A multiple alignment of the capsid protein sequences of nepoviruses and comoviruses suggests a common structure

Population genetics of cycas necrotic stunt virus and the development of multiplex RT-PCR diagnostics

Cycas necrotic stunt virus (CNSV) has an extensive host range and is detected in an accelerated pace around the globe in several agricultural crops. One of the plant species affected is peony (Paeonia lactiflora Pall.). The virus is asymptomatic in most peony cultivars, but there have been reports of symptoms in others. It is thus important to study CNSV and its population structure to gain insights into its evolution and epidemiology. The outputs of this study, in addition to the in-depth analysis of the virus population structure, include the development of a multiplex RT-PCR detection protocol that can amplify all published CNSV isolate sequences; allowing for accurate, reliable detection of the virus and safeguarding its susceptible, clonally-propagated hosts.

Characterization of a New Nepovirus Infecting Grapevine

In 2012, dormant canes of a proprietary wine grape (Vitis vinifera L.) accession were included in the collection of the University of California-Davis Foundation Plant Services. No virus-like symptoms were elicited when bud chips from propagated own-rooted canes of the accession were graft-inoculated onto a panel of biological indicators. However, chlorotic ringspot symptoms were observed on sap-inoculated Chenopodium amaranticolor Coste & A. Rein and C. quinoa Willd. plants, indicating the presence of a mechanically transmissible virus. Transmission electron microscopy of virus preparations from symptomatic C. quinoa revealed spherical, nonenveloped virions about 27 nm in diameter. Nepovirus-like haplotypes of sequence contigs were detected in both the source grape accession and symptomatic C. quinoa plants via high-throughput sequencing. A novel bipartite nepovirus-like genome was assembled from these contigs, and the termini of each RNA segment were verified by rapid amplification of complementary DNA ends assays. The RNA1 (7,186-nt) of the virus encodes a large polyprotein 1 of 231.1 kDa, and the RNA2 (4,460-nt) encodes a large polyprotein 2 of 148.9 kDa. Each of the polyadenylated RNA segments is flanked by 5'- (RNA1 = 156-nt; RNA2 = 170-nt) and 3'- (RNA1 = 834-nt; RNA2 = 261-nt) untranslated region sequences with >90% identities. Maximum likelihood phylogenetic analyses of the conserved Pro-Pol amino acid sequences revealed the clustering of the new virus within the genus Nepovirus of the family Secoviridae. Considering its biological and molecular characteristics, and based on current taxonomic criteria, we propose that the novel virus, named grapevine nepovirus A, be assigned to the genus Nepovirus.

Caraway yellows virus, a novel nepovirus from Carum carvi

A novel nepovirus was identified and characterised from caraway, and tentatively named caraway yellows virus (CawYV). Tubular structures with isomeric virus particles typical for nepoviruses were observed in infected tissues by electron microscopy. The whole genome of CawYV was identified by high throughput sequencing (HTS). It consists of two segments with 8026 nt for RNA1 and 6405 nt for RNA2, excluding the poly(A) tails. CawYV-RNA1 shared closest nt identity to peach rosette mosaic virus (PRMV) with 63%, while RNA2 shared 41.5% with blueberry latent spherical virus (BLSV). The amino acid sequences of the CawYV protease-polymerase (Pro-Pol) and capsid protein (CP) regions share the highest identities with those of the subgroup C nepoviruses. The Pro-Pol region shared highest aa identity with PRMV (80.1%), while the CP region shared 39.6% to soybean latent spherical virus. Phylogenetic analysis of the CawYV-Pro-Pol and -CP aa sequences provided additional evidence of their association with nepoviruses subgroup C. Based on particle morphology, genomic organization and phylogenetic analyses, we propose CawYV as a novel species within the genus Nepovirus subgroup C.

A new nepovirus identified in mulberry (Morus alba L.) in China

An isometric virus was identified in mulberry leaves showing symptoms of mulberry mosaic leaf roll (MMLR) disease. Its genome consists of two (+)ssRNAs. RNA1 and RNA2 have 7183 and 3742 nucleotides, excluding the 3'-terminal poly(A) tail. Based on phylogenetic analysis of the RNA1-encoded polyprotein and CP amino acid sequences, the properties of the the 3'-UTR of RNA1 and RNA2, and <75 % identity in the CP amino acid sequence, this virus is proposed to be a new member of the genus Nepovirus, subgroup A. Since a causal relationship between this virus and MMLR has not been established, it is tentatively referred to as MMLR-associated virus.

Characterization of a putative novel nepovirus from Aeonium sp

A virus was isolated from potted plants of an unidentified species of Aeonium, a succulent ornamental very common in Southern Italy, showing chlorotic spots and rings on both leaf surfaces. It was successfully transmitted by sap inoculation to a limited range of hosts, including Nicotiana benthamiana which was used for ultrastructural observations and virus purification. Virus particles are isometric, ca. 30nm in diameter, have a single type of coat protein (CP) subunits 54kDa in size, that encapsidate single-stranded positive-sense RNA species of 7549 (RNA1) and 4010 (RNA2) nucleotides. A third RNA molecule 3472 nts in size entirely derived from RNA2 was also found. The structural organization of both genomic RNAs and the cytopathological features were comparable to those of nepoviruses. In addition, amino acid sequence comparisons of CP and the Pro-Pol region (a sequence containing parts of the proteinase and polymerase) with those of other nepoviruses showed that the Aeonium virus belongs to the subgroup A of the genus Nepovirus and is phylogenetically close to, but serologically distinct from tobacco ringspot virus (TRSV). Based on the species demarcation criteria for the family Secoviridae, the virus under study appears to be a novel member of the genus Nepovirus for which the name of Aeonium ringspot virus (AeRSV) is proposed.

Identification and characterization of blueberry latent spherical virus, a new member of subgroup C in the genus Nepovirus

A new member of the genus Nepovirus was isolated from blueberry in Japan. The virus was associated with latent infection of blueberry trees and provisionally named blueberry latent spherical virus (BLSV). BLSV was found to have isometric particles approximately 30 nm in diameter, which were composed of a single coat protein (CP) of 55 kDa. The viral genome consisted of two positive-sense single-stranded RNA species (RNA1 and RNA2), which were 7,960 and 6,344 nucleotides (nt) long, respectively. The organization of RNA1 and RNA2 was similar to that of nepoviruses. The 3' non-coding regions of RNA1 and RNA2 were 1,379 nt and 1,392 nt long, respectively. The amino acid sequences of the BLSV polymerase and CP shared the highest amino acid sequence similarities with those of the subgroup C nepoviruses (57% and 43%, respectively). Additionally, the BLSV genome, in contrast to other nepovirus genomes, was predicted to encode a serine protease.

A novel member of the genus Nepovirus isolated from Cucumis melo in Japan

An unusual virus was isolated from a Japanese Cucumis melo cv. Prince melon plant showing mild mottling of the leaves. The virus had a broad experimental host range including at least 19 plant species in five families, with most infected plants showing no symptoms on inoculated and uninoculated systemically infected leaves. The virus particles were spherical, approximately 28 nm in diameter, and the coat protein (CP) had an apparent molecular mass of about 55 kDa. The virus possessed a bi-partite genome with two RNA species, of approximately 8,000 and 4,000 nucleotides. Both genome components for the new virus were sequenced. Amino acid sequence identities in CP between the new virus and previously characterized nepoviruses were found to be low (less than 27%); however, in phylogenetic reconstructions the closest relationship was revealed between the new virus and subgroup A nepoviruses. These results suggest that the new virus represents a novel member of the genus Nepovirus. A new name, Melon mild mottle virus, has been proposed for this new virus.

Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)

The genus Nepovirus (family Comoviridae) was known both for a good level of homogeneity and for the presence of atypical members. In particular, the atypical members of the genus differed by the number of capsid protein (CP) subunits. While typical nepoviruses have a single CP subunit with three structural domains, atypical nepoviruses have either three small CP subunits, probably corresponding to the three individual domains, or a large and a small subunit, probably containing two and one structural domains, respectively. These differences are corroborated by hierarchical clustering based on sequences derived from both genomic RNAs. Therefore, these atypical viruses are now classified in two distinct genera, Cheravirus (three CP subunits; type species Cherry rasp leaf virus) and Sadwavirus (two CP subunits; type species Satsuma dwarf virus).

Complete Nucleotide Sequence of the RNA-2 of Grapevine Deformation and Grapevine Anatolian Ringspot Viruses

The nucleotide sequence of RNA-2 of Grapevine Anatolian ringspot virus (GARSV) and Grapevine deformation virus (GDefV), two recently described nepoviruses, has been determined. These RNAs are 3753 nt (GDefV) and 4607 nt (GARSV) in size and contain a single open reading frame encoding a polyprotein of 122 kDa (GDefV) and 150 kDa (GARSV). Full-length nucleotide sequence comparison disclosed 71-73% homology between GDefV RNA-2 and that of Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV), and 62-64% homology between GARSV RNA-2 and that of Grapevine chrome mosaic virus (GCMV) and Tomato black ring virus (TBRV). As previously observed in other nepoviruses, the 5' non-coding regions of both RNAs are capable of forming stem-loop structures. Phylogenetic analysis of the three proteins encoded by RNA-2 (i.e. protein 2A, movement protein and coat protein) confirmed that GDefV and GARSV are distinct viruses which can be assigned as definitive species in subgroup A and subgroup B of the genus Nepovirus, respectively.

Black currant reversion virus, a mite-transmitted nepovirus

SUMMARY Taxonomy: Black currant reversion virus (BRV) is the first identified mite-transmitted member of the genus Nepovirus (family Comoviridae). A few systematic studies have been performed to compare virus isolates from different geographical locations. Physical properties: Purified preparations contain two closely sedimenting centrifugal components (B and M for RNA1 and RNA2, respectively) at varying ratios, and occasionally a T component (for satellite RNA). The BRV capsids have a diameter of 27 nm and they are putatively composed of 60 copies of a single species of capsid (coat) protein assembled in an icosahedral lattice. Diluted plant sap loses its infectivity within 1 day at 20 degrees C and in 4-8 days at 4 degrees C. Hosts: The natural host range of BRV is limited; it infects black currant (Ribes nigrum L.) and some related Ribes species. The transmission of the virus is by the eriophyid gall mite of black currant (Cecidophyopsis ribis). A number of herbaceous plants can be infected experimentally. BRV is the agent of black currant reversion disease (BRD), which is economically the most significant virus disease in Ribes species. BRV and BRD occur widely in locations where black currant is cultivated commercially.

Satsuma dwarf and related viruses belong to a new lineage of plant picorna-like viruses

Satsuma dwarf virus (SDV) and two closely related viruses, Citrus mosaic (CiMV), and Naval orange infectious mottling (NIMV), seriously affect citrus varieties grown in Japan and East Asia. All three viruses have icosahedral particles built of two proteins encapsidating two single-stranded genomic RNAs. The natural mode of transmission of these SDV-like viruses is unknown, and they were previously placed among tentative members of the family Comoviridae. Recently, a complete genome of SDV was sequenced, and its replication-related proteins were found only distantly related to those of viruses from the family Comoviridae (Iwanami T., Kondo Y., and Karasev A.V. J Gen Virol 80, 793-797, 1999). Here we present a partial genome sequence for another SDV-like virus, NIMV, and a thorough phylogenetic analysis of the gene products encoded by SDV, CiMV, and NIMV to assess their relationships with picorna-like viruses infecting plants, insects, and vertebrates. The RdRp's of SDV-like viruses form a new lineage, separate from members of Como- and Sequiviridae families. Phylogenetic analysis suggests that SDV-like viruses may represent a new family of plant picorna-like viruses. Sequence analysis of the capsid proteins (CPs) encoded by the SDV-like viruses revealed a region of similarity to CPs of animal calici- and picornaviruses that encompasses the structural core of the eight-strand beta-barrel characteristic of picornaviral CPs. These data suggest that SDV and related bipartite viruses evolved separately from the viruses in the family Comoviridae and that the split of an ancestor, monopartite picorna-like virus genome might have occurred more than once.

Differences between the coat protein amino acid sequences of English and Scottish serotypes of Raspberry ringspot virus exposed on the surface of virus particles

The region of the RNA 2 coding for the putative helper/movement protein and the coat protein (CP) of each of six isolates of Raspberry ringspot virus was sequenced and these sequences were compared with the published sequence of the Scottish type isolate. Minimal differences were detected among the putative translations of the helper/movement proteins, however, multiple alignment and phylogenetic analysis of the putative CPs separated the English and Scottish serotypes into two distinct clades. Superimposing the amino acid sequences of the CPs of these two serotypes on the 3D model for the CP of a comovirus/nepovirus, showed that eight of the differences identified between the two serotypes occurred on the surface of the protein. Inspection of the recently reported structure of the capsid protein of Tobacco ringspot virus, the type member of the genus Nepovirus, indicated identical locations for these differences. The change of H (Scottish isolates) to R (English isolates) at position 219 in the amino acid sequences of the viruses occurred on an exposed, erect surface loop. The potential role of this change, and other unique differences between the amino acid sequences of the two serotypes, in the specificity of nematode transmission of the virus is discussed.

The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily

BACKGROUND

Tobacco ringspot virus (TRSV) is a member of the nepovirus genus of icosahedral RNA plant viruses that cause disease in fruit crops. Nepoviruses, comoviruses and picornaviruses are classified in the picornavirus superfamily. Crystal structures of comoviruses and picornaviruses and the molecular mass of the TRSV subunit (sufficient to accommodate three beta-barrel domains) suggested that nepoviruses may represent a link in the evolution of the picornavirus capsids from a T = 3 icosahedral virus. This evolutionary process is thought to involve triplication of the capsid protein gene, to encode a three-domain polyprotein, followed by development of cleavage sites in the interdomain linking regions. Structural studies on TRSV were initiated to determine if the TRSV subunit corresponds to the proposed uncleaved three-domain polyprotein.

RESULTS

The 3.5 A resolution structure of TRSV shows that the capsid protein consists of three beta-barrel domains covalently linked by extended polypeptides. The order of connectivity of the domains in TRSV confirms the proposed connectivity for the precleaved comovirus and picornavirus capsid polyprotein. Structural differences between equivalent domains in TRSV and comoviruses are confined to the external surface loops, interdomain connecting polypeptides and N termini. The three different domains within TRSV and comoviruses are more closely related at the structural level than the three individual domains within picornaviruses.

CONCLUSIONS

The structural results confirm the notion of divergent evolution of the capsid polyproteins of nepoviruses, comoviruses and picornaviruses from a common ancestor. A number of residues were found to be conserved among various nepoviruses, some of which stabilize the quaternary structure of the three domains in the TRSV capsid protein subunit. Two conserved regions were identified on the external surface of TRSV, however, mutational studies will be needed to understand their functional significance. Nepoviruses transmitted by the same nematode species do not share regions with similar amino acid composition on the viral surface.

Characterization of the coat protein gene of mite-transmitted blackcurrant reversion associated nepovirus

The nucleotide sequence of the 3' terminal 3105 nucleotides (nt) of RNA2 of blackcurrant reversion associated virus (BRAV), the first mite-transmitted member of the nepovirus group, has been determined. The sequence contains an open reading frame of 1744 nt in the virus-sense strand, a 3' untranslated region of 1360 nt and a 3' poly(A) tail. Analysis of the amino-terminal residues of purified coat protein (CP) suggests that the CP gene is located between nts 1361 and 2959 (from the 3' terminus) in the RNA2, and that Asp/Ser is the proteolytic cleavage site of CP in the RNA2 encoded polyprotein. The predicted translation product from the CP gene is a polypeptide of 533 amino acids with a calculated Mr of 57 561. The amino acid sequence of BRAV CP showed highest similarity to blueberry leaf mottle virus (BLMV), and tomato ringspot virus (ToRSV), two members of the proposed sub-group three of nepoviruses possessing large RNA2 components. Nucleic and amino acid sequence comparisons between BRAV CP and the CPs of other nepoviruses indicate that specific conserved nepovirus CP domains occur in the BRAV CP thus confirming that BRAV is a member of the subgroup three of nepoviruses. reserved.