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00.067.0.01.005. Rice yellow mottle virus

Cite this publication as: ICTVdB Management (2006). 00.067.0.01.005. Rice yellow mottle virus. In: ICTVdB - The Universal Virus Database, version 4. Büchen-Osmond, C. (Ed), Columbia University, New York, USA

Cite this site as: ICTVdB - The Universal Virus Database, version 4. http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/

Table of Contents

Isolate Description

Location: Kisumu, Western part; Kenya.

Host of Isolate and Habitat Details
Source of isolate: Oryza sativa.

Natural host and symptoms
Oryza sativa — yellow or orange leaves, stunting, reduced tillering and sterility.

Oryza longistaminata — chlorosis and mottling.

Reference to Isolation Report
Bakker (1970).

Classification

This is a description of a plant virus at the species level with data on all virus properties from morphology to genome, replication, antigenicity and biological properties.

ICTVdB Virus Code: 00.067.0.01.005. Virus accession number: 67001005. Obsolete virus code: 67.0.1.0.005; superceded accession number: 67010005.
NCBI Taxon Identifier NCBI Taxonomy ID: 31744.

Name, Synonyms and Lineage

ICTV approved acronym: RYMV. Virus is an ICTV approved species of the genus 00.067.0.01. Sobemovirus; not assigned to a family.

Virion Properties

Morphology

Virions consist of a capsid. Virus capsid is not enveloped, round with icosahedral symmetry (T=3). The capsid is isometric and has a diameter of 29-32.2 nm. Capsids appear hexagonal in outline. The capsomer arrangement is clearly visible.

Electron microscopic preparation and references: Virus preparation contains many virions. Reference for electron microscopic methods: Bakker (1975, Fauquet and Thouvenel (1977).

Capsid structures, detailed structural and computational analysis are found in the Protein Data Bank (PDB) using VIPERdB, the VIrus Particle ExploreR 1f2n.

Physicochemical and Physical Properties

Virions have a buoyant density in CsCl of 1.359 g cm-3. There are 1 sedimenting component(s) found in purified preparations. The sedimentation coefficient is 116 S20w. Isoelectric point pH is 6. A260/A280 ratio is 1.46-1.54. The thermal inactivation point (TIP) is at 65-70°C (in sap from infected rice). The longevity in vitro (LIV) is 99 days (at 20°C), or 260 days (at 4°C). Although the titer is dependent on the host, the decimal exponent (DEX) of the dilution end point is usually around 6-9. The infectivity is not changed by treatment with ether.

Nucleic Acid

The Mr of the genome constitutes 23% of the virion by weight. The genome is monopartite. Only one particle size of linear, positive-sense, single-stranded RNA is recovered. The complete genome is 4200 nucleotides long, is fully or partially sequenced, complete sequence is 4200 nucleotides long. Sequence has the accession number

[L20893] Em(40)_vi:RYVCGEN Gb(84)_vi:RYVCGEN Rice yellow mottle virus complete genome. 2/94 4,450bp.
[U23142] Em(43)_vi:Ry23142 Gb(89)_vi:Ryu23142 Rice yellow mottle virus from Nigeria, complete genome. 4/95 4,451bp.

The genome has a base ratio of 29 % guanine; 21 % adenine; 25 % cytosine; 25 % uracil.

GenBank records for nucleotide sequences; complete genome sequences.

Proteins

Proteins constitute about 77% of the particle weight.

The viral genome encodes structural proteins and non-structural proteins located in the capsid.

Structural Proteins: Capsid protein has a molecular mass of 26108 Da (239 AA) with 180 copies per virion; sequence has the accession number [Q86527]; is the coat protein.

Lipids

Lipids are not reported.

Antigenicity

The virus does not show serological relationships to cocksfoot mottle and cocksfoot mild mosaic (syn. phleum mottle) viruses.

Biological Properties

Natural Host

Domain
Viral hosts belong to the Domain Eucarya.

Domain Eucarya
Kingdom Plantae.

Kingdom Plantae
Phylum Magnoliophyta (Angiosperms, Class Liliopsida (Monocotyledonae).

Severity and Occurrence of Disease

Host: Signs and symptoms persist.

Transmission and Vector Relationships

Virus is transmitted by a vector. Virus is transmitted by mechanical inoculation; not transmitted by seeds.

Vector Transmission:
Virus is transmitted by arthropods, by insects of the order Coleoptera; Sesselia pusilla, Chaetocnema pulla, Trichispa serica and Dicladispa viridicyanea. Virus is transmitted in a semi-persistent manner; lost by the vector when it moults; does not replicate in the vector; not transmitted congenitally to the progeny of the vector; does not require a helper virus for vector transmission.

Experimental Hosts and Symptoms

Under experimental conditions susceptibility to infection by virus is found in few families. Susceptible host species are found in the Family Gramineae. The following species were susceptible to experimental virus infection: Dinebra retroflexa, Oryza barthii, Oryza longistaminata, Oryza punctata, Oryza sativa, Phleum arenarium.

Diagnostic Hosts

Diagnostic host species and symptoms:

Oryza sativa — chlorotic dotting of leaf bases, elongating parallel to veins to produce mottling, stunting.

Oryza barthii — yellow spots and vein streaking.

Oryza punctata — systemic chlorotic dots.

Dinebra retroflexa — mild systemic mottling.

Phleum arenarium — systemic mottling and leaf death.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are Oryza sativa cv. Sindano.

Assay Hosts

Host: Assay hosts (for Local lesions or Whole plants):
Oryza sativa cvs Sindano and IR 20 (W).

References to host data: Bakker (1970, 1974).

Histopathology: Virus can be best detected in mesophyll and epidermis. Virions are found in the cytoplasm.

Cytopathology: Inclusions are not present in infected cells.

Geographical Distribution

The virus occurs in Burkina Faso, Cote d'Ivoire, Kenya, Liberia, Mali, Niger, Nigeria, Sierra Leone, and Tanzania (and, possibly, Zanzibar).

Ecology, Epidemiology and Control

Studies reported by Bakker (1970, 1971, 1974, Fauquet and Thouvenel (1977, Rossel et al. (1982, John et al. (1984).

References

Bakker, W. (1970). Neth. J. Pl. Path 76: 53.

Bakker, W. (1971). Neth J. Pl. Path. 77: 201.

Bakker, W. (1974). Agric. Res. Reports 829: 152 pp.

Bakker, W. (1975). CMI/AAB Descr. Pl. Viruses No. 149, 4pp.

Fauquet, C. and Thouvenel, JC (1977). Pl. Dis. Reptr 61: 443.

John, V.T., Thottappilly, G. and Awoderu, V.A. (1984). FAO Pl. Prot. Bull. 32: 86.

Rossel, H.W., Thottappilly, G. and Buddenhagen, I.W. (1982). FAO Pl. Prot. Bull. 30: 137.

The following generic references are cited in the most recent ICTV Report.

PubMed References.

VIDEdB, the plant virus database developed at the Australian National University by Adrian J. Gibbs and collaborators, contains an earlier description with the number 697 by A.A. Brunt and W. Bakker, 1987.

A description of the virus is found in DPV, a database for plant viruses developed by the Association of Applied Biologists (AAB), with the number 149.



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DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia. ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses by Dr Cornelia Büchen-Osmond is written in DELTA. The virus descriptions in ICTVdB are coded by, or using data from experts in the field of virology or members ICTV. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations are automatically generated and formatted for display on the Web from the descriptions in DELTA-format. The description has been generated automatically from DELTA files. DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia.

ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses (ICTV) by Dr Cornelia Büchen-Osmond, is written in DELTA. The virus descriptions in ICTVdB are coded by ICTV members and experts, or by the ICTVdB Management using data provided by the experts, the literature or the latest ICTV Report. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations from the encoded descriptions are automatically generated and formatted for display on the Web.

Developer of the DELTA software: M. J. Dallwitz, T. Paine and E. Zurcher

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Last updated on 25 April 2006 by Cornelia Büchen-Osmond
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