Secoviridae

Genus: Nepovirus


Genus: Nepovirus

Distinguishing features

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).

Virion

See discussion under family description.

Genome organization and replication

See discussion under family description.

Biology

See discussion under family description.

Species demarcation criteria

See discussion under family description.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)
Aeonium ringspot virusAeonium ringspot virusScafati-2011RNA-1: JX304792; RNA-2: JQ670669Complete genomeAeRSV-Scafati-2011
Apricot latent ringspot virusapricot latent ringspot virusModestoAJ278875Partial genomeALRSV-Modesto
Arabis mosaic virusArabis mosaic virusNWRNA-1: AY303786; RNA-2: AY017339RNA-1: NC_006057; RNA-2: NC_006056Complete genomeArMV-NW
Arracacha virus AArracacha virus ANo entry in GenbankAVA
Artichoke Aegean ringspot virusartichoke Aegean ringspot virusNo entry in GenbankAARSV
Artichoke Italian latent virusartichoke Italian latent virusX87254Partial genomeAILV
Artichoke yellow ringspot virusartichoke yellow ringspot virusAM087671Partial genomeAYRSV
Beet ringspot virusbeet ringspot virus; tomato black ring virusSRNA-1: D00322; RNA-2: X04062RNA-1: NC_003693; RNA-2: NC_003694Complete genomeBRSV-S
Blackcurrant reversion virusblackcurrant reversion virusLatvalaRNA-1: AF368272; RNA-2: AF020051RNA-1: NC_003509; RNA-2: NC_003502Complete genomeBRV-Latvala
Blueberry latent spherical virusblueberry latent spherical virusJapan:Iwate, Takizawa-mura RNA-1: AB649296; RNA-2: AB649297Complete genomeBLSV-Japan
Blueberry leaf mottle virusblueberry leaf mottle virusU20621Partial 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 virusE395 RNA-1: FR851461; RNA-2: FR851462RNA-1: NC_015414; RNA-2: NC_015415CLRV-E395
Chicory yellow mottle viruschicory yellow mottle virusNo entry in GenbankChYMV
Cocoa necrosis viruscocoa necrosis virusATTC PV283EU741694Partial genomeCoNV-ATTC PV283
Crimson clover latent viruscrimson clover latent virusNo entry in GenbankCCLV
Cycas necrotic stunt virusCycas necrotic stunt virusIwanamiRNA-1: AB073147; RNA-2: AB073148RNA-1: NC_003791; RNA-2: NC_003792CNSV-Iwanami
Grapevine Anatolian ringspot virusgrapevine Anatolian ringspot virusA34 RNA-1: HE774604; RNA-2: AY291207RNA-1: NC_018383; RNA-2: NC_018384GARSV-A34
Grapevine Bulgarian latent virusgrapevine Bulgarian latent virusSerb1 RNA-1: FN691934; RNA-2: FN691935RNA-1: NC_015492; RNA-2: NC_015493GBLV-Serb1
Grapevine chrome mosaic virusgrapevine chrome mosaic virusBraultRNA-1: X15346; RNA-2: X15163RNA-1: NC_003622; RNA-2: NC_003621GCMV-Brault
Grapevine deformation virusgrapevine deformation virusN66 RNA-1: HE613269; RNA-2: AY291208RNA-1: NC_017939; RNA-2: NC_017938GDefV-N66
Grapevine fanleaf virusgrapevine fanleaf virusF13RNA-1: D00915; RNA-2: X16907RNA-1: NC_003615; RNA-2: NC_003623GFLV-F13
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-Tottori RNA-1: AB518485; RNA-2: AB518486Complete genomeMMMoV-Japan-Tottori
Mulberry mosaic leaf roll associated virusmulberry mosaic leaf roll associated viruszjRNA-1: KC904083; RNA-2: KC904084Complete genomeMMLRaV-zj
Mulberry ringspot virusmulberry ringspot virusNo entry in GenbankMRSV
Myrobalan latent ringspot virusmyrobalan latent ringspot virusNo entry in GenbankMLRSV
Olive latent ringspot virusolive latent ringspot virusItalyAJ277435Partial genomeOLRSV-Italy
Peach rosette mosaic viruspeach rosette mosaic virusPRMV2-1RNA-1: KJ572573; RNA-2: KJ572574Partial genomePRMV-2-1
Potato black ringspot viruspotato black ringspot virusPRI-Ec RNA-1: KC832887; RNA-2: KC832892RNA-1: NC_022798; RNA-2: NC_022799Complete genomePBRSV-PRI-Ec
Potato virus Upotato virus UNo entry in GenbankPVU
Raspberry ringspot virusraspberry ringspot viruscherryRNA-1: AY303787; RNA-2: AY303788RNA-1: NC_005266; RNA-2: NC_005267Complete genomeRpRSV-cherry
Tobacco ringspot virustobacco ringspot virusSK RNA-1: U50869; RNA-2: AY363727RNA-1: NC_005097; RNA-2: NC_005096Complete genomeTRSV-SK
Tomato black ring virustomato black ring virusMJRNA-1: AY157993; RNA-2: AY157994RNA-1: NC_004439; RNA-2: NC_004440Complete genomeTBRV-MJ
Tomato ringspot virustomato ringspot virusRaspberryRNA-1: L19655; RNA-2: D12477RNA-1: NC_003840; RNA-2: NC_003839Complete genomeToRSV-Rasberry

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.

Related, Unclassified Viruses

Virus name

Accession number

Virus abbreviation

potato virus B

RNA-1: KX656670; RNA-2: KX656671

PVB

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.

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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  • When: Mar 22, 2017 5:22 PM
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