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00.060.0.08.001. Rice dwarf virus

Cite this publication as: ICTVdB Management (2006). 00.060.0.08.001. Rice dwarf 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: Shiga; Japan.

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

Natural host and symptoms
Echinochloa crus-galli, Paspalum thumbergii, Oryza sativa, Alopecurus aequalis — stunting, white chlorotic specks on leaves.

Reference to Isolation Report
Takada (1895 and 1896).

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: 00.060.0.08.001. Virus accession number: 60008001. Obsolete virus code: 60.0.8.0.001; superceded accession number: 60080001.
NCBI Taxon Identifier NCBI Taxonomy ID: 10991.

Name, Synonyms and Lineage

ICTV approved acronym: RDV. Virus is the type of the genus 00.060.0.08. Phytoreovirus in the family 00.060. Reoviridae.

Virion Properties

Morphology

Virions consist of a capsid, a core, and a nucleoprotein complex. Virus capsid is not enveloped. Capsid/nucleocapsid is isometric with icosahedral symmetry and has a diameter of 70 nm. The capsid shells of virions are composed of two layers. All shells are usually present. Capsids appear round. The capsomer arrangement is clearly visible.

Electron microscopic preparation and references: Virus preparation contains many virions. Reference for electron microscopic methods: Iida et al. (1972).

Physicochemical and Physical Properties

Virions have a buoyant density in CsCl of 1.26 g cm-3 (T), or 1.38 g cm-3 (M1), or 1.43 g cm-3 (M2), or 1.46 g cm-3 (B). There are 2 sedimenting component(s) found in purified preparations. The sedimentation coefficient is 510 S20w. A260/A280 ratio is 1.4. The thermal inactivation point (TIP) is at 45-50°C. The longevity in vitro (LIV) is 10 days (at 4°C). Although the titer is dependent on the host, the decimal exponent (DEX) of the dilution end point is usually around 3-4 (in sap from rice leaves). The infectivity is not changed by treatment with ether; lost when deproteinized with phenol or detergent.

Nucleic Acid

The Mr of the genome constitutes 20% of the virion by weight. The genome is segmented and consists of twelve segments of linear, double -stranded RNA. The complete genome is 25130 nucleotides long, is fully sequenced, or partially sequenced, complete sequence is 4354 nucleotides long. Sequence has the accession number

[D00241] Em(40)_vi:RDVS10 Gb(84)_vi:RDVS10 Rice dwarf virus segment S10 mRNA, encoding an ORF, complete cds. 7/90 1,319bp.
[D00465] Em(40)_vi:RDVSEG9 Gb(84)_vi:RDVSEG9 Rice dwarf virus segment 9 RNA, complete sequence. 3/91 1,305bp.
[D00473] Em(40)_vi:RDVS10A Rice dwarf virus genome segment 10, complete sequence. 7/90 1,321bp.
[D00536] Em(40)_vi:RDVS8 Gb(84)_vi:RDVS8 Rice dwarf virus outer capsid protein RNA (S8), complete cds. 3/91 1,424bp.
[D00607] Em(40)_vi:RDVSEG3 Gb(84)_vi:RDVSEG3 Rice dwarf virus genome segment 3, complete sequence. 11/90 3,195bp.
[D00608] Em(40)_vi:RDVSEG4 Gb(84)_vi:RDVSEG4 Rice dwarf virus genome segment 4, complete sequence. 3/91 2,468bp.
[D00639] Em(40)_vi:RDVS7 Gb(84)_vi:RDVS7 Rice dwarf virus genome segment 7, complete sequence. 3/91 1,696bp.
[D00693] Em(40)_vi:RDVS3CP Gb(84)_vi:RDVS3CP Rice dwarf virus genome segment S3 encoding 114K core protein. 2/92 3,130bp.
[D10218] Em(40)_vi:RDVSEG7RD Gb(84)_vi:RDVSEG7RD Rice dwarf virus segment 7, complete sequence. 3/94 1,696bp.
[D10219] Em(40)_vi:RDVSEG8RD Gb(84)_vi:RDVSEG8RD Rice dwarf virus segment 8, complete sequence. 3/94 1,427bp.
[D10220] Em(40)_vi:RDVSEG9RD Gb(84)_vi:RDVSEG9RD Rice dwarf virus segment 9, complete sequence. 3/94 1,305bp.
[D10221] Em(40)_vi:RDVSEG10R Gb(84)_vi:RDVSEG10RD Rice dwarf virus segment 10, complete sequence. 3/94 1,321bp.
[D10222] Em(40)_vi:RDVSEG1H Gb(84)_vi:RDVSEG1H Rice dwarf virus segment 1, RNA-dependent RNA polymerase. 12/92 4,423bp.
[D10249] Em(40)_vi:RDVS11 Gb(84)_vi:RDVS11 Rice dwarf virus segment S11 mRNA. 2/93 1,067bp.
[D11369] Em(40)_vi:RDVGS12 Gb(84)_vi:RDVGS12 Rice dwarf virus genome segment 12, complete cds. 10/92 1,066bp.
[D13404] Em(40)_vi:RDVS9 Gb(84)_vi:RDVS9 Rice dwarf virus segment 9 RNA. 1/93 1,305bp.
[D13773] Em(40)_vi:RDVSS8 Gb(84)_vi:RDVSS8 Rice dwarf virus RNA for outer capsid protein. 4/94 1,427bp.
[D90033] Em(40)_vi:RDVAS5 Gb(84)_vi:RDVAS5 Rice dwarf virus A segment 5, complete. 5/92 2,570bp.
[D90198] Em(40)_vi:RDVS1 Gb(84)_vi:RDVSEG1A Rice dwarf virus segment 1, RNA-dependent RNA polymerase mRNA. 11/92 4,423bp.
[D90199] Em(40)_vi:US11 Rice dwarf virus segment 11 mRNA. 8/92 1,067bp.
[D90200] Em(40)_vi:RDVS12 Gb(84)_vi:RDVS12 Rice dwarf virus segment 12 mRNA. 2/93 1,066bp.
[M35118] Em(40)_vi:RDVS1001 Gb(84)_vi:RDVS10A Rice dwarf virus segment 10 RNA, encoding an ORF, complete cds. 2/91 1,321bp.
[M91653] Em(40)_vi:RDVASEG6 Gb(84)_vi:RDVASEG6 Rice dwarf virus segment 6, complete. 3/93 1,699bp.
[S77255] Em(40)_vi:S77255 Gb(84)_vi:S77255 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77256] Em(40)_vi:S77256 Gb(84)_vi:S77256 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77257] Em(40)_vi:S77257 Gb(84)_vi:S77257 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77258] Em(40)_vi:S77258 Gb(84)_vi:S77258 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77259] Em(40)_vi:S77259 Gb(84)_vi:S77259 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77260] Em(40)_vi:S77260 Gb(84)_vi:S77260 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77261] Em(40)_vi:S77261 Gb(84)_vi:S77261 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77262] Em(40)_vi:S77262 Gb(84)_vi:S77262 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77263] Em(40)_vi:S77263 Gb(84)_vi:S77263 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77264] Em(40)_vi:S77264 Gb(84)_vi:S77264 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77265] Em(40)_vi:S77265 Gb(84)_vi:S77265 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77266] Em(40)_vi:S77266 Gb(84)_vi:S77266 (3' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77279] Em(40)_vi:S77279 Gb(84)_vi:S77279 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77280] Em(40)_vi:S77280 Gb(84)_vi:S77280 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77281] Em(40)_vi:S77281 Gb(84)_vi:S77281 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77282] Em(40)_vi:S77282 Gb(84)_vi:S77282 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77283] Em(40)_vi:S77283 Gb(84)_vi:S77283 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77284] Em(40)_vi:S77284 Gb(84)_vi:S77284 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77285] Em(40)_vi:S77285 Gb(84)_vi:S77285 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77286] Em(40)_vi:S77286 Gb(84)_vi:S77286 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77287] Em(40)_vi:S77287 Gb(84)_vi:S77287 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77288] Em(40)_vi:S77288 Gb(84)_vi:S77288 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77289] Em(40)_vi:S77289 Gb(84)_vi:S77289 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[S77290] Em(40)_vi:S77290 Gb(84)_vi:S77290 (5' terminus) rice dwarf virus RDV, Genomic RNA, 10 nt. 12/93 10bp.
[X16017] Em(40)_vi:RDVSEG5A Gb(84)_vi:RDVSEG5A Rice Dwarf Virus RNA for genomic segment 5. 9/93 2,552bp.
[X54620] Em(40)_vi:RDVSEG3A Gb(84)_vi:RDVSEG3A Rice dwarf virus S3 mRNA for segment 3. 9/93 3,195bp.
[X54622] Em(40)_vi:RDVSEG4A Gb(84)_vi:RDVSEG4A Rice dwarf virus S4 mRNA for segment 4. 9/93 2,468bp.
[S72083] Gb(89)_vi:S72083 P12...P120Pa (segment 12) rice dwarf virus RDV, RDV-H, Genomic RNA, 3 genes, 1066 nt). 10/94
[S72085] Gb(89)_vi:S72085 P12...P120Pb (segment 12) rice dwarf virus RDV, RDV-AKITA, Genomic RNA, 3 genes, 1066 nt). 1
[S74804] Gb(89)_vi:S74804 polyprotein (S2, segment 2) (rice dwarf virus, RDV-H, Genomic RNA, 3512 nt). 5/95 3,5
[S74805] Gb(89)_vi:S74805 polyprotein (S2, segment 2) (rice dwarf virus, RDV-Akita, Genomic RNA, 3512 nt). 5/95
[U25671] Gb(89)n:Rdu25671 Rice dwarf virus segment 10 nonstructural protein gene, complete cds. 6/95 1,164bp. Sequence is is about 3385 nucleotides long, is sequenced, but only an estimate is given, complete sequence is 3195 nucleotides long, has been sequenced, but only an estimate is provided; complete sequence is 2468 nucleotides long and has been sequenced, but only an estimate is presented, complete sequence is 2570 nucleotides long. RNA-6 has been fully sequenced, complete sequence is 1699 nucleotides long. RNA-7 has been sequenced, but only an estimate is presented, complete sequence is 1696 nucleotides long. RNA-8 has been sequenced, but only an estimate is available, complete sequence is 1424 nucleotides long. RNA-9 has been sequenced, complete sequence is about 1305 nucleotides long. RNA-10 has been sequenced, but only an estimate is available; complete sequence is 1319 nucleotides long, has been sequenced, but only an estimate is given; complete sequence is 887 nucleotides long, has been sequenced, but only an estimate is available; complete sequence is 828 nucleotides long. The genome has a guanine + cytosine content of 42.3-48.1 %. The 5'-end of the genome has shows the sequence of GGCA or GGUA. Reference to nucleotide sequence Kimura et al. (1987).

GenBank records for nucleotide sequences; complete genome sequences.

Proteins

Proteins constitute about 80% of the particle weight.

The viral genome encodes structural proteins and non-structural proteins. Virions consist of 6 structural protein(s).

Lipids

Lipids are absent.

Transcription: Sub-genomic RNA is absent from infected cells.

Translation: The genome replicates in the cytoplasm.

Replication cycle Features: the genome has s3 has an ORF which encodes 114000 polypeptide; s4 ORF encodes 79800 polypeptide; s5 ORF encodes 90500 polypeptide; s6 ORF encodes 57400 polypeptide; s7 ORF encodes 55300 polypeptide; s8 ORF encodes 46400 polypeptide; s9 ORF encodes 38900 polypeptide; s10 ORF encodes 39100 or 39200 polypeptide; s11 ORF encodes 20800 polypeptide.

Antigenicity

The virus is serologically related to rice gall dwarf virus. The virus does not show serological relationships to clover wound tumour virus.

Each segment has a high homology with corresponding segments of clover wound tumour and rice gall dwarf viruses.

Diagnostics and Reference Collections

The best tests for diagnosis are distinguish by characteristic symptoms and serological tests.

Biological Properties

Natural Host

Domain
Viral hosts belong to the Domain Eucarya.

Domain Eucarya
Kingdom Plantae.

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

General Symptoms in Plants Symptoms stunting, fine chlorotic specks on leaves.

Severity and Occurrence of Disease

Host: Signs and symptoms persist.

Transmission and Vector Relationships

Virus is transmitted by a vector. Virus is not transmitted by mechanical inoculation; not transmitted by contact between hosts; not transmitted by seeds; not transmitted by pollen.

Vector Transmission:
Virus is transmitted by arthropods, by insects of the order Hemiptera, family Cicadellidae; Nephotettix cincticeps, N. apicalis, N. nigropictus, N. virescens, Recilia dorsalis. The principal natural vector(s) are Nephotettix cincticeps. Virus is transmitted in a persistent manner; retained when the vector moults; replicates in the vector; transmitted congenitally to the progeny of the vector.

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: Alopecurus aequalis, Alopecurus japonicus, Avena sativa, Echinochloa crus-galli, Hordeum sativum, Hordeum vulgare, Oryza cubensis, Oryza sativa, Panicum miliaceum, Paspalum thumbergii, Poa annua, Secale cereale, Triticum aestivum.

Host:
Experimentally infected hosts mainly show symptoms of stunting, white specks on leaves, darker leaf colour.

Experimentally infected insusceptible Hosts: Families containing insusceptible hosts: Gramineae. Species inoculated with virus that do not show signs of susceptibility: Andropogon sorghum, Setaria italica, Zea mays.

Diagnostic Hosts

Diagnostic host species and symptoms:

Alopecurus japonicus, A aequalis, Avena sativa, Echinochloa crus-galli, Hordeum sativum, Oryza cubensis, O. sativa, Panicum miliaceum, Poa annua, Secale cereale, Triticum aestivum — stunting and systemic chlorotic specks.

Diagnostic host: insusceptible host species Andropogon sorghum, Setaria italica, Zea mays.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are Alopecurus japonicus, Oryza sativa.

Assay Hosts

Host: Assay hosts (for Local lesions or Whole plants):
Oryza sativa (W).

References to host data: Fukushi (1934, Shinkai (1962).

Histopathology: Virus can be best detected in leaves, mesophyll, epidermis, vascular parenchyma and all parts of the host plant. Virions are found in the cytoplasm.

Cytopathology: Inclusions are present in infected cells. Inclusion bodies in the host cell are found in the cytoplasm. Cytoplasmic inclusions are viroplasma. Inclusions contain mature virions.

Geographical Distribution

The virus occurs in China, Japan, Korea (North), Korea (South), and Nepal.

References

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 686 by A.J. Gibbs, 1990; H. Hibino, 1992.

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 102.

Taxonomic Proposals and Changes

A taxonomic proposal has been submitted to the ICTV by the Plant Virus Subcommittee and Vertebrate Virus Subcommittee, Study Group for Reoviridae to reclassify the position of type species. The proposal has been approved by postal ballot following discussions at the meeting of the Executive Committee in San Diego, 1998, the taxon has been designated as Species.



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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.

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