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Research Project: NEW AND EMERGING VIRAL AND BACTERIAL DISEASES OF ORNAMENTAL PLANTS: DETECTION, IDENTIFICATION, AND CHARACTERIZATION

Location: Floral and Nursery Plants Research

Title: Create four new unassigned species in the family Tombusviridae

Author
item Scheets, Kay - Oklahoma State University
item Hernandez, Carmen - Polytechnic University Of Valencia (UPV)
item Jordan, Ramon
item White, Andy - York University

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/9/2014
Publication Date: 9/26/2014
Publication URL: http://www.ictvonline.org/proposals-14/2014.006aP.A.v2.Tombusviridae_4sp.pdf
Citation: Scheets, K., Hernandez, C., Jordan, R.L., White, A. 2014. Create four new unassigned species in the family Tombusviridae. Archives of Virology. DOI:10.1007/s00705-015-2500-5.

Interpretive Summary: A significant factor in the continued growth of the ornamentals industry is the introduction of new plant species and varieties to the trade; however the introduction of new plant materials also brings the risk of new viral diseases as new crops are introduced or grown in new areas. Viral diseases cause significant losses to production and/or quality, and are impossible to control directly with agrochemicals. Methods to reliably and rapidly detect and identify viruses are necessary for the production of pathogen-free or pathogen-indexed plants, and for general virological investigations. Improved knowledge on genomes and genetic relationships are also essential for epidemiological studies and disease diagnosis and control. Understanding viral genome structures and functions, and the mechanisms of viral and bacterial pathogenicity, will lead to a better understanding of host-pathogen interactions and mechanisms of plant disease resistance. Over the past several years research on established and new or emerging viruses of geranium and roses has revealed that several of these viruses posses unique biochemical and genomic features that differentiate them from other presumably related viruses. This report proposes to establish a new plant virus genus in the family Tombusviridae. The distinct properties of the proposed six species are described and delineated, the species type member is designated, and the new genus name, Pelarspovirus, is given. Characterization and classification of the viruses infecting ornamental and agronomic plants will add to our knowledge of the taxonomy and biology of these viral plant pathogens and will be applied to the detection and identification of new and emerging viruses infecting ornamentals. Improved detection and differentiation methods for these pathogens will be used by state and federal regulatory officials to make timely and appropriate recommendations in safeguarding the movement of horticultural and agricultural products into and through the United States.

Technical Abstract: The proposed genus Pelarspovirus contains six viral species with similar biological, morphological, physicochemical, and ultrastructural properties. These viruses are Elderberry latent virus, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. No vector is known although transmission is by grafting and, mechanical inoculation, and dispersal is through infected propagating material. Virions are spherical and ~30-32 nm in diameter with a single capsid protein of 35-37 kDa and do not contain lipids or carbohydrates. The single-stranded, positive sense RNA genome is ~ 3883-3971 nucleotides in size and is made up of five open reading frames (ORFs). ORF1 encodes a 27-kDa peptide (p27). ORF2 shares a common start codon with ORF1 and continues through the amber stop codon of p27 to produce an 87-kDa protein (p87) with amino acid sequence similarity to the RNA-dependent RNA polymerases (RdRp) of members of the family Tombusviridae. ORF3 encodes a putative 7-kDa peptide designated movement protein 1 (MP1). ORF4, predicted to initiate with a non-canonical start codon, encodes MP2 (p9). The coat protein is encoded by ORF5. When analyzed, two major dsRNAs of ~4.0kb and 1.6-1.8kb are detected in infected plants. The genome structure and organization (i.e. number and order of genes) closely resembles that of the genus Carmovirus. However, unlike carmoviruses which produce two sgRNAs, these viruses are known or predicted to produce only one sgRNA encoding genes in the 3' half of their genomes. Thus, leaky scanning of MP1 and MP2 start codons allows production of three proteins from one sgRNA. Phylogenetic analyses of the predicted proteins results in a cluster separate from the other Tombusviridae members, including carmoviruses. Suggested species demarcation criteria in the new genus include <75% amino acid sequence identity in RdRp proteins and <75% identity in coat proteins. Pelargonium line pattern virus is the well-characterized member and is designated as type species. The origin of the new genus name is the sigla from Pelargonium ringspot virus, the first of these viruses to be named and described.