Genus: Nepovirus

Genus: Nepovirus

Distinguishing features

Nepoviruses are the only known members of the family that encode a single large capsid protein (CP) of 52–60 kDa (Fuchs et al., 2016). These viruses are transmitted by nematode vectors and through pollen.

Virion

See discussion under family description.

Genome organisation and replication

Genome organization and expression are similar to those of comoviruses, except that RNA-2 specifies a single polyprotein of 105–207 kDa. Nepoviruses can be divided into three subgroups based on their sequences, genome organization and cleavage sites. Subgroup A has an RNA-2 of 3,700–4,000 bases, present in both M and B components. Subgroup B has an RNA-2 of 4,400–4,700 bases, present only in the M component. Potato virus B and red clover nepovirus A are newly characterized viruses with phylogenetic relationships to nepoviruses of subgroup B (De Souza et al., 2016, Koloniuk et al., 2018). Subgroup C has an RNA-2 of 6,400–7,300 bases, present in M component particles that are sometimes barely separable from those of B component. The three subgroups also differ in the cleavage sites recognized by their proteinase (Table 3.Secoviridae).

Additional linear or circular satellite RNAs, which sometimes modulate symptoms, are found associated with several nepoviruses of all three subgroups. They are either linear (1100–1800 bases) with a 5ʹ-linked VPg, a 3ʹ-poly(A) tail and encoding a 36–48 kDa polypeptide, or circular (300–460 bases) and apparently non-coding (Feldstein et al., 1997, Chay et al., 1997). They are present in some natural isolates but are not necessary for virus accumulation (Gottula et al., 2013). In aeonium plants infected with aeonium ringspot virus there is an additional species of RNA-2 (RNA-2′) in addition to the full-length RNA-2. The smaller length of this RNA-2′ is the result of a 537 nt deletion in the predicted movement protein (MP) region (Sorrentino et al., 2013).

The RNA-2-encoded polyprotein of subgroup A and B nepoviruses is processed into three domains. In grapevine fanleaf virus (GFLV), the N-terminal protein of the RNA-2-encoded polyprotein (P2A) is involved in RNA-2 replication (Gaire et al., 1999). The two other protein domains are the MP and the unique CP. Both are required for cell-to-cell movement of the virus. Similarly to comoviruses, the MP has a LPL motif, interacts with the CP and is a structural component of tubular structures containing virus-like particles and traversing the cell wall. Cell-to-cell movement depends on the secretory pathway and the cytoskeleton and requires class XI myosin motors (Laporte et al., 2003, Amari et al., 2011). In tomato ringspot virus (ToRSV) (subgroup C), the N-terminal region of the RNA-2-encoded polyprotein is cleaved at an additional site, defining two domains (X3 and X4) (Carrier et al., 2001). The X3 protein contains some sequence similarity with the P2A protein of GFLV but the X4 protein is a unique protein of unknown function. The RNA-1 of nepoviruses is translated into a single polyprotein that is processed into six domains. The C-terminal region of the polyprotein contains the replication block, and is similar to that of comoviruses (NTB-VPg-Pro-Pol). In contrast, the N-terminal region of the polyprotein contains an additional cleavage site defining two protein domains (X1 and X2) instead of the single domain present upstream of NTB in the comovirus genome. Cleavage at this additional site was demonstrated for arabis mosaic virus (subgroup A) and ToRSV (subgroup C) (Wetzel et al., 2008, Wang and Sanfacon 2000). A cleavage site at this position has been proposed for other nepoviruses. The function of X1 is unknown. X2 contains a sequence motif in common with the comovirus Co-Pro protein but does not seem to modulate the activity of the proteinase. However, similarly to the comovirus Co-Pro, the X2 protein of ToRSV associates with ER-derived membranes and a role in viral replication has been proposed (Zhang and Sanfacon 2006). When comparing RNA-1 and RNA-2, the 5ʹ- and 3ʹ- UTRs are similar in sequence but not identical in subgroup A nepoviruses. In subgroup B nepoviruses, the 5ʹ-UTRs also show sequence similarity between RNA-1 and RNA-2, while the 3ʹ-UTRs are identical in both RNAs. In subgroup C nepoviruses, both UTRs are identical or nearly identical between RNA-1 and RNA-2. The region of sequence similarity extends into part of the coding region of the polyproteins in ToRSV, but not in blackcurrant reversion virus (Walker et al., 2015).

Biology

Nepoviruses are widely distributed in temperate regions. The natural host range of nepoviruses varies from wide to restricted, depending on the virus. Ringspot symptoms are characteristic, but mottling and spotting are equally frequent. Viruses of twelve species are acquired and transmitted non-persistently by longidorid nematodes (Xiphinema, Longidorus or Paralongidorus spp), three are transmitted by pollen, and viruses of one species are transmitted by mites (blackcurrant reversion virus). The others have no known biological vector (Susi 2004). Seed and/or pollen transmission is very common. In herbaceous plants, the symptoms induced by nepoviruses are often transient, with newly emerging leaves appearing symptomless a few weeks after infection (the so-called “recovery” phenomenon). Symptom recovery is associated with induction of RNA silencing, an antiviral defence, and is sometimes (but not always) accompanied with reduced concentration of viral RNAs (Ghoshal and Sanfacon 2015).

Species demarcation criteria

See discussion under family description.

Member species

Exemplar isolate of the species
SpeciesVirus nameIsolateAccession numberRefSeq numberAvailable sequenceVirus Abbrev.
Aeonium ringspot virusAeonium ringspot virusScafati/2011RNA-1: JX304792;
RNA-2: JQ670669
All
RNA-1: NC_038762;
RNA-2: NC_038761
All
Complete genomeAeRSV
Apricot latent ringspot virusapricot latent ringspot virusModestoAJ278875NC_043411Partial genomeALRSV
Arabis mosaic virusArabis mosaic virusNWRNA-1: AY303786;
RNA-2: AY017339
All
RNA-1: NC_006057;
RNA-2: NC_006056
All
Complete genomeArMV
Arracacha virus AArracacha virus ANo entry in GenbankAVA
Artichoke Aegean ringspot virusartichoke Aegean ringspot virusNo entry in GenbankAARSV
Artichoke Italian latent virusartichoke Italian latent virusVRNA-1: LT608395;
RNA-2: LT608396
All
RNA-1: NC_043684;
RNA-2: NC_043685
All
Complete genomeAILV
Artichoke yellow ringspot virusartichoke yellow ringspot virusAM087671NC_038862Partial genomeAYRSV
Beet ringspot virusbeet ringspot virus; tomato black ring virusSRNA-1: D00322;
RNA-2: X04062
All
RNA-1: NC_003693;
RNA-2: NC_003694
All
Complete genomeBRSV
Blackcurrant reversion virusblackcurrant reversion virusLatvalaRNA-1: AF368272;
RNA-2: AF020051
All
RNA-1: NC_003509;
RNA-2: NC_003502
All
Complete genomeBRV
Blueberry latent spherical virusblueberry latent spherical virusJapanRNA-1: AB649296;
RNA-2: AB649297
All
RNA-1: NC_038764;
RNA-2: NC_038763
All
Complete genomeBLSV
Blueberry leaf mottle virusblueberry leaf mottle virusU20621NC_043076Partial genomeBLMoV
Cassava American latent viruscassava American latent virusNo entry in GenbankCsALV
Cassava green mottle viruscassava green mottle virusNo entry in GenbankCsGMV
Cherry leaf roll viruscherry leaf roll virusE395RNA-1: FR851461;
RNA-2: FR851462
All
RNA-1: NC_015414;
RNA-2: NC_015415
All
Complete genomeCLRV
Chicory yellow mottle viruschicory yellow mottle virusNo entry in GenbankChYMV
Cocoa necrosis viruscocoa necrosis virusATTC PV-283EU741694NC_043077Partial genomeCoNV
Crimson clover latent viruscrimson clover latent virusNo entry in GenbankCCLV
Cycas necrotic stunt virusCycas necrotic stunt virusIwanamiRNA-1: AB073147;
RNA-2: AB073148
All
RNA-1: NC_003791;
RNA-2: NC_003792
All
Complete coding genomeCNSV
Grapevine Anatolian ringspot virusgrapevine Anatolian ringspot virusA34RNA-1: HE774604;
RNA-2: AY291207
All
RNA-1: NC_018383;
RNA-2: NC_018384
All
Complete genomeGARSV
Grapevine Bulgarian latent virusgrapevine Bulgarian latent virusSerb1RNA-1: FN691934;
RNA-2: FN691935
All
RNA-1: NC_015492;
RNA-2: NC_015493
All
Complete genomeGBLV
Grapevine chrome mosaic virusgrapevine chrome mosaic virusBraultRNA-1: X15346;
RNA-2: X15163
All
RNA-1: NC_003622;
RNA-2: NC_003621
All
Complete genomeGCMV
Grapevine deformation virusgrapevine deformation virusN66RNA-1: HE613269;
RNA-2: AY291208
All
RNA-1: NC_017939;
RNA-2: NC_017938
All
Complete genomeGDefV
Grapevine fanleaf virusgrapevine fanleaf virusF13RNA-1: D00915;
RNA-2: X16907
All
RNA-1: NC_003615;
RNA-2: NC_003623
All
Complete genomeGFLV
Grapevine Tunisian ringspot virusgrapevine Tunisian ringspot virusNo entry in GenbankGTRSV
Hibiscus latent ringspot virusHibiscus latent ringspot virusNo entry in GenbankHLRSV
Lucerne Australian latent viruslucerne Australian latent virusNo entry in GenbankLALV
Melon mild mottle virusmelon mild mottle virusJapan/TottoriRNA-1: AB518485;
RNA-2: AB518486
All
RNA-1: NC_038765;
RNA-2: NC_038766
All
Complete genomeMMMoV
Mulberry mosaic leaf roll associated virusmulberry mosaic leaf roll associated viruszjRNA-1: KC904083;
RNA-2: KC904084
All
RNA-1: NC_038767;
RNA-2: NC_038768
All
Complete genomeMMLRaV
Mulberry ringspot virusmulberry ringspot virusNo entry in GenbankMRSV
Myrobalan latent ringspot virusmyrobalan latent ringspot virusNo entry in GenbankMLRSV
Olive latent ringspot virusolive latent ringspot virusItalyAJ277435NC_038863Partial genomeOLRSV
Peach rosette mosaic viruspeach rosette mosaic virus43771RNA-1: KY646466;
RNA-2: KJ572573
All
RNA-1: NC_034214;
RNA-2: NC_034215
All
Complete genomePRMV
Potato black ringspot viruspotato black ringspot virusPRI-EcRNA-1: KC832887;
RNA-2: KC832892
All
RNA-1: NC_022798;
RNA-2: NC_022799
All
Complete genomePBRSV
Potato virus Bpotato virus BPasco-01RNA-1: KX656670;
RNA-2: KX656671
All
RNA-1: NC_043447;
RNA-2: NC_043448
All
Complete genomePVB
Potato virus Upotato virus UNo entry in GenbankPVU
Raspberry ringspot virusraspberry ringspot viruscherryRNA-1: AY303787;
RNA-2: AY303788
All
RNA-1: NC_005266;
RNA-2: NC_005267
All
Complete genomeRpRSV
Soybean latent spherical virussoybean latent spherical virusND1RNA-1: KX424571;
RNA-2: KX424572
All
RNA-1: NC_032270;
RNA-2: NC_032271
All
Complete genomeSLSV
Tobacco ringspot virustobacco ringspot virusSKRNA-1: U50869;
RNA-2: AY363727
All
RNA-1: NC_005097;
RNA-2: NC_005096
All
Complete genomeTRSV
Tomato black ring virustomato black ring virusMJRNA-1: AY157993;
RNA-2: AY157994
All
RNA-1: NC_004439;
RNA-2: NC_004440
All
Complete genomeTBRV
Tomato ringspot virustomato ringspot virusRasberryRNA-1: L19655;
RNA-2: D12477
All
RNA-1: NC_003840;
RNA-2: NC_003839
All
Complete genomeToRSV

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

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

red clover nepovirus A

RNA-1: MG253828; RNA-2: MG253829

RCNVA

Virus names and virus abbreviations are not official ICTV designations.
red clover nepovirus A (Koloniuk et al., 2018)