Ophioviridae


Ophioviridae

Chapter Contents

Ophioviridae: The Family

Ophioviridae: Member Taxa

Ophioviridae: Supporting Information

  • Authors - Corresponding author: María Laura García (garcia_m@biol.unlp.edu.ar)
  • Resources - Sequence alignments and tree files
  • Further Reading - Reviews and additional information
  • References - Literature cited

Citation

A summary of this ICTV online (10th) report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows: 

María Laura García, Elena Dal Bó, John V. da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A. Navarro, Carina A. Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E. Tzanetakis, Anna María Vaira, Martin Verbeek, and ICTV Report Consortium, 2017, ICTV Virus Taxonomy Profile: Ophioviridae, Journal of General Virology, 98: 11611162.

Summary

The Ophioviridae is a family of filamentous plant viruses, with single stranded negative, and possibly ambisense, RNA genomes of 11.3–12.5 kb divided into 3–4 segments. Virions are naked filamentous nucleocapsids, non-enveloped, in the shape of kinked circles of at least two different contour lengths. Since only one genus is currently recognized, the family description corresponds to the genus Ophiovirus, and the type species is Citrus psorosis virus. The family includes seven members, of which four are known to be soil-transmitted. Natural hosts of the ophioviruses include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots.

Table 1.Ophioviridae. Characteristics of the family Ophioviridae

Characteristic

Description

Typical member

citrus psorosis virus P-121 (RNA1: AY654892; RNA2: AY654893; RNA3: AY654894), species Citrus psorosis virus, genus Ophiovirus

Virion

Non-enveloped, naked filamentous nucleocapsids about 3 nm in diameter, forming kinked circles of at least two different contour lengths (700 nm and about 2000 nm). Pseudo-linear duplex structures are about 9–10 nm in diameter

Genome

11.3–12.5 kb of negative-sense, segmented RNA (3 or 4 segments)

Replication

Not characterized

Translation

From mRNAs, which are complementary to the vRNAs,

Host Range

Citrus, blueberry, pittosporum, lettuce, sowthistle, tulip, ranunculus, anemone, lachenalia and freesia

Taxonomy

One genus, Ophiovirus, including 7 species

Virion

Morphology

The particles are naked filamentous nucleocapsids about 3 nm in diameter (Figure 1.Ophioviridae), forming kinked (probably internally coiled) circles of at least two different contour lengths, the shortest being about 700 nm. The circles (open form) can collapse to form pseudo-linear duplex structures of 9–10 nm in diameter (collapsed form) (Milne et al., 1996).

Figure 1.Ophioviridae. Negative contrast electron micrograph (uranyl acetate) of FreSV and CPsV particles. The bar represents 100 nm. (A) Open form of the large particle (CPsV), and (B) collapsed form (FreSV) (Courtesy of R. G. Milne)

Physicochemical and physical properties

The relative molecular masses and sedimentation coefficients of virions are unknown. The particles are unstable in CsCl but the buoyant density in cesium sulfate has been determined to be 1.22 g cm−3 for both Ranunculus white mottle virus [RWMV, Rn3 isolate], and Mirafiori lettuce big-vein virus [MiLBVV, I-47 isolate] (Roggero et al., 2000, Vaira et al., 1997). The particles are unstable between pH 6 and 8. Viruses lose infectivity in crude sap held at 50 °C for 10 min (40–45 °C for tulip mild mottle mosaic virus, TMMMV) (Morikawa et al., 1995). Virus structures are resistant to limited treatment with organic solvents and nonionic or zwitterionic detergents.

Nucleic acid

Single stranded negative, and possibly ambisense, RNA genome (11.3–12.5 kb in total) divided into 3 or 4 segments. The virions encapsidate both the viral and viral complementary RNAs (vRNA and vcRNA), but a larger amount of vRNA (negative polarity) is detected in purified virion preparations (Roggero et al., 2000, Garcia et al., 1991, Naum-Ongania et al., 2003, Sánchez de la Torre et al., 1998, van der Wilk et al., 2002). As virions appear circularized, the presence of panhandle structures has been suggested; however, significant sequence complementarity was not found between the 5′- and the 3′-terminal sequences of genomic RNAs of citrus psorosis virus (CPsV), MiLBVV or blueberry mosaic associated virus (BlMaV) (Naum-Ongania et al., 2003, van der Wilk et al., 2002, Thekke-Veetil et al., 2014). At the 5′ and 3′ ends of MiLBVV genomic RNAs, there are orthomyxovirus-like palindromic sequences that could fold into a symmetrically hooked conformation. These structures could not be predicted for other sequenced members.

The size of the RNAs is 7.5-8.2 kb for RNA1, 1.6-1.9 kb for RNA2 and 1.4-1.5 kb for RNA3. A fourth genomic RNA of about 1.4 kb has been reported for MiLBVV and lettuce ring necrosis virus (LRNV). In the case of CPsV, RWMV, freesia sneak virus (FreSV) and BlMaV the RNA4 was not found, and no information is available for TMMMV (Vaira et al., 1997, Morikawa et al., 1995, Naum-Ongania et al., 2003, Sánchez de la Torre et al., 1998, Thekke-Veetil et al., 2014, Sánchez de la Torre et al., 2002, Torok and Vetten 2002, Torok and Vetten 2003, Vaira et al., 2003, Vaira et al., 2009, Vaira et al., 1996).

Proteins

The virions consist of a single type of coat protein (CP) subunits of 43–50 kDa, varying in size according to species and isolate (Roggero et al., 2000, Vaira et al., 1997, Morikawa et al., 1995, Sánchez de la Torre et al., 1998, van der Wilk et al., 2002, Torok and Vetten 2003, Derrick et al., 1988, Garcia et al., 1994, Jeong et al., 2014, Navas‐Castillo et al., 1993).  

Genome organization and replication

The genome of ophioviruses consists of three or four individually encapsidated vRNA segments (Figure 2.Ophioviridae) although vcRNAs are also encapsidated (Vaira et al., 1997, Naum-Ongania et al., 2003, Sánchez de la Torre et al., 1998, van der Wilk et al., 2002, Thekke-Veetil et al., 2014, Sánchez de la Torre et al., 2002, Vaira et al., 2003, Martin et al., 2005). The vcRNA1, the longest RNA segment (7.5–8.2 kb), contains two ORFs. The ORF located at its 5´ end encodes a protein with a predicted molecular mass of 22-25 kDa. The 24K ortholog of CPsV localizes at the nucleus and was reported to be involved in miRNA misprocessing in citrus (Reyes et al., 2016), and to possess RNA silencing suppressor activity (Robles Luna et al., 2017). Separated by an intergenic region of about a hundred nucleotides, a second ORF in the same strand encodes a protein (261-280 kDa) that contains the core polymerase module with the characteristic five conserved motifs (A-E) of the RNA-dependent RNA polymerases (RdRP). The SDD sequence, a signature for segmented negative-stranded RNA viruses (Orthomyxoviridae, Arenaviridae and Bunyaviridae) occurs in motif C of the RdRP (Naum-Ongania et al., 2003). Since no segmented-RNA virus has two ORFs coded in the vcRNA of the larger segment (RNA1), this genomic organization is a particular feature of this family.

Figure 2.Ophioviridae. Genome organization of the genus Ophiovirus. MiLBVV is shown here (modified from (van der Wilk et al., 2002)). Boxes represent ORFs. The length of the RNA segments and the predicted sizes of the ORF products are indicated. v, viral RNA; vc, viral complementary RNA. RNA4 is not reported for all ophioviruses. RdRP, RNA polymerase; MP, movement protein; CP, coat protein. 

The vcRNA2 (1.6-1.9 kb) of CPsV, LRNV, FreSV and BlMaV contains a single ORF, whereas for MiLBVV a second ORF in the vRNA2 encoding a putative protein of 37-38 kDa of unknown function has been reported. This would make MiLBVV the sole ophiovirus with ambisense RNA2 (van der Wilk et al., 2002). The vcRNA 2 encodes the cell-to-cell movement protein (MP) of 50-58 kDa, which has been characterized for CPsV (54K) and MiLBVV (55K) (Hiraguri et al., 2013, Robles Luna et al., 2013). The MP is also involved in RNA silencing suppression activity (Robles Luna et al., 2017). The vcRNA3 codes for the CP (Roggero et al., 2000, Sánchez de la Torre et al., 1998, Vaira et al., 2011), which show homologous interaction and localizes in the cytoplasm of N. benthamiana epithelial cells (Peña et al., 2012). RWMV CP accumulates in the cytoplasm of parenchyma cells (Roggero et al., 2000). The CPs of MiLBVV and CPsV interact with the virus-specific MP in the cytoplasm suggesting a potential role of the CP in ophiovirus movement (Robles Luna et al., 2013).

RNA4 (ca. 1.4 kb) has been identified only from MiLBVV and LRNV (Roggero et al., 2000, Torok and Vetten 2003). Whereas the vcRNA4 of LRNV potentially encodes only one protein (ca. 38 kDa) of unknown function, that of MiLBVV contains two ORFs overlapping by 38 nt, potentially encoding a 37- and 10.6-kDa proteins. The second ORF lacks an initiation codon and is proposed to be expressed by a +1 translational frameshift (van der Wilk et al., 2002).

Nuclear localization signals (NLS) have been reported for the CPsV, MiLBVV, BlMaV and RWMV polymerases, for the MPs of CPsV and MiLBVV and for the 23K protein of BlMaV (Naum-Ongania et al., 2003, van der Wilk et al., 2002, Thekke-Veetil et al., 2014, Sánchez de la Torre et al., 2002).

For CPsV and BlMaV, the 5′ ends of the vcRNA1, vcRNA2 and vcRNA3 are identical, GATAC(T)7, but the 3′ ends are all different. For MiLBVV, the respective 5′ and 3′ ends are conserved among the four viral RNA segments. In addition, the vRNA terminal ends are able to anneal and fold into structures resembling the ‘corkscrew’ conformation of the RNA termini of the Orthomyxoviridae (van der Wilk et al., 2002).

For BlMaV, there are indications of natural reassortments between RNAs 2 and 3 (Thekke-Veetil et al., 2015). Natural reassortments between RNAs 1 and 3 of CPsV have been suggested (Martin et al., 2006), and genome compatibility, between the bottom (RNA1) and top (RNAs 2 and 3) components of two CPsV isolates, has been observed in the experimental host Chenopodium quinoa (Garcia et al., 1993).

Antigenicity

The CP is the only significant antigenic element. In Western blots, the CPs of RWMV, TMMMV, MiLBVV and LRNV, but not CPsV, appear to be serologically related to varying degrees (Roggero et al., 2000).

Biology

Ophioviruses can be mechanically transmitted to a limited range of test plants, the most used being Nicotiana benthamiana and N. occidentalis P1, inducing local lesions and systemic mottle, and Chenopodium quinoa producing local lesions. The natural hosts of CPsV, RWMV, MiLBVV and LRNV are dicotyledonous plants of widely differing taxonomy. In contrast, TMMMV and FreSV infect monocots. CPsV is commonly transmitted by vegetative propagation of the host. Although natural dispersion of psorosis disease has been observed in Texas and Argentina (Danós 1990, Timmer and Garnsey 1980) no natural vector has been identified, since limited vector-transmission experiments have been performed (Beñatena and Portillo 1984, Palle et al., 2004). No vector is known for either RWMV or BlMaV. The zoospores of Olpidium virulentus or O. brassicae transmit MiLBVV, TMMMV, LRNV and FreSV (Lot et al., 2002, Meekes and Verbeek 2011, Navarro et al., 2004, Sasaya and Koganezawa 2006, Vaira et al., 2006). MiLBVV has been shown to be present in the weed Sonchus oleraceus which can act as a natural reservoir for lettuce infection by means of the fungus vector (Navarro et al., 2005).

CPsV has a wide geographical distribution in Citrus spp. and citrus relatives in the Americas, in the Mediterranean basin, New Zealand and South Africa (Quemin et al., 2011, Roistacher 1993, Sippel et al., 2015).

RWMV has been reported in two species of the family Ranunculacae from Northern Italy (ranunculus and anemone hybrids) (Vaira et al., 1997, Vaira et al., 2003), in lettuce in France and Germany (Torok and Vetten 2010) and recently in the evergreen shrub Pittosporum tobira in Southern Italy (Morelli et al., 2015).

FreSV has been reported in Europe, South Africa, North America, South Korea and New Zealand (Vaira et al., 2009, Jeong et al., 2014, Vaira et al., 2006, Pearson et al., 2009, Vaira et al., 2007, Verbeek et al., 2004) in freesia (Freesia refracta hyb. Iridaceae) and in lachenalia (Lachenalia hyb. Hyacinthaceae).

TMMMV has been reported in tulips (Tulipa hyb. Liliaceae) in Japan (Morikawa et al., 1995). MiLBVV is the causal agent of big-vein symptoms (zones cleared of chlorophyll, parallel to the veins) in lettuce; this widespread and damaging disease probably occurs worldwide. 

LRNV is closely associated with lettuce ring necrosis disease in The Netherlands and Belgium (Torok and Vetten 2002). BlMaV has been reported in blueberry (Vaccinium spp. Ericaceae) in several regions of North America as well as several other parts of the globe including South America, Europe, New Zealand, South Africa and Japan (Isogai et al., 2016, Martin et al., 2012).

Derivation of name

Ophio: from the Greek ophis, “snake”, referring to the snaky appearance of the virion (Garcia et al., 1994).

Phylogenetic relationships

Ophiovirus-specific primers, based on a highly conserved sequence of RNA1, have been tested in RT-PCR with all ophiovirus species. In all cases, a 136 bp fragment was amplified (Vaira et al., 2003). Phylogenetic analysis of the coat protein from one isolate for each species (Figure 3.Ophioviridae) supported the positions of each species and indicated a closer relationship between MiLBVV and TMMMV, as already suggested by coat protein serological tests. BlMaV and CPsV cluster in a distinct clade and seem more distantly related to the other ophioviruses by molecular characteristics. These differences, if reinforced, might also lead to the re-assignment of the existing species into two separate genera in the family. Analysis of the conserved RdRP motifs show again a distinct clade of CPsV and BlMaV, as well as higher identities between the orthologous CP and MP, with respect to the rest of the ophioviruses (Thekke-Veetil et al., 2015).

Figure 3.Ophioviridae. Unrooted phylogenetic tree based on the predicted coat protein amino acid sequences encoded by RNA3, obtained from 7 ophiovirus species. Alignment was obtained using ClustalW, and analyzed by the neighbor-joining method, with 1000 bootstrap replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches (when >50%). The evolutionary distances were computed using the p-distance method.

Similarity with other taxa

Ophiovirus virion morphology resembles that of viruses in the genus Tenuivirus, family Phenuiviridae, and the internal nucleocapsid component resembles that of members of the family Tospoviridae. Unlike tenuiviruses, ophioviruses do not infect plants in the Gramineae, and unlike members of the family Tospoviridae, there is no evidence of enveloped virions. Moreover, ophioviruses do not have the conserved identical nucleotides at the genomic RNA termini that are typical of these two families. MiLBVV appears to have a terminal “corkscrew”-like conformation similar to that in viruses in the Orthomyxoviridae. RdRP aa sequences show ophioviruses to be similar to members of the families Paramyxoviridae, Pneomoviridae, Rhabdoviridae, Bornaviridae and Filoviridae (Figure 4.Ophioviridae). The RdRP also contains the SDD sequence in motif C, a signature for segmented negative-stranded RNA viruses (families Orthomyxoviridae, Arenaviridae and order Bunyavirales). However, phylogenetic reconstructions using sequences of the core module of RdRPs of representative negative-stranded RNA viruses reinforce the phylogenetic relatedness of the ophioviruses and suggest their separation as a monophyletic group (Figure 4.Ophioviridae). 

Figure 4A.Ophioviridae. Unrooted phylogenetic tree of members of the family Ophioviridae and other negative stranded RNA viruses based on the amino acid sequences of their conserved RdRP core modules. The tree was generated by the neighbor-joining method and bootstrap values (indicated for each branch node when >50%) were estimated using 100 replicates. 

Figure 4B.Ophioviridae. Midpoint phylogenetic tree of members of the family Ophioviridae and other negative stranded RNA viruses based on the amino acid sequences of their conserved RdRP core modules. The tree was generated by the neighbor-joining method and bootstrap values (indicated for each branch node when >50%) were estimated using 100 replicates. 

Related, Unclassified viruses

There are two reports regarding ophiovirus-like isolates. In one study, RdRP sequences corresponding to 3 negative-stranded RNA viruses  (Rhizoctonia solani negative-stranded RNA viruses 1 to 3, RsNSRV-1, -2, and -3) were found in the transcriptome of Rhizoctonia solani (Marzano et al., 2016) . The predicted amino acid sequences of RsNSRV-1, -2, and -3 were similar to those of the RdRP encoded by the RNA1 of LRNV and other members of the family Ophioviridae. The second report describes the detection of an RdRP sequence (Fusarium poae negative-stranded RNA virus (FpNSV) 1) in metagenomic data from Fusarium poae with 23% identity to the RdRP of MiLBVV (Osaki et al., 2016). Further characterization, including particle morphology, will be required in order to decide if these (putative) ophiovirus-like viruses belong to the family Ophioviridae; if so they are unlikely to belong to the genus Ophiovirus.

Virus name

Accession number

Virus abbreviation

Rhizoctonia solani negative-stranded RNA virus-1

KP900919

RsNSRV-1

Rhizoctonia solani negative-stranded RNA virus-2

KP900920

RsNSRV-2

Rhizoctonia solani negative-stranded RNA virus-3

KP900903

RsNSRV-3

Fusarium poae negative-stranded RNA virus-1

LC150618

FpNSV1

 


Genus: Ophiovirus


Since only one genus (Ophiovirus) is currently recognized in the family Ophioviridae, the family description above corresponds to the genus description. For clarity, the additional information that can be found on the genus page is also presented below.

Species demarcation criteria

The different criteria considered for species demarcation in the genus are:

  • differences in CP size
  • no or distant serological relationship between CPs
  • differences in natural host range
  • different number, organization and/or size of genome segments.

Alignments between CPsV, FreSV, MiLBVV, LRNV, BlMaV and RWMV (partial sequence) CP amino acid sequences show 31–52% identity, whereas isolates of the same species show over 92% identity. Since CPs of MiLBVV and TMMMV (partial cds) share about 80% amino acid sequence identity, this may warrant the establishment of the following molecular criterion for ophiovirus species demarcation: CP amino acid sequence identity <85%.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)Isolate Abbreviation
Blueberry mosaic associated ophiovirusblueberry mosaic associated virusArkansas5RNA1: KJ704366; RNA2: KJ704367; RNA3: KJ704368Complete genomeBlMaV
Citrus psorosis ophioviruscitrus psorosis virusP/121RNA1: AY654892; RNA2: AY654893; RNA3: AY654894RNA1: NC_006314; RNA2: NC_006315; RNA3: NC_006316Complete genomeCPsV
Freesia sneak ophiovirusfreesia sneak virusFFr220205/9RNA3: DQ885455Partial genomeFreSV
Lettuce ring necrosis ophioviruslettuce ring necrosis virusBelg/2RNA1: AY535016; RNA2: AY535017; RNA3: AY535018; RNA4: AY535019RNA1: NC_006051; RNA2: NC_006052; RNA3: NC_006053; RNA4: NC_006054Complete genomeLRNV
Mirafiori lettuce big-vein ophiovirusMirafiori lettuce big-vein virusLS301/ORNA1: AF525933; RNA2: AF525934; RNA3: AF525935; RNA4: AF525936RNA1: NC_004779; RNA2: NC_004781; RNA3: NC_004782; RNA4: NC_004780Complete genomeMLBVV
Ranunculus white mottle ophiovirusranunculus white mottle virusRn3RNA1: AF335429Partial genomeRWMV
Tulip mild mottle mosaic ophiovirustulip mild mottle mosaic virusBas/1RNA3: AY542958Partial genomeTMMMV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.