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.
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).
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.
|Species||Virus name||Isolate||Accession number||RefSeq number||Available sequence||Virus Abbrev.|
|Aeonium ringspot virus||Aeonium ringspot virus||Scafati/2011||RNA-1: JX304792;|
|Apricot latent ringspot virus||apricot latent ringspot virus||Modesto||AJ278875||NC_043411||Partial genome||ALRSV|
|Arabis mosaic virus||Arabis mosaic virus||NW||RNA-1: AY303786;|
|Arracacha virus A||Arracacha virus A||No entry in Genbank||AVA|
|Artichoke Aegean ringspot virus||artichoke Aegean ringspot virus||No entry in Genbank||AARSV|
|Artichoke Italian latent virus||artichoke Italian latent virus||V||RNA-1: LT608395;|
|Artichoke yellow ringspot virus||artichoke yellow ringspot virus||AM087671||NC_038862||Partial genome||AYRSV|
|Beet ringspot virus||beet ringspot virus; tomato black ring virus||S||RNA-1: D00322;|
|Blackcurrant reversion virus||blackcurrant reversion virus||Latvala||RNA-1: AF368272;|
|Blueberry latent spherical virus||blueberry latent spherical virus||Japan||RNA-1: AB649296;|
|Blueberry leaf mottle virus||blueberry leaf mottle virus||U20621||NC_043076||Partial genome||BLMoV|
|Cassava American latent virus||cassava American latent virus||No entry in Genbank||CsALV|
|Cassava green mottle virus||cassava green mottle virus||No entry in Genbank||CsGMV|
|Cherry leaf roll virus||cherry leaf roll virus||E395||RNA-1: FR851461;|
|Chicory yellow mottle virus||chicory yellow mottle virus||No entry in Genbank||ChYMV|
|Cocoa necrosis virus||cocoa necrosis virus||ATTC PV-283||EU741694||NC_043077||Partial genome||CoNV|
|Crimson clover latent virus||crimson clover latent virus||No entry in Genbank||CCLV|
|Cycas necrotic stunt virus||Cycas necrotic stunt virus||Iwanami||RNA-1: AB073147;|
|Complete coding genome||CNSV|
|Grapevine Anatolian ringspot virus||grapevine Anatolian ringspot virus||A34||RNA-1: HE774604;|
|Grapevine Bulgarian latent virus||grapevine Bulgarian latent virus||Serb1||RNA-1: FN691934;|
|Grapevine chrome mosaic virus||grapevine chrome mosaic virus||Brault||RNA-1: X15346;|
|Grapevine deformation virus||grapevine deformation virus||N66||RNA-1: HE613269;|
|Grapevine fanleaf virus||grapevine fanleaf virus||F13||RNA-1: D00915;|
|Grapevine Tunisian ringspot virus||grapevine Tunisian ringspot virus||No entry in Genbank||GTRSV|
|Hibiscus latent ringspot virus||Hibiscus latent ringspot virus||No entry in Genbank||HLRSV|
|Lucerne Australian latent virus||lucerne Australian latent virus||No entry in Genbank||LALV|
|Melon mild mottle virus||melon mild mottle virus||Japan/Tottori||RNA-1: AB518485;|
|Mulberry mosaic leaf roll associated virus||mulberry mosaic leaf roll associated virus||zj||RNA-1: KC904083;|
|Mulberry ringspot virus||mulberry ringspot virus||No entry in Genbank||MRSV|
|Myrobalan latent ringspot virus||myrobalan latent ringspot virus||No entry in Genbank||MLRSV|
|Nepovirus CawYV||caraway yellows virus||MK492273;|
|Nepovirus GNVA||grapevine nepovirus A||MT507290;|
|Nepovirus GSPNeV||green Sichuan pepper nepovirus||MH323435;|
|Nepovirus PCMoV||petunia chlorotic mottle virus||KX812815;|
|Nepovirus PoLNVA||poaceae Liege nepovirus A||MW289235;|
|Nepovirus RCNA||red clover nepovirus A||MG253828;|
|Olive latent ringspot virus||olive latent ringspot virus||Italy||AJ277435||NC_038863||Partial genome||OLRSV|
|Peach rosette mosaic virus||peach rosette mosaic virus||43771||RNA-1: KY646466;|
|Potato black ringspot virus||potato black ringspot virus||PRI-Ec||RNA-1: KC832887;|
|Potato virus B||potato virus B||Pasco-01||RNA-1: KX656670;|
|Potato virus U||potato virus U||No entry in Genbank||PVU|
|Raspberry ringspot virus||raspberry ringspot virus||cherry||RNA-1: AY303787;|
|Soybean latent spherical virus||soybean latent spherical virus||ND1||RNA-1: KX424571;|
|Tobacco ringspot virus||tobacco ringspot virus||SK||RNA-1: U50869;|
|Tomato black ring virus||tomato black ring virus||MJ||RNA-1: AY157993;|
|Tomato ringspot virus||tomato ringspot virus||Rasberry||RNA-1: L19655;|
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Related, unclassified viruses
red clover nepovirus A