papa A, Niedrig M, Bramson JL, Richner JM, Palù G, Diamond MS, Ulbert S. Distinguishing West Nile virus infection using a recombinant envelope protein with mutations in the conserved fusion-loop. BMC Infect Dis 2014; 14:246. [PMID: 24884467 PMCID: PMC4028281 DOI: 10.1186/1471-2334-14-246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND West Nile Virus (WNV) is an emerging mosquito-transmitted flavivirus that continues to spread and cause disease throughout several parts of the world, including Europe and the Americas. Specific diagnosis of WNV infections using current serological testing is complicated by the high degree of cross-reactivity between antibodies against other clinically relevant flaviviruses, including dengue, tick-borne encephalitis (TBEV), Japanese encephalitis (JEV), and yellow fever (YFV) viruses. Cross-reactivity is particularly problematic in areas where different flaviviruses co-circulate or in populations that have been immunized with vaccines against TBEV, JEV, or YFV. The majority of cross-reactive antibodies against the immunodominant flavivirus envelope (E) protein target a conserved epitope in the fusion loop at the distal end of domain II. METHODS We tested a loss-of-function bacterially expressed recombinant WNV E protein containing mutations in the fusion loop and an adjacent loop domain as a possible diagnostic reagent. By comparing the binding of sera from humans infected with WNV or other flaviviruses to the wild type and the mutant E proteins, we analyzed the potential of this technology to specifically detect WNV antibodies. RESULTS Using this system, we could reliably determine WNV infections. Antibodies from WNV-infected individuals bound equally well to the wild type and the mutant protein. In contrast, sera from persons infected with other flaviviruses showed significantly decreased binding to the mutant protein. By calculating the mean differences between antibody signals detected using the wild type and the mutant proteins, a value could be assigned for each of the flaviviruses, which distinguished their pattern of reactivity. CONCLUSIONS Recombinant mutant E proteins can be used to discriminate infections with WNV from those with other flaviviruses. The data have important implications for the development of improved, specific serological assays for the detection of WNV antibodies in regions where other flaviviruses co-circulate or in populations that are immunized with other flavivirus vaccines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sebastian Ulbert
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany.
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11
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B cell response and mechanisms of antibody protection to West Nile virus. Viruses 2014; 6:1015-36. [PMID: 24594676 PMCID: PMC3970136 DOI: 10.3390/v6031015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 01/03/2023] Open
Abstract
West Nile virus (WNV) has become the principal cause of viral encephalitis in North America since its introduction in New York in 1999. This emerging virus is transmitted to humans via the bite of an infected mosquito. While there have been several candidates in clinical trials, there are no approved vaccines or WNV-specific therapies for the treatment of WNV disease in humans. From studies with small animal models and convalescent human patients, a great deal has been learned concerning the immune response to infection with WNV. Here, we provide an overview of a subset of that information regarding the humoral and antibody response generated during WNV infection.
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12
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Replication cycle and molecular biology of the West Nile virus. Viruses 2013; 6:13-53. [PMID: 24378320 PMCID: PMC3917430 DOI: 10.3390/v6010013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/27/2022] Open
Abstract
West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated.
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13
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Chabierski S, Makert GR, Kerzhner A, Barzon L, Fiebig P, Liebert UG, Papa A, Richner JM, Niedrig M, Diamond MS, Palù G, Ulbert S. Antibody responses in humans infected with newly emerging strains of West Nile Virus in Europe. PLoS One 2013; 8:e66507. [PMID: 23776680 PMCID: PMC3680493 DOI: 10.1371/journal.pone.0066507] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/06/2013] [Indexed: 11/18/2022] Open
Abstract
Infection with West Nile Virus (WNV) affects an increasing number of countries worldwide. Although most human infections result in no or mild flu-like symptoms, the elderly and those with a weakened immune system are at higher risk for developing severe neurological disease. Since its introduction into North America in 1999, WNV has spread across the continental United States and caused annual outbreaks with a total of 36,000 documented clinical cases and ∼1,500 deaths. In recent years, outbreaks of neuroinvasive disease also have been reported in Europe. The WNV strains isolated during these outbreaks differ from those in North America, as sequencing has revealed that distinct phylogenetic lineages of WNV concurrently circulate in Europe, which has potential implications for the development of vaccines, therapeutics, and diagnostic tests. Here, we studied the human antibody response to European WNV strains responsible for outbreaks in Italy and Greece in 2010, caused by lineage 1 and 2 strains, respectively. The WNV structural proteins were expressed as a series of overlapping fragments fused to a carrier-protein, and binding of IgG in sera from infected persons was analyzed. The results demonstrate that, although the humoral immune response to WNV in humans is heterogeneous, several dominant peptides are recognized.
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Affiliation(s)
- Stefan Chabierski
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Gustavo R. Makert
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Alexandra Kerzhner
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Petra Fiebig
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Uwe G. Liebert
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Justin M. Richner
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Missouri, St. Louis, United States of America
| | | | - Michael S. Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, Missouri, St. Louis, United States of America
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Sebastian Ulbert
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- * E-mail:
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14
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Izzi V, Chiurchiù V, Doldo E, Palumbo C, Tresoldi I, Bei R, Albonici L, Modesti A. Interleukin-17 Produced by Malignant Mesothelioma-Polarized Immune Cells Promotes Tumor Growth and Invasiveness. EUR J INFLAMM 2013. [DOI: 10.1177/1721727x1301100119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Malignant mesothelioma (MM) is a highly fatal tumor of inner body membranes, the extensive growth of which is supported by both a weak immunogenicity and the ability to reprogram surrounding immune cells towards tumor-supporting phenotypes. Interleukin-17 (IL-17) is a major inflammatory cytokine which is now accepted as the paradigmatic cytokine of many autoimmune diseases; however, its role in tumor immunology has only been partially unraveled, and no data exist regarding its possible involvement in MM. Thus, in this work we evaluated the ability of MM to induce IL-17 production in immune cells and the effects of IL-17 on MM growth and invasiveness. Our data show for the first time that macrophages and CD4+ T-cells are polarized by MM to produce IL-17, and that this cytokine exerts multiple tumor-supporting effects on both cell growth and invasiveness. These data provide novel evidence of the crosstalk occurring between MM and immune cells and suggest potential targets for the development of new pharmacological approaches for MM treatment.
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Affiliation(s)
- V. Izzi
- Center for Cell-Matrix Research and Biocenter Oulu, Department of Medical Biochemistry and Molecular Biology, University of Oulu, Oulu, Finland
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - V. Chiurchiù
- European Center for Brain Research (CERC)/Santa Lucia Foundation I.R.C.C.S., Rome, Italy
| | - E. Doldo
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - C. Palumbo
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - I. Tresoldi
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - R. Bei
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - L. Albonici
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - A. Modesti
- Department of Clinical Sciences and Translational Medicine, Faculty of Medicine, University of Rome “Tor Vergata”, Rome, Italy
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