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      ICTV Virus Taxonomy Profile: Potyviridae

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          Abstract

          The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide. There are eight genera, distinguished by the host range, genomic features and phylogeny of the member viruses. Genomes range from 8.2 to 11.3 kb, with an average size of 9.7 kb. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Potyviridae, which is available at www.ictv.global/report/potyviridae.

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          Molecular criteria for genus and species discrimination within the family Potyviridae.

          J Antoniw, C Fauquet, J. Adams (2005)
          A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.
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            RNA polymerase slippage as a mechanism for the production of frameshift gene products in plant viruses of the potyviridae family.

            Bernardo Rodamilans, Adrián Valli, Ares Mingot … (2015)
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              An unusual structure at one end of potato potyvirus particles.

              Kristiina Mäkinen, Rasa Gabrenaite-Verkhovskaya, M. E. Taliansky … (2006)
              The particles of potato virus Y (PVY) and potato virus A (PVA) potyviruses are helically constructed filaments that are thought to contain a single type of coat protein subunit. Examination of negatively stained virions by electron microscopy reveals flexuous rod-shaped particles with no obvious terminal structures. It is known that some helically constructed rod-shaped virus particles incorporate additional minor protein components, which form stable complexes that mediate particle disassembly, movement or transmission by vectors. Some of this information has been obtained using imaging techniques such as atomic force microscopy. The particles of PVY and PVA were examined by atomic force microscopy and immunogold labelling electron microscopy. Our results show that some of the potyvirus particles contain a protruding tip at one end of the virus particles, which is presumably associated with the 5'-end of viral RNA. The tip contains the virus-encoded proteins genome-linked protein and helper-component proteinase. The composition and possible roles of the terminal tip structures in virus biology are discussed.
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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): March 2017
                Publication date (Electronic): 1 April 2017
                Publication date PMC-release: 1 April 2017
                Volume: 98
                Issue: 3
                Pages: 352-354
                Affiliations
                [ 1​ ]State Agricultural Biotechnology Centre, Murdoch University , Perth, Western Australia 6150, Australia
                [ 2​ ]24 Woodland Way , Stevenage, Herts SG2 8BT, UK
                [ 3​ ]Division of Plant Quarantine, ICAR – National Bureau of Plant Genetic Resources , Pusa Campus, New Delhi 110012, India
                [ 4​ ]International Potato Center (CIP) , Apartado 1558, Lima 12, Peru
                [ 5​ ]Centre for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB, Campus Bellaterra , 08193 Barcelona, Spain
                [ 6​ ]Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga 840-8502, Japan
                [ 7​ ]Division of Biochemistry, Indian Agricultural Research Institute , New Delhi 110012, India
                [ 8​ ]Institute for Epidemiological and Pathogen Diagnosis, Julius Kuhn Institut , Quedlinburg, Saxony-Anhalt, Germany
                [ 9​ ]Crop Diseases, Pests, Genetics, ARS, USDA , 9611 S. Riverbend Ave., Parlier, CA 93648, USA
                [ 10​ ]London Research and Development Centre, Agriculture and Agri-Food Canada , 1391 Sandford St., London, Ontario N5V 4T3, Canada
                [ 11​ ]Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa , Viçosa, MG, 36570-900, Brazil
                Author notes
                *Correspondence: Stephen J. Wylie, s.wylie@ 123456murdoch.edu.au
                Article
                Publisher ID: 000740
                DOI: 10.1099/jgv.0.000740
                PMC ID: 5797945
                PubMed ID: 28366187
                SO-VID: 77d1e30f-a347-4509-94ea-1fa032e6c425
                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 : 02 February 2017
                Date accepted : 09 February 2017
                Funding
                Funded by: Wellcome Trust
                Award ID: WT108418AIA
                Categories
                Subject: ICTV Virus Taxonomy Profiles
                Subject: Plant
                Subject: RNA Viruses
                Custom metadata
                OpenAccessEmbargo 0

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: potyviridae,ictv report,taxonomy
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: potyviridae, ictv report, taxonomy

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