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00.088.0.01.001.00.002. Beet necrotic yellow vein virus, Japanese S43 isolate

Cite this publication as: ICTVdB Management (2006). 00.088.0.01.001.00.002. Beet necrotic yellow vein virus, Japanese S43 isolate. 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

Isolate designation: S (145–1, H20, S4, S7, pMPCRD5, pMPCRSX19, pMRP70, pMSD25).

Location: Japan.

Isolate Host and Habitat Details
Source of isolate: Beta vulgaris; lab host Tetragonia expansa.

Collection and Isolation Details Virus was isolated by T; Tamada. Tadahiko Kiguchi; Hokkaido Central Agricultural Experiment Station, Plant Biotechnology; 6 Kita 15; Higashi; Naganuma, Hokkaido; 069–13

; Japan.

Reference of Isolation Report Reference: Saito,M., Kiguchi,T., Kusume,T. and Tamada,T. (1996). Complete nucleotide sequence of the Japanese isolate S of beet necrotic yellow vein virus RNA and comparison with European isolates. Arch. Virol. 141:2163–2175.

Classification

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

ICTVdB Virus Code: 00.088.0.01.001. Virus accession number: 88021001. NCBI Taxon Identifier NCBI Taxonomy ID: 31721.

Name, Synonyms and Lineage

ICTV approved acronym: BNYVV. Virus is assigned to species 00.088.0.01.001. Beet necrotic yellow vein virus of the genus 00.088.0.01. Benyvirus ; not assigned to a family.

Virion Properties

Morphology

Virions consist of a capsid. Virus capsid is not enveloped. Capsid/nucleocapsid is elongated and exhibits helical symmetry. Virus preparations contain more than one particle component. The capsid is rod-shaped, straight and fragile; has a herring–bone pattern. Segments have different predominant lengths; with clear predominate lengths; with a length of 390 nm; 265 nm; 100 nm; 70 nm; width of about 20 nm. Axial canal is distinct. Basic helix is obvious. Pitch of helix is 2.6 nm. The nucleocapsid CP is segmented.

Electron microscopic preparation and references Virus preparation contains few virions.

Physicochemical and Physical Properties

There are 4 sedimenting component(s) found in purified preparations. The thermal inactivation point (TIP) is at 65–70°C. The longevity in vitro (LIV) is 5–8 days. Although the titer is dependent on the host, the decimal exponent (DEX) of the dilution end point is usually around 4–5. The infectivity is 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 multipartite. Segments are distributed over several particles of varying size, depending on the length of the genome enclosed. The genome consists of five segments of linear, positive-sense, single-stranded RNA. Minor species of non–genomic nucleic acid are not found in virions. The complete genome is 14600 nucleotides long (excluding poly(A) tails). Sequence can be accessed from EBI-EMBL, GenBank, and Rothamsted; the RNA-1 is fully sequenced, complete sequence is 6749 nucleotides long and encodes 237k protein. Sequence has the accession number [D84410]. RNA-2 is fully sequenced, complete sequence is 4609 nucleotides long and encodes the readthrough 75k protein that produces pot. 54k and coat protein; the transport proteins of 15k; 42k and 13k; the 14k protein which has no function assigned, has the accession number [D84411]. RNA-3 is fully sequenced, complete sequence is 1774 nucleotides long and encodes a 25k protein, has the accession number [D84412]. RNA-4, has been fully sequenced, complete sequence is 1465 nucleotides long and encodes 31k protein;  has the accession number [D84413]. RNA-5, has been fully sequenced, complete sequence is 1320 nucleotides long and encodes 26kDa protein, has the accession number [D63936]. The genome has a base ratio of 24 % guanine; 26 % adenine; 15 % cytosine; 34 % uracil. The 5'–terminus has a long non-coding region; is 445 nucleotides in length and has a methylated nucleotide cap; 5'–end of the genome has of RNA–3 and RNA–4 unusually long non-coding regions; they are 445 (RNA–3) and 379 (RNA–4) nucleotides long; cap sequence type is m7GpppA. The 3'–terminus has a poly (A) tract 65–140 nucleotides in length. The 3'–terminus has no tRNA–like structure. The multipartite genome is divided among more than one type of particle and the segments are distributed between 2 different types of particles. The largest particles contain RNA-1. The medium sized particles contain RNA-2. The smallest particles contain deletion mutants in the shortest particles.

GenBank records for nucleotide sequence(s); 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).

Non-Structural Proteins: Virus–coded non–structural proteins have been identified by sequence analysis and 7 non-structural protein(s) are found. The virus codes for read-through polypeptides, movement proteins, replication-associated proteins, transmission helper proteins, interacting with the vector, and symptom enhancing proteins. In addition to the polymerase, the virus codes for enzymes such as papain-like protease, helicase, methyl-transferase, and replicase. The non-structural protein is associated with the capsid; proteins function in the cytoplasm of infected cells. Non-structural protein is translated from the first AUG at position 154, has a molecular mass of 237 kDa. The protein is coded from RNA-1 of ORF1; a replication-associated protein and possesses a its N-terminal part a methyltransferase motif (Mt), at the central part a helicase (Hel) and a papain-like protease motif (Prot), and at its C-terminal part a RNA-dependent RNA polymerase (RdRp) motif. Non-structural protein is translated from the downstream AUG at position 496 onwards, has a molecular mass of 220 kDa. The protein of ORF2. The protein is a replication-associated protein and possesses a its N-terminal part a methyltransferase motif (Mt), at the central part a helicase (Hel) and a papain-like protease motif (Prot), and at its C-terminal part a RNA-dependent RNA polymerase (RdRp) motif. Non-structural protein cell to cell movement protein, has a molecular mass of 13, 15, and 42 kDa. The protein is coded from RNA-2; of ORF5-ORF7. The protein is presumably viral movement; possesses helicase motif. Non-structural protein CP read-through; the protein is coded from RNA-2 of ORF3. Its role is initiating encapsidation and enabling transmission (at the C-terminal part).

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. The genome expression is based on RNA production which can be analyzed by the dsRNA patterns found in the infected tissues. Usually there are 4 virus specified dsRNA species found in infected cells.

Biological Properties

Natural Host

Domain Viral hosts belong to the Domain Eucarya.

Domain Eucarya Kingdom Plantae.

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

Class Magnoliopsida (Dicotyledonae)
Subclass CARYOPHYLLIDAE.

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 contact between hosts; not transmitted by seeds; not transmitted by pollen.

Vector Transmission: Virus is transmitted by fungi; of the order Plasmodiophorales; Polymyxa betae. Virus is not transmitted by Polymyxa graminis, Myzus persicae, Acyrthosiphon (Aulacorthum) solani.

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 Tetragoniaceae. The following species were susceptible to experimental virus infection: Tetragonia tetragonioides.

Host: Experimentally infected hosts mainly show symptoms of chlorotic local lesions.

Maintenance and Propagation Hosts

Most commonly used maintenance and propagation host species are Tetragonia expansa.

Assay Hosts

Host: Assay hosts (for Local lesions or Whole plants):
Tetragonia expansa (L).

Histopathology: Virions are found in the cytoplasm.

Cytopathology: Inclusions are not present in infected cells.

Geographical Distribution

The virus is probably distributed worldwide (where there are major sugar beet industries). The virus spreads in East Asia. The virus occurs in Japan.

References

PubMed References. 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 .

Contributor

Data have been submitted online to ICTVdB by
Büchen-Osmond C



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Comments to ICTVdB Management

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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Comments to ICTVdB Management
Last updated on 25 April 2006 by Cornelia Büchen-Osmond
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