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00.072.0.01.001. Tobacco rattle virus

Cite this publication as: ICTVdB Management (2006). 00.072.0.01.001. Tobacco rattle 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: Germany.

Host of Isolate and Habitat Details
Source of isolate: Nicotiana tabacum.

Natural host and symptoms
Stellaria media, Viola arvensis — few symptoms, mottling.

Beta vulgaris, Spinacia oleracea — chlorotic or necrotic local lesions; systemic mottle.

Capsicum annuum — ringspots or line patterns.

Solanum tuberosum — necrotic local lesions; systemic chlorotic or necrotic spots and streaks.

Nicotiana tabacum — necrotic local lesions, necrotic or chlorotic ringspots; systemic necrosis, ringspots or line patterns, mottling.

Narcissus pseudonarcissus, Tulipa sp., Hyacinthus sp. — mottling.

Reference to Isolation Report
Büning (1931).

Classification

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

ICTVdB Virus Code: 00.072.0.01.001. Virus accession number: 72001001. Obsolete virus code: 72.0.1.0.001; superceded accession number: 72010001.
NCBI Taxon Identifier NCBI Taxonomy ID: 12295.

Name, Synonyms and Lineage

Synonym(s): aster ringspot virus, belladonna mosaic virus, paeony mosaic virus (Brierley, 1944), paeony ringspot virus (Chang et al., 1976; Jones and Young, 1978; Martin, 1929), potato corky ringspot virus, potato stem mottle virus, stengelbonk virus (Rozendaal and van der Want, 1948), ratel virus, Tabakmauche Virus, Tabakstreifen- und Kr"uselkrankheit Virus, spinach yellow mottle virus, tulip white streak virus (Smith, 1950). ICTV approved acronym: TRV. Virus is the type species of the genus 00.072.0.01. Tobravirus; not assigned to a family.

Virion Properties

Morphology

Virions consist of a capsid. Virus capsid is not enveloped. Capsid/nucleocapsid is elongated with helical symmetry. Virus preparations contain more than one particle component. The capsid is rod-shaped, straight; has a herring-bone pattern (of 4-5 nm) with clear predominate lengths with a length of (L) 180-215 nm, or 46-115 nm ((S). Many strains produce in addition small amounts of shorter particles) and a width of in electron microscopy 21.3-23.1 nm, or 20.5-22.5 nm (in X-ray diffraction). Axial canal is distinct; 4 nm in diameter. Basic helix is obvious. Pitch of helix is 2.5 nm.

Electron microscopic preparation and references: Virus preparation contains few virions. Reference for electron microscopic methods: Harrison and Nixon (1959, Lister and Bracker (1969).

Physicochemical and Physical Properties

Virions have a buoyant density in CsCl of 1.306-1.324 g cm-3 (not fixed with aldehydes). There are 2 sedimenting component(s) found in purified preparations. The sedimentation coefficient is B 300 S20w. A260/A280 ratio is 1.1-1.15. The thermal inactivation point (TIP) is at 80-85°C. The longevity in vitro (LIV) is 40-50 days. Although the titer is dependent on the host, the decimal exponent (DEX) of the dilution end point is usually around 6. The infectivity is not changed by treatment with ether; retained when deproteinized with proteases; retained when deproteinized with phenol or detergent.

Nucleic Acid

The Mr of the genome constitutes 5% of the virion by weight. The genome is segmented and consists of two segments of linear, positive-sense, single-stranded RNA. Minor species of non-genomic nucleic acid are also found in virions. The encapsidated nucleic acid is mainly of genomic origin, but virions may also contain subgenomic RNA that is mRNA (in 3 parts namely RNA-3, RNA-4 and RNA-5). The complete genome is 9090-11515 nucleotides long, is fully and partially sequenced, complete sequence is 7272 nucleotides long (RNA-1 from B component virions). Sequence has the accession number

[D00155] Gb(84)_vi:MTRRNA1 Tobacco rattle virus (TRV), RNA-1, complete cds. 1/92 6,791bp
[J04347] Em(40)_vi:TOBMTRCP Gb(84)_vi:MTRCPSA Tobacco Rattle virus coat protein, 16K protein, and 13K protein genes, complete cds. 3/92 2,1
[X03241] Em(40)_vi:TOBTRVR2 Gb(84)_vi:TOBTRVR2 Tobacco rattle virus RNA-2 (CAM strain) for capsid protein. 11/93 1,799bp.
[X03685] Em(40)_vi:TOTRVRG1 Gb(84)_vi:TOTRVRG1 Tobacco rattle virus strain PSG RNA1 3' terminal sequence (2 kb). 9/93 2,077bp.
[X03686] Em(40)_vi:TOTRVRG2 Gb(84)_vi:TOTRVRG2 Tobacco rattle virus strain PSG RNA2. 9/93 1,905bp.
[X03955] Em(40)_vi:TOTRVRN2 Gb(84)_vi:TOTRVRN2 Tobacco rattle virus (TRV) strain TCM RNA2 sequence. 9/93 3,389bp.
[X06172] Em(40)_vi:TOTRRNA1 Gb(84)_vi:TOTRRNA1 Tobacco Rattle virus (TRV) RNA-1 complete sequence. 9/93 6,791bp.
[S72875] Gb(89)_un:S72876s2 (RNA-2 5' and 3' regions) (tobacco rattle virus TRV, TCM, I6, Genomic RNA, 565 nt, segment 2
[S72876] Gb(89)_un:S72876s1 (RNA-2 5' and 3' regions) (tobacco rattle virus TRV, TCM, I6, Genomic RNA, 369 nt, segment 1
[Z36974] Em(43)_vi:Trvrna2cp Gb(89)_vi:Trvrna2cp Tobacco rattle virus genes for coat protein, 28.7 kDa & 32.8 kDa proteins. 3/95 3,856bp.
[Z36983] Em(43)_vi:Trvpprncp Gb(89)_vi:Trvpprncp Tobacco rattle virus coat protein gene. 9/94 627bp. Sequence is fully sequenced, complete sequence is 1818-4242 nucleotides long (RNA-2 from T component virions). The genome has a base ratio of 24-25 % guanine; 26-29 % adenine; 17-18 % cytosine; 29-32 % uracil. The 5'-end of the genome has a methylated nucleotide cap (in RNA-2; not yet found on RNA-1, cap sequence type is m7GpppA. The multipartite genome is divided among more than one type of particle and the segments are distributed between 2 different types of particles. Reference to nucleotide sequence Minson and Darby (1973, Abou Harter and Hirth (1977).

GenBank records for nucleotide sequences; complete genome sequences.

Proteins

Proteins constitute about 95% of the particle weight.

The viral genome encodes structural proteins and non-structural proteins. Virions consist of 1 structural protein(s).

Structural Proteins: Reference to method of preparation: Semancik (1970, Ghabrial and Lister (1973).

Reference to amino acid sequence or composition Cornelissen et al. (1986, Offord and Harris (1965, Offord (1966, Semancik (1966, Miki and Okada (1970, Ghabrial and Lister (1973).

Non-Structural Proteins: Virus-coded non-structural proteins have been isolated and 2 non-structural protein(s) are found.

Lipids

Lipids are not reported.

Genome Organization and Replication

By itself, genomic nucleic acid is infectious.

Transcription: Sub-genomic RNA is present in infected cells.

Translation: Coat protein mRNA is translated in the cytoplasm.

Antigenicity

The virus is serologically related to some isolates of pea early browning are distantly related.

The genomes of different strains differ in size, especially their RNA-2s.

Biological Properties

Natural Host

Domain
Viral hosts belong to the Domain Eucarya.

Domain Eucarya
Kingdom Plantae.

Kingdom Plantae
Phylum Magnoliophyta (Angiosperms, Class Magnoliopsida (Dicotyledonae).

Severity and Occurrence of Disease

Host: Signs and symptoms persist (some strains), or vary seasonally, or disappear soon after infection.

Transmission and Vector Relationships

Virus is transmitted by a vector. Virus is transmitted by mechanical inoculation; transmitted by grafting; not transmitted by contact between hosts; transmitted by seeds (up to 40% in Viola arvensis or only to 1% in Capsella bursa-pastoris).

Vector Transmission:
Virus is transmitted by nematodes; family Trichodoridae; Paratrichodorus allius, P. anemones, P. christiei, P. nanus, P. pachydermus, P. teres, Trichodorus minor, T. primitivus, T. viruliferus.

Experimental Hosts and Symptoms

Under experimental conditions susceptibility to infection by virus is found in many families. Susceptible host species are found in the Family Alliaceae, Amaranthaceae, Amaryllidaceae, Apocynaceae, Boraginaceae, Campanulaceae, Caryophyllaceae, Chenopodiaceae, Compositae, Cruciferae, Cucurbitaceae, Euphorbiaceae, Gramineae, Hyacinthaceae, Labiatae, Leguminosae-Papilionoideae, Liliaceae, Linaceae, Phytolaccaceae, Scrophulariaceae, Solanaceae, Tropaeolaceae, Umbelliferae, Violaceae. The following species were susceptible to experimental virus infection: Allium cepa, Amaranthus caudatus, Amaranthus retroflexus, Antirrhinum majus, Arachis hypogaea, Avena sativa, Bellis perennis, Beta vulgaris, Brassica campestris, Brassica campestris ssp. napus, Brassica campestris ssp. pekinensis, Brassica juncea, Calendula officinalis, Capsella bursa-pastoris, Capsicum annuum, Catharanthus roseus, Cheiranthus cheiri, Chenopodium album, Chenopodium amaranticolor, Chenopodium foetidum, Chenopodium quinoa, Coriandrum sativum, Cucumis melo, Cucumis sativus, Glycine max, Gomphrena globosa, Gypsophila elegans, Helianthus annuus, Hyacinthus, Hyoscyamus niger, Lactuca sativa, Lathyrus odoratus, Linum usitatissimum, Lobelia erinus, Lupinus mutabilis, Lycopersicon esculentum, Lycopersicon pimpinellifolium, Melilotus albus, Momordica balsamina, Myosotis sylvatica, Narcissus pseudonarcissus, Nicandra physalodes, Nicotiana benthamiana, Nicotiana clevelandii, Nicotiana glutinosa, Nicotiana rustica, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana x edwardsonii, Ocimum basilicum, Petunia x hybrida, Phaseolus vulgaris, Phytolacca americana, Pisum sativum, Raphanus sativus, Ricinus communis, Salvia splendens, Senecio vulgaris, Solanum melongena, Solanum nigrum, Solanum tuberosum, Spinacia oleracea, Stellaria media, Trifolium pratense, Trifolium repens, Tropaeolum majus, Tulipa, Vicia faba, Vicia villosa, Viola arvensis.

Experimentally infected insusceptible Hosts: Families containing insusceptible hosts: Caryophyllaceae, Compositae, Cruciferae, Cucurbitaceae, Gesneriaceae, Gramineae, Polemoniaceae, or Polygonaceae, Rosaceae, Rutaceae, Solanaceae, Umbelliferae. Species inoculated with virus that do not show signs of susceptibility: Citrus medica, Cucurbita pepo, Datura ferox, Datura metel, Datura stramonium, Daucus carota, Dianthus barbatus, Dianthus caryophyllus, Fragaria vesca, Hordeum vulgare (probably), Matthiola incana, Phlox drummondii, Physalis floridana, Rumex acetosa, Secale cereale, Sinningia speciosa, Triticum aestivum, Zea mays, Zinnia elegans.

Diagnostic Hosts

Diagnostic host species and symptoms:

Chenopodium amaranticolor, C. quinoa, Cucumis sativus — necrotic and chlorotic local lesions; no systemic infection.

Phaseolus vulgaris cv. The Prince, Pisum sativum, Vicia faba — necrotic local lesions; no systemic infection.

Nicotiana clevelandii — necrotic and chlorotic local lesions; few systemic symptoms, mottle, necrosis.

N. tabacum cv. Samsun NN — necrotic local lesions and ringspots; systemic necrosis, ringspots, mottle. Diagnostic host: insusceptible host species probably Hordeum vulgare.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are Nicotiana clevelandii, N. tabacum.

Assay Hosts

Host: Assay hosts (for Local lesions or Whole plants):
Chenopodium amaranticolor (L), Phaseolus vulgaris (L), Nicotiana tabacum for some strains (L).

References to host data: Schmelzer (1957, Uschdraweit and Valentin (1956, Noordam (1956).

Histopathology: Virus can be best detected in all parts of the host plant. Virions are found in the cytoplasm (where they stack on the surface of the mitochondria).

Cytopathology: Inclusions are present in infected cells (some strains). Inclusion bodies in the host cell are found in the cytoplasm. Cytoplasmic inclusion bodies are associated with the cluster of abnormal mitochondria. Inclusions contain mature virions. Other cellular changes include chloroplast break down.

Geographical Distribution

The virus spreads in Eurasia, North America, and South and Central Americas. The virus occurs in China, Japan, and the USSR (former). The virus is found, but with no evidence of proliferation, in New Zealand and Australia.

List of Strains and Isolates in the Species

Fraxinus virus (Cooper et al., 1983), Oregon yellow virus, PRN (Scottish type strain), spinach yellow mottle. NM isolates, which lack the smaller part of the genome and do not produce nucleoprotein, can be prepared from all strains.

References

Abou Harter, M. and Hirth, L. (1977). Virology 76: 173.

Böning, K. (1931). Z. ParasitKde. 3: 103.

Brierley, P. (1944). Pl. Dis. Reptr 150 Suppl.: 410.

Chang, M.U., Doi, Y. and Yora, K. (1976). Ann. Phytopath. Soc. Japan 42: 325.

Cooper, J.I., Edwards, M.L., Arnold, M.K. and Massalski, P.R. (1983). Pl. Path. 32: 469.

Cornelissen, B.J.C., Linthorst, H.J.M., Brederode F.Th. and Bol, J.F. (1986). Nucl. Acids Res. 14: 2157.

Ghabrial, S.A. and Lister, RM (1973). Virology 52: 1.

Gugerli, P., Darby, G. and Minson, AC. (1978). J. gen. Virol. 38: 273.

Harrison, BD (1970). CMI/AAB Descr. Pl. Viruses No. 12, 4 pp.

Harrison, BD and Nixon, H.L. (1959). J. gen. Microbiol. 21: 569.

Harrison, BD and Robinson, D.J. (1978). Adv. Virus Res. 23: 25

Harrison, BD and Robinson, D.J. (1981). In: Handbook of Plant Virus Infections, p. 515; ed. E. Kurstak. Elsevier/North Holland Biomedical Press, Amsterdam.

Jones, AT and Young, B.R. (1978). Pl. Dis. Reptr 62: 925.

Lister, RM and Bracker, C.E. (1969). Virology 37: 262.

Martin, GH (1929). Pl. Dis. Reptr Suppl. 73: 390.

Miki, T. and Okada, Y. (1970). Virology 42: 993.

Minson, T. and Darby, G. (1973). J. mol. Biol. 77: 337.

Noordam, D. (1956). Tijdschr. Plziekt. 62: 219.

Offord, R.E. and Harris, J.I. (1965). Proc. FEBS Meeting, p. 216.

Offord, R.E. (1966). Ph.D. Thesis, University of Cambridge, England.

Robinson, D.J. (1977). J. gen. Virol. 35: 37.

Robinson, D.J. and Harrison, BD (1989). CMI/AAB Descr. Pl. Viruses No. 346, 6 pp.

Rozendaal, A and van der Want, J.P.H. (1948). Tijdschr. PlZiekt. 54: 113.

Schmelzer, K. (1957). Phytopath. Z. 30: 281.

Semancik, J.S. (1966). Phytopathology 56: 1190.

Semancik, J.S. (1970). Virology 40: 618.

Smith, K.M. (1950). J. R. hort. Sci. 75: 350.

Uschdraweit, H.A. and Valentin, H. (1956). NachrBl. dtsch. Pflschutz., Braunschweig 8: 132.

Van Hoof, H.A. (1968). Nematologica 14: 20.

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 808 by B.D. Harrison and D.J. Robinson, 1984.

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 12.

Images

Taxon images: • EM from IACR Rothamsted.



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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.

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