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Nepoviruses are the only known members of the family that encode a single large CP of 52-60 kDa (Fuchs et al., 2016). 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 nt in length, present in both M and B components. Subgroup B has an RNA-2 of 4,400-4-700 nt in length, present only in the M component. Subgroup C has an RNA-2 of 6,400-7,300 nt in length, 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 nt) with a 5ʹ-linked VPg, a 3ʹ poly(A) tail and encoding a 36–48 kDa polypeptide, or circular (300-460 nt) 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 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) was shown to be 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 putative cleavage site at this position has been implied 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).
See discussion under family properties
potato virus B
RNA-1, KX656670; RNA-2, KX656671
Potato virus B is a newly characterized virus with phylogenetic relationships to nepoviruses of subgroup B (De Souza et al., 2016)
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