Genus: Allexivirus

Genus: Allexivirus

Distinguishing features

Allexiviruses are distinguished by mite transmission and by the presence of a large conserved ORF4 or 5 after the position where the third, and smallest, of the triple gene block (TGB) proteins, TGB3, is found in the other plant-infecting members of the family. Whereas the start codon is missing for the TGB3 ORF in most (but not all) genus members, the coding capacity is conserved and the ORF may be translated through alternative mechanisms. 

Virion

Morphology

Virions are highly flexible filamentous particles, about 800 nm in length and 12 nm in diameter. They resemble potyviruses in their length, but closteroviruses in their flexibility and cross-banded substructure (Figure 1.Alphaflexiviridae).

Physicochemical and physical properties

Virions of shallot virus X sediment with an S20,w of about 170S in 0.1 M Tris-HC1, pH 7.5 at 20°C and have a buoyant density in CsCl of 1.33 g cm−3.

Nucleic acid

Virions contain a single molecule of linear single-stranded RNA, of about 9.0 kb, with a 3′-poly(A) tract. The genomic RNA contains six large ORFs and short untranslated regions (UTR) at the 5′- and 3′-termini (Figure 2.Alphaflexiviridae).

Proteins

Virions are composed of a 25–32 kDa polypeptide as a major capsid protein (CP). A 42 kDa polypeptide is a minor component of virions. 

Carbohydrates

None reported.

Genome organization and replication

The genomic RNA contains six large ORFs and short UTRs at the 5′- and 3′-termini (Kanyuka et al., 1992) (Figure 1.Allexivirus) The ORFs code for polypeptides of about 195, 27, 11, 42, 28 and 15 kDa, respectively from the 5′-end to the 3′-end. The 195 kDa polypeptide is the replication-associated (Rep) protein. The 26 and 11 kDa proteins are similar to the first two proteins encoded by the TGB of related plant viruses and are probably involved in cell-to-cell movement of the virus. There is a coding sequence for a third small (7–8 kDa) TGB protein but the initiation AUG-codon is lacking in most, but not all member species. The 42 kDa polypeptide (ORF4) has no significant homology with any known protein; in plants infected with an isolate of the type species, the 42 kDa protein was expressed in relatively large amounts and was shown to be involved in virion assembly. The 28 kDa polypeptide is the CP. In SDS-polyacrylamide gel electrophoresis it migrates as an apparently 32–36 kDa protein, which could be due to its high hydrophilicity. The 15 kDa protein has a zinc-binding finger motif and an ability to bind nucleic acids. The function of this polypeptide is not known.

Figure 1.Allexivirus. Genome organization and translation strategy of shallot virus X showing the relative positions of the ORFs and their expression products. Mtr, methyltransferase; Hel, helicase; RdRP, RNA-directed RNA polymerase; TGB, triple gene block; CP, capsid protein; NB, nucleic acid binding protein. 

Biology

Host range

The host range of allexiviruses that encode a 15 kDa RNA-binding protein is mainly restricted to Allium species. Some isolates from shallot, onion, garlic and sand leek have been experimentally transmitted to Chenopodium murale, in which they induced local lesions. Viruses lacking the RNA-binding protein infect hosts other than Allium including vanilla, alfalfa, groundnut and blackberry.

Transmission

Allexiviruses are thought to be mite-borne. Garlic viruses C and D have been shown to be transmitted by the eriophyd mite, Aceria tulipae. All are manually transmissible by sap inoculation to healthy host plants. None could be transmitted by aphids.

Geographical distribution

Allexiviruses are widely distributed and probably occur wherever their host plants are grown.

Cytopathic effects

Most allexiviruses induce no visible or only very mild symptoms, although certain isolates can cause severe damage to crops. In infected tissue, allexiviruses can induce the formation of granular inclusion bodies and small bundles of flexible particles.

Antigenicity

Allexivirus particles are immunogenic. Some members of the genus are serologically related. Specific antisera and monoclonal antibodies against virus particles as well as antisera against recombinant CPs have been used for differentiation purposes.

Derivation of names 

Allexi: from Allium (the genus name for the principal host, shallot) and exi, a phonetic version of “X”.

Species demarcation criteria

The criteria demarcating species in the genus are:

  • Members of different species have less than 72% nt identity (or 80% aa identity) in their CP or Rep genes.
  • Members of different species react differently with antisera.

Member species

Exemplar isolate of the species
SpeciesVirus nameIsolateAccession numberRefSeq numberAvailable sequenceVirus Abbrev.
Alfalfa virus SAlfalfa virus S98.3AKY696659NC_034622Complete genomeAVS
Arachis pintoi virusArachis pintoi virusVar AKX058345NC_032104Complete genomeApV
Blackberry virus Eblackberry virus EBB_Ellis-1JN053266NC_015706Complete genomeBVE
Garlic mite-borne filamentous virusgarlic mite-borne filamentous virusX98991NC_038864Partial genomeGarMbFV
Garlic virus Agarlic virus ASumiAB010300NC_003375Complete genomeGarVA
Garlic virus Bgarlic virus BMesi 13KM379144NC_025789Complete genomeGarVB
Garlic virus Cgarlic virus CSumiAB010302NC_003376Complete genomeGarVC
Garlic virus Dgarlic virus DSW10KF555653NC_022961Complete genomeGarVD
Garlic virus Egarlic virus EYHAJ292230NC_004012Complete genomeGarVE
Garlic virus Xgarlic virus XKoreaU89243NC_001800Complete genomeGarVX
Shallot virus Xshallot virus XKanyukaM97264NC_003795Complete genomeShVX
Vanilla latent virusVanilla latent virusCRV2148ALLMF150239NC_035201Complete genomeVLV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Related, unclassified viruses 

Virus name

Accession number

Virus abbreviation

allexivirus DS-2013/CZE  

JX682826

 

Cassia mild mosaic virus  

GU481094

 

Senna severe yellow mosaic virus 

MN031278

 

shallot mite-borne latent virus

EU835196

 

Virus names and virus abbreviations are not official ICTV designations.