Virology Division News : The new plant virus family Flexiviridae and assessment of molecular criteria for species demarc
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The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation M. J. Adams1 , J. F. Antoniw1 , M. Bar-Joseph2 , A. A. Brunt3 , T. Candresse4 , G. D. Foster5 , G. P. Martelli6 , R. G. Milne7 , and C. M. Fauquet8 1 Plant
Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts, U.K. 2 Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel 3 Department of Microbiology and Plant Pathology, Horticulture Research International, Wellesbourne, U.K. 4 Equipe de Virologie, UMR GD2P, Villenave d’Ornon, France 5 School of Biological Sciences, University of Bristol, Bristol, U.K. 6 Dipartimento di Protezione delle Piante e Microbiologia Applicata, Bari, Italy 7 Istituto di Virologia Vegetale CNR, Torino, Italy 8 ILTAB, Danforth Plant Science Center, St Louis, Missouri, U.S.A. Received October 31, 2003; accepted January 29, 2004 c Springer-Verlag 2004 Published online May 2, 2004
Summary. The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fullysequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes. Introduction The International Committee on Taxonomy of Viruses (ICTV) has recently approved a proposal to create a plant virus family Flexiviridae. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus together with the new genus Mandarivirus,
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and some related viruses not assigned to any genus. The chief characteristics of members of the family are: 1. Flexuous filamentous virions 12–13 nm in diameter 2. Monopartite, positive sense, ssRNA genomes with a 3 -polyA tail 3. Translation of at least some ORFs from subgenomic mRNAs (there is increasing evidence that viruses in the family employ both 5 - and 3 -coterminal subgenomic mRNAs [7, Bar-Joseph unpublished data]) 4. Up to 6 open reading frames ordered from 5 to 3 : a) An alpha-like replication protein (150–250 kDa) containing conserved methyl transferase, helicase and RNA-dependent RNA polymerase (RdRp) motifs [9] b) One or more movement proteins (MP) c) A single capsid (coat) protein (CP) (22–44 kDa) d) A sixth ORF in some virus
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