Historically, two genera of unsegmented plant rhabdoviruses (Nucleorhabdovirus and Cytorhabdovirus) were established based on the sites of virus replication and morphogenesis. Nucleorhabdoviruses replicate and mature in the nuclei of infected cells. Recently, following the creation of the genus Dichorhavirus, for rhabdoviruses with bi-segmented genomes that are related to nucleorhabdoviruses, the genus Nucleorhabdovirus was split into three new genera Alphanucleorhabdovirus, Betanucleorhabdovirus and Gammanucleorhabdovirus. This reclassification became necessary since phylogenetic analyses of new plant rhabdovirus genomes consistently showed that nucleorhabdoviruses did not form a monophyletic clade upon analysis of complete L protein sequence alignments.
Based on well-supported Maximum Likelihood trees inferred from complete L protein sequences, viruses classified in the genus Alphanucleorhabdovirus form a monophyletic cluster clearly distinguished from beta- and gammanucleorhabdoviruses and from dichorhaviruses, as well as from other plant rhabdoviruses.
Physicochemical and physical properties
Virus particles sediment at 800–1000 S in sucrose gradients and the buoyant density of virions is 1.18 g cm−3 in isopycnic sucrose gradients (Goodin and Jackson 2002).
The negative-sense, single-stranded RNA genome of 12.0–14.5 kb is unsegmented. Six or seven mRNAs, one for each of the encoded proteins identified in infected plants.
N, P, M, G and L represent the five canonical rhabdovirus structural proteins. Rice yellow stunt virus (RYSV) P6 has RNA silencing suppressor activity (Jackson et al., 2005a, Guo et al., 2013). The RYSV P3 protein, encoded by an ORF between the P and M ORFs, has been shown to have cell-to-cell movement activity in a heterologous virus trans-complementation assay (Huang et al., 2005). The Y proteins of potato yellow dwarf virus (PYDV) and eggplant mottled dwarf virus (EMDV), also encoded by an ORF between the P and M ORFs, are thought to be movement proteins (Jackson et al., 2005a, Bandyopadhyay et al., 2010, Pappi et al., 2013).
PYDV M can induce the intranuclear accumulation of the inner nuclear membrane in the absence of any other viral protein (Bandyopadhyay et al., 2010). Protein interaction studies for PYDV in live plants have identified binary interactions between N:N, N:P, N:M, M:M, M:Y, M:G, G:G and Y:Y (Bandyopadhyay et al., 2010).
The lipoprotein envelope is derived from the host plant or insect vector (Jackson et al., 2005a). Lipid composition is unknown.
Genome organisation and replication
The PYDV genome (12.9 kb) contains seven genes in the order 3′-N-X-P-Y-M-G-L-5′, which likely encode the nucleocapsid protein (N), phosphoprotein (polymerase cofactor) (P), movement protein (Y), matrix protein (M), glycoprotein (G) and RNA-directed RNA polymerase (L), respectively (Figure 1.Alphanucleorhabdovirus). The function of the protein encoded in the X gene has not been determined. The genome organisation of EMDV and Physostegia chlorotic mottle virus (PhCMoV) resembles that of PYDV. The PYDV coding sequences are flanked by a 3′-leader RNA of 149 nt and a 5′-trailer RNA of 97 nt, with genes separated by conserved intergenic “gene junction” regions that are similar in both length and sequence to those of other rhabdoviruses.
The genomes of RYSV and wheat yellow striate virus (WYSV) have gene orders similar to that of maize mosaic virus (MMV), except for the presence of an additional small gene P6 between the G gene and the L gene, which in RYSV encodes a virion-associated protein. The genomes of maize Iranian mosaic virus (MIMV), taro vein chlorosis virus (TaVCV) and Morogoro maize-associated virus (MMaV) are approximately 12.0–12.4 kb with a gene order resembling that of MMV.
Figure 1.Alphanucleorhabdovirus. Schematic representation of alphanucleorhabdovirus genome organisations. N, P, M, G and L represent ORFs encoding the structural proteins. ORFs encoding putative cell-to-cell movement proteins are highlighted (blue). Other ORFs encode putative accessory proteins of unknown function, including sets of small homologous proteins located between the N gene and P gene of potato yellow dwarf virus, Physostegia chlorotic mottle virus and eggplant mottled dwarf virus (orange), and between the G gene and L gene of rice yellow stunt virus and wheat yellow striate virus (green).
Nucleorhabdoviruses replicate in the nuclei of plant cells, which become greatly enlarged and develop large granular nuclear inclusions that are thought to be sites of virus replication (Jackson et al., 2005a).
A wide variety of monocot and dicot plants are susceptible to infection by alphanucleorhabdoviruses although each virus usually has a restricted host range (Jackson et al., 2005a, Goodin and Jackson 2002). Alphanucleorhabdoviruses are transmitted by leafhoppers (RYSV, WYSV, EMDV, PYDV) or planthoppers (MMV, MIMV). Some viruses are also transmitted during vegetative propagation, and some can be transmitted mechanically from infected sap. In all carefully examined cases, viruses replicate in cells of the insect vector as well as in the plant host (Jackson et al., 2005a).
Species demarcation criteria
Viruses assigned to different species within the genus Alphanucleorhabdovirus have several of the following characteristics: A) the nucleotide sequence identity of complete genomes is lower than 75%; B) they occupy different ecological niches as evidenced by differences in hosts and/or arthropod vectors; and C) they can be clearly distinguished in serological tests or by nucleic acid hybridisation.
Alphanucleorhabdovirus species are primarily differentiated by plant host range and vector specificity of the virus. Nucleic acid hybridisation has been used to provide confirmation of identification and serological criteria have enabled verification of common viruses that infect different hosts. However, no alphanucleorhabdovirus species have been defined unambiguously using serology. Complete genome nucleotide sequences are available for all 9 viruses currently assigned to species in the genus. RT-PCR-based assays and fluorescent viral protein localisation have proven to be useful tools for species demarcation. Hybridisation using cloned probes and RT-PCR has been used to diagnose viruses.
|Species||Virus name||Isolate||Accession number||RefSeq number||Available sequence||Virus Abbrev.|
|Constricta yellow dwarf alphanucleorhabdovirus||constricta yellow dwarf virus||PV-233||KY549567||Complete genome||CYDV|
|Eggplant mottled dwarf alphanucleorhabdovirus||eggplant mottled dwarf virus||Agapanthus||KJ082087||NC_025389||Complete genome||EMDV|
|Maize Iranian mosaic alphanucleorhabdovirus||maize Iranian mosaic virus||Fars||MF102281||NC_036390||Complete genome||MIMV|
|Maize mosaic alphanucleorhabdovirus||maize mosaic virus||USA||AY618418||NC_005975||Complete genome||MMV|
|Morogoro maize-associated alphanucleorhabdovirus||Morogoro maize-associated virus||16-0112||MK063878||Complete genome||MMaV|
|Peach alphanucleorhabdovirus||peach virus 1||NSTT||MN520414||Complete genome||PeV1|
|Physostegia chlorotic mottle alphanucleorhabdovirus||Physostegia chlorotic mottle virus||PV-1182||KX636164||Complete genome||PhCMoV|
|Potato yellow dwarf alphanucleorhabdovirus||potato yellow dwarf virus||SYDV||GU734660||NC_016136||Complete genome||PYDV|
|Rice yellow stunt alphanucleorhabdovirus||rice yellow stunt virus||China||AB011257||NC_003746||Complete genome||RYSV|
|Taro vein chlorosis alphanucleorhabdovirus||taro vein chlorosis virus||Fiji||AY674964||NC_006942||Complete genome||TaVCV|
|Wheat yellow striate alphanucleorhabdovirus||wheat yellow striate virus||SX-HC||MG604920||Complete genome||WYSV|
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Related, unclassified viruses
constricta yellow dwarf virus
peach virus 1