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      ICTV Virus Taxonomy Profile: Picornaviridae

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          Abstract

          The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal–oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.

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          VIPERdb2: an enhanced and web API enabled relational database for structural virology

          Mauricio Carrillo-Tripp, Craig Shepherd, Ian A. Borelli … (2009)
          VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ (Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
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            Picornavirus morphogenesis.

            Ping Jiang, Ying Liu, Hsin-Chieh Ma … (2014)
            The Picornaviridae represent a large family of small plus-strand RNA viruses that cause a bewildering array of important human and animal diseases. Morphogenesis is the least-understood step in the life cycle of these viruses, and this process is difficult to study because encapsidation is tightly coupled to genome translation and RNA replication. Although the basic steps of assembly have been known for some time, very few details are available about the mechanism and factors that regulate this process. Most of the information available has been derived from studies of enteroviruses, in particular poliovirus, where recent evidence has shown that, surprisingly, the specificity of encapsidation is governed by a viral protein-protein interaction that does not involve an RNA packaging signal. In this review, we make an attempt to summarize what is currently known about the following topics: (i) encapsidation intermediates, (ii) the specificity of encapsidation (iii), viral and cellular factors that are required for encapsidation, (iv) inhibitors of encapsidation, and (v) a model of enterovirus encapsidation. Finally, we compare some features of picornavirus morphogenesis with those of other plus-strand RNA viruses.
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              Structural insights into viral IRES-dependent translation mechanisms.

              Gloria Lozano, Encarnación Martínez-Salas (2015)
              A diverse group of viruses subvert the host translational machinery to promote viral genome translation. This process often involves altering canonical translation initiation factors to repress cellular protein synthesis while viral proteins are efficiently synthesized. The discovery of this strategy in picornaviruses, which is based on the use of internal ribosome entry site (IRES) elements, opened new avenues to study alternative translational control mechanisms evolved in different groups of RNA viruses. IRESs are cis-acting RNA sequences that adopt three-dimensional structures and recruit the translation machinery assisted by a subset of translation initiation factors and various RNA binding proteins. However, IRESs present in the genome of different RNA viruses perform the same function despite lacking conservation of primary sequence and secondary RNA structure, and differing in host factor requirement to recruit the translation machinery. Evolutionary conserved motifs tend to preserve sequences impacting on RNA structure and RNA-protein interactions important for IRES function. While some motifs are found in various picornavirus IRESs, others occur only in one type reflecting specialized factor requirements. This review is focused to describe recent advances on the principles and RNA structure features of picornavirus IRESs.
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Gen Virol
                Journal ID (iso-abbrev): J. Gen. Virol
                Journal ID (publisher-id): JGV
                Title: The Journal of General Virology
                Publisher: Microbiology Society
                ISSN (Print): 0022-1317
                ISSN (Electronic): 1465-2099
                Publication date (Print): October 2017
                Publication date (Electronic): 8 September 2017
                Publication date PMC-release: 8 September 2017
                Volume: 98
                Issue: 10
                Pages: 2421-2422
                Affiliations
                [ 1​ ] Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University , Jena, Germany
                [ 2​ ] Department of Laboratory Medicine, Blood System Research Institute, University of California , San Francisco, CA, USA
                [ 3​ ] Department of Medical Microbiology, Leiden University Medical Center , Leiden, The Netherlands
                [ 4​ ] National Institute for Health and Welfare (THL) , Helsinki, Finland
                [ 5​ ] The Pirbright Institute , Woking, Surrey, UK
                [ 6​ ] Department of Chemistry and Biomedical Sciences, Linnaeus University , Kalmar, Sweden
                [ 7​ ] Division of Viral Diseases, Centers for Disease Control and Prevention (CDC) , Atlanta, GA, USA
                [ 8​ ] Department of Biochemistry, Institute for Molecular Virology , Madison, WI, USA
                [ 9​ ] Department of Medical Microbiology and Immunology, University of Pécs , Pécs, Hungary
                [ 10​ ] Nuffield Department of Medicine, University of Oxford , Oxford, UK
                [ 11​ ] Max F. Perutz Laboratories, Medical University of Vienna , Vienna, Austria
                [ 12​ ] Department of Biological Sciences, University of Essex , Colchester, UK
                [ 13​ ] Department of Food Science and Nutrition, Faculty of Health and Nutrition, Shubun University , Aichi, Japan
                Author notes
                *Correspondence: R. Zell, Roland.Zell@ 123456med.uni-jena.de
                Article
                Publisher ID: 000911
                DOI: 10.1099/jgv.0.000911
                PMC ID: 5725991
                PubMed ID: 28884666
                SO-VID: c0eebbdb-d96c-4e63-b4f2-5e21e53cacbe
                Copyright statement: Copyright @ 2017
                License:

                This is an open access article under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 22 June 2017
                Date accepted : 01 August 2017
                Funding
                Funded by: Wellcome Trust
                Award ID: WT108418AIA
                Categories
                Subject: ICTV Virus Taxonomy Profiles
                Subject: Animal
                Subject: Positive-strand RNA Viruses
                Custom metadata
                OpenAccessEmbargo 0

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: picornaviridae,ictv,taxonomy,poliovirus,foot-and-mouth disease virus,rhinovirus,enterovirus
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: picornaviridae, ictv, taxonomy, poliovirus, foot-and-mouth disease virus, rhinovirus, enterovirus

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