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N. Yoshikawa - One of the best experts on this subject based on the ideXlab platform.
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spherical virus: a new virus classified into the family
2013Co-Authors: N. Yoshikawa, T Takahashi, T Ito, K Yoshida, H KoganezawaAbstract:A virus with isometric virus particles (ca. 25 nm) was isolated from an apple tree and named Apple latent spherical virus (ALSV). Virus particles purified from infected Chenopodium quinoa formed two bands with densities of 1�41 and 1�43 g/cm 3 in CsCl equilibrium density-gradient centrifugation, indicating that the virus is composed of two components. The virus had two ssRNA species (RNA1 and RNA2) and three capsid proteins (Vp25, Vp24 and Vp20). The complete nucleotide sequences of RNA1 and RNA2 were determined to be 6815 nt and 3384 nt excluding the 3� poly(A) tail, respectively. RNA1 contains two partially overlapping ORFs encoding polypeptides of molecular mass 23 kDa (‘23K’; ORF1) and 235 kDa (‘235K’; ORF2); RNA2 has a single ORF encoding a polypeptide of 108 kDa (‘108K’). The 235K protein has, in order, consensus motifs of the protease cofactor, the NTP-binding helicase, the cysteine protease and the RNA polymerase, in good agreement with the gene arrangement of viruses in the Comoviridae. The 108K protein contains an LPL movement protein (MP) motif near the N terminus. Direct sequencing of the N-terminal amino acids of the three capsid proteins showed that Vp25, Vp20 and Vp24 are located in this order in the C-terminal region of the 108K protein. The cleavage sites of the 108K polyprotein were Q/G (MP/Vp25 and Vp25/Vp20) and E/G (Vp20/Vp24). Phylogenetic analysis of the ALSV RNA polymerase domain showed that ALSV falls into a cluster different from the nepo-, como- and fabavirus lineages
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Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)
Archives of Virology, 2007Co-Authors: O. Gall, Alexander Karasev, Joan Wellink, K Lehto, M. Ikegami, T. Iwanami, T. Jones, T. Wetzel, N. YoshikawaAbstract: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 ).
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Nucleotide sequence and genome organization of apple latent spherical virus: a new virus classified into the family Comoviridae.
The Journal of general virology, 2000Co-Authors: N. Yoshikawa, T Takahashi, T Ito, K Yoshida, H KoganezawaAbstract:A virus with isometric virus particles (ca. 25 nm) was isolated from an apple tree and named Apple latent spherical virus (ALSV). Virus particles purified from infected Chenopodium quinoa formed two bands with densities of 1.41 and 1.43 g/cm(3) in CsCl equilibrium density-gradient centrifugation, indicating that the virus is composed of two components. The virus had two ssRNA species (RNA1 and RNA2) and three capsid proteins (Vp25, Vp24 and Vp20). The complete nucleotide sequences of RNA1 and RNA2 were determined to be 6815 nt and 3384 nt excluding the 3' poly(A) tail, respectively. RNA1 contains two partially overlapping ORFs encoding polypeptides of molecular mass 23 kDa ('23K'; ORF1) and 235 kDa ('235K'; ORF2); RNA2 has a single ORF encoding a polypeptide of 108 kDa ('108K'). The 235K protein has, in order, consensus motifs of the protease cofactor, the NTP-binding helicase, the cysteine protease and the RNA polymerase, in good agreement with the gene arrangement of viruses in the COMOVIRIDAE: The 108K protein contains an LPL movement protein (MP) motif near the N terminus. Direct sequencing of the N-terminal amino acids of the three capsid proteins showed that Vp25, Vp20 and Vp24 are located in this order in the C-terminal region of the 108K protein. The cleavage sites of the 108K polyprotein were Q/G (MP/Vp25 and Vp25/Vp20) and E/G (Vp20/Vp24). Phylogenetic analysis of the ALSV RNA polymerase domain showed that ALSV falls into a cluster different from the nepo-, como- and fabavirus lineages.
Helene Sanfacon - One of the best experts on this subject based on the ideXlab platform.
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secoviridae a family of plant picorna like viruses with monopartite or bipartite genomes
eLS, 2015Co-Authors: Helene SanfaconAbstract:Members of the family Secoviridae, referred to as secovirids, are plant viruses that share features with animal and human viruses of the family Picornaviridae and other insect or marine viruses of the order Picornavirales. These common features include a conserved structure of the icosahedral virus particles, the expression of viral proteins by proteolytic cleavage of large polyproteins and viral replication proteins with conserved sequence motifs, including the viral RNA-dependent RNA polymerase and protease. Secovirids also share the distinguishing feature of encoding specialised proteins that enable their movement in plant and counteract plant defence mechanisms, such as RNA silencing. The family Secoviridae includes eight genera. Members of the genera Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus and Torradovirus have a bipartite positive-strand RNA genome, whereas members of the genera Sequivirus and Waikavirus have a monopartite genome. Key Concepts Many plant viruses are related to animal and human viruses of the family Picornaviridae and to other picorna-like viruses infecting algae and arthropods. A recent update in the taxonomy of plant picorna-like viruses has led to the creation of the family Secoviridae which amalgamates the previous families Comoviridae and Sequiviridae as well as the genera Cheravirus, Sequivirus and Torradovirus. Secovirids share common characteristics including having both similar virus particle structures and genomic organizations and requiring specialised proteins to facilitate their movement within the host plant or counteract plant defence mechanism. Secovirids produce their proteins in the form of large polyproteins that are cleaved at specific sites by a viral protease. Replication of the viral RNA occurs in large protein complexes in association with intracellular membranes from the host. Plant cells infected with secovirids generally display tubular structures that are composed of the viral movement protein, contain virus-like particles and traverse the cell wall. These tubular structures are involved in the movement of the virus from cell to cell. Secovirids can be transmitted through seeds and pollen or with the help of nematode or arthropod vectors and their spread in the field is largely dependent on their mode of transmission. Some secovirids have been successfully exploited as plant vectors, allowing epitope presentation for vaccine production, expression of proteins in plants and silencing of endogenous plant genes. Keywords: picornavirales; protease; virus taxonomy; plant–virus interactions; cell-to-cell movement; virus replication
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Insertion of large amino acid repeats and point mutations contribute to a high degree of sequence diversity in the X4 protein of tomato ringspot virus (genus Nepovirus)
Archives of Virology, 2009Co-Authors: Bita Jafarpour, Helene SanfaconAbstract:Tomato ringspot virus (ToRSV) is a serious pathogen of small fruits and fruit trees in North America [14]. Several ToRSV isolates have been described that differ in natural host range and intensity of symptoms in herbaceous hosts [3, 17]. Tomato ringspot virus is a species of the genus Nepovirus [15], which has recently been reassigned to the proposed new family ‘‘Secoviridae’’ (subfamily ‘‘Comovirinae’’) within the order Picornavirales [16]. Nepoviruses have a bipartite positive-strand RNA genome. Each RNA encodes a polyprotein that is cleaved by the viral proteinase (Pro) at specific cleavage sites. RNA1 encodes replication proteins, while RNA2 codes for the coat protein (CP), movement protein (MP) and other protein(s) of less defined function. Using in vitro processing assays, three proteinase cleavage sites have been identified in the RNA2encoded polyprotein of ToRSV (a subgroup C nepovirus), allowing the definition of four protein domains (X3, X4, MP and CP) [4, 5]. In contrast, only three protein domains are present in the polyprotein of subgroup A and B nepoviruses (2a, MP and CP; see Fig. 1a). The ToRSV X3 protein shares conserved sequence motifs with the 2a protein of subgroup A and B nepoviruses [12]. The 2a protein of grapevine fanleaf virus has been shown to play a role in the replication of RNA2 [7]. The ToRSV X4 protein does not have significant sequence identity with proteins available in the database and does not have a functional equivalent in the genome of nepoviruses of subgroups A and B (Fig. 1a). The only other nepovirus of subgroup C for which the entire nucleotide sequence is available is blackcurrant reversion virus (BRV). The extent of sequence identity between ToRSV and BRV is very low in the deduced amino acid (a.a.) sequence of the X4 protein (8%) but higher in the deduced a.a. sequence of the CP (29%), VPg (viral protein linked to the genome), Pro and polymerase (Pol) (36%). In this study, we examined the extent of sequence diversity in the X4 protein among closely related ToRSV isolates. We show that there is a high degree of sequence diversity in the X4 protein, which is due in part to the insertion of multiple copies of two types of large amino acid repeats.
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secoviridae the amalgamation of the families sequiviridae and comoviridae
eLS, 2009Co-Authors: Helene SanfaconAbstract:Several plant viruses share features with animal and human viruses of the family Picornaviridae, including a conserved structure of both the virus particle and the viral genome, expressing viral proteins by proteolytic cleavage of large polyproteins and encoding replication proteins with conserved sequence motifs. Members of the family Comoviridae were originally described as the only plant picorna-like viruses. Other plant picorna-like viruses were later discovered and classified in the family Sequiviridae. Sequiviridae and Comoviridae are related to each other in phylogenetic studies and share the common property of encoding specialized proteins to enable their movement in the plant. Recently, it was proposed to regroup plant picorna-like viruses into a single family termed ‘secoviridae’. The proposed family amalgamates the families Comoviridae and Sequiviridae, and incorporates other plant picorna-like viruses currently classified in the genera Sadwavirus and Cheravirus, and the proposed genus ‘Torradovirus’. Key concepts: Many plant viruses are related to the animal and human picornaviridae and to other picorna-like viruses infecting algae and arthropods. A recent update in the taxonomy of plant picorna-like viruses has lead to the creation of the family ‘secoviridae’ which amalgamates the families Comoviridae and Sequiviridae as well as the existing genera Cheravirus, Sequivirus and the proposed genus ‘torradovirus’. Secoviridae share many common characteristics including having both similar virus particle structures and genomic organizations, and requiring a specialized protein to facilitate their movement within the host plant. Secoviridae produce their proteins in the form of large polyproteins that are cleaved at specific sites by a viral proteinase. Replication of the viral RNA occurs in large protein complexes in association with intracellular membranes from the host. Plant cells infected with secoviridae generally display tubular structures that are composed of the viral movement protein, contain virus-like particles and traverse the cell wall. These tubular structures are probably involved in the movement of the virus from cell to cell. Secoviridae can be transmitted through seeds and pollen or with the help of nematode or arthropod vectors and their spread in the field is largely dependent on their mode of transmission. Keywords: picornavirales; proteinase; virus taxonomy; plant–virus interactions; cell-to-cell movement; virus replication
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Characterization of Membrane Association Domains within the Tomato Ringspot Nepovirus X2 Protein, an Endoplasmic Reticulum-Targeted Polytopic Membrane Protein
Journal of virology, 2006Co-Authors: Guangzhi Zhang, Helene SanfaconAbstract:Replication of nepoviruses (family Comoviridae) occurs in association with endoplasmic reticulum (ER)-derived membranes. We have previously shown that the putative nucleoside triphosphate-binding protein (NTB) of Tomato ringspot nepovirus is an integral membrane protein with two ER-targeting sequences and have suggested that it anchors the viral replication complex (VRC) to the membranes. A second highly hydrophobic protein domain (X2) is located immediately upstream of the NTB domain in the RNA1-encoded polyprotein. X2 shares conserved sequence motifs with the comovirus 32-kDa protein, an ER-targeted protein implicated in VRC assembly. In this study, we examined the ability of X2 to associate with intracellular membranes. The X2 protein was fused to the green fluorescent protein and expressed in Nicotiana benthamiana by agroinfiltration. Confocal microscopy and membrane flotation experiments suggested that X2 is targeted to ER membranes. Mutagenesis studies revealed that X2 contains multiple ER-targeting domains, including two C-terminal transmembrane helices and a less-well-defined domain further upstream. To investigate the topology of the protein in the membrane, in vitro glycosylation assays were conducted using X2 derivatives that contained N-glycosylation sites introduced at the N or C termini of the protein. The results led us to propose a topological model for X2 in which the protein traverses the membrane three times, with the N terminus oriented in the lumen and the C terminus exposed to the cytoplasmic face. Taken together, our results indicate that X2 is an ER-targeted polytopic membrane protein and raises the possibility that it acts as a second membrane anchor for the VRC.
Joan Wellink - One of the best experts on this subject based on the ideXlab platform.
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Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus
Archives of Virology, 2009Co-Authors: Joan Wellink, Olivier Gall, Alexander Karasev, René Vlugt, Thierry WetzelAbstract:The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus , Fabavirus and Nepovirus ) and Sequiviridae (genera Sequivirus and Waikavirus ) and into the unassigned genera Cheravirus and Sadwavirus . These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus , Fabavirus , Nepovirus , Cheravirus , Sadwavirus , Sequivirus and Waikavirus . Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae.
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Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)
Archives of Virology, 2007Co-Authors: O. Gall, Alexander Karasev, Joan Wellink, K Lehto, M. Ikegami, T. Iwanami, T. Jones, T. Wetzel, N. YoshikawaAbstract: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 ).
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Comoviridae: plant picorna-like viruses
2000Co-Authors: Le Gall, Joan WellinkAbstract:The Comoviridae are plant viruses that share many structural and functional features with animal and human viruses of the family Picornaviridae.
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The cowpea mosaic virus RNA 1-encoded 112 kDa protein may function as a VPg precursor in
1995Co-Authors: Er A. Peters, Joan Wellink, Jean-michel T Mesnard, Ingeborg M. Kooter, Jan Verver, Ab Van KammenAbstract:Processing of the 112 kDa ( ' 112K') protein encoded by cowpea mosaic virus RNA 1 was examined in cowpea mesophyll protoplasts using a transient expression system. Cleavage of the 112K protein occurred via two alternative pathways either into VPg and l l0K (24K+ 87K) or into 26K (VPg +24K) and 87K proteins. The 26K protein can be further cleaved into VPg and 24K proteins. The results support a model in which the 112K protein functions as the precursor of VPg during initiation of replication. Cowpea mosaic virus (CPMV), the type member of the family Comoviridae, is a positive-strand RNA plant virus with a bipartite genome. Both RNA 1 and RNA 2 have a small protein, VPg (viral protein genome linked), at their 5 ' end, are polyadenylated at the 3 " end and ar
Nitin Kamath - One of the best experts on this subject based on the ideXlab platform.
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An Evolutionary Analysis of the Secoviridae Family of Viruses
2016Co-Authors: Jeremy R. Thompson, Nitin Kamath, Keith L. PerryAbstract:The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.2961023 to 2.7461023 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in
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An evolutionary analysis of the Secoviridae family of viruses.
PLOS ONE, 2014Co-Authors: Jeremy R. Thompson, Nitin Kamath, Keith L. PerryAbstract:The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.
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Maximum likelihood inferred phylogenetic trees for the six main functional domains of the Secoviridae.
2014Co-Authors: Jeremy R. Thompson, Nitin KamathAbstract:The putative movement protein or 2N terminal protein, 2N(MP); the coat protein (CP); the putative protease cofactor or 1N terminal protein, 1N(ProCo); the helicase (HEL), the protease (Pro), and the RNA-dependent RNA polymerase (RdRp). Designated viral lineages are contained within the polygons, in descending order: green, Comovirinae; blue, Nepovirus; yellow, Fabavirus; yellow/green, Comovirus; orange, Sadwavirus; red/green, Cheravirus; grey, Sequivirus, Waikavirus; red, Torradovirus. Numbers at nodes refer to bootstrap values, with any branch below 70% being collapsed. The outgroup (black oval) for all trees is the corresponding functional gene of the Potato virus Y (PVY). PVY is type member of the potyvirus genus in the Potyviridae family – a group of plant infecting picorna-like viruses that lies outside the Picornavirales order [74]. Apple latent spherical virus (ALSV), Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Beet ringspot virus (BRSV), Black raspberry necrosis virus (BRNV), Blackcurrant reversion virus (BRV), Broad bean wilt virus-1 (BBWV1), Broad bean wilt virus-2 (BBWV2), Cherry rasp leaf virus (CRLV), Cowpea mosaic virus (CPMV), Cowpea severe mosaic virus (CPSMV), Cycas necrotic stunt virus (CNSV), Grapevine chrome mosaic (GCMV), Grapevine fanleaf virus (GFLV), Maize chlorotic dwarf virus (MCDV), Parsnip yellow fleck virus (PYFV), Radish mosaic virus (RaMV), Red clover mottle virus (RCMV), Rice tungro spherical virus (RTSV), Satsuma dwarf virus (SDV), Squash mosaic virus (SqMV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tobacco ringspot virus (TRSV), Tomato marchitez virus (ToMarV) and Tomato ringspot virus (ToRSV), Tomato torrado virus (ToTV).
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Coalescent tree for the subfamily Comovirinae using coat protein sequences.
2014Co-Authors: Jeremy R. Thompson, Nitin Kamath, Keith L. PerryAbstract:Bayesian priors were set for a lognormal relaxed molecular clock at the most conservative mean species nucleotide substitution estimate of 2.74×10-3 (for ToRSV) using a constant tree prior with all species’ sequences ‘time-stamped’. Horizontal blue bars show the 95% highest posterior density (HPD) ranges for each node. The presence of the HPD bar denotes a node posterior probability greater than 0.9. Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Broad bean wilt virus-2 (BBWV-2), Blackcurrant reversion virus (BRV), Grapevine fanleaf virus (GFLV), Tomato ringspot virus (ToRSV) and Tobacco ringspot virus (TRSV). The equivalent tree generated using a strict clock is shown in the supplemental data.
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Host distribution of known related virus sequences.
2014Co-Authors: Jeremy R. Thompson, Nitin Kamath, Keith L. PerryAbstract:a) three putative models for assigning directionality of colonization based on diversity (proportional to the diameter of circle); the greater the diversity the older the population. In model three the distributions have reached an ‘equilibrium’ due to the limits of detection (ie the most divergent viruses cannot be identified), b) the distribution of the total number (in parentheses) of recognized ICTV classified viruses according to eukaryotic host. c) distribution, within the framework of the models proposed in a), of related ICTV-recognized virus species (black numbers) for the coat protein (CP, left) and the protease (Pro, right). Circles are proportional to number of species (orange – vertebrate host, blue – insect host). Arrow sizes are proportional to the ratio of the number of species in each host type (e.g. animal species:plant species or plant species:animal species). Absence of the thin black vertical line means that no significant animal homolog was identified. The rounded blue boxes contain members of the subfamily Comovirinae. Broad bean wilt virus-1 (BBWV1), Cherry rasp leaf virus (CRLV), Grapevine fanleaf virus (GFLV), Rice tungro spherical virus (RTSV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tobacco ringspot virus (TRSV), and Tomato torrado virus (ToTV).
Alexander Karasev - One of the best experts on this subject based on the ideXlab platform.
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Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus
Archives of Virology, 2009Co-Authors: Joan Wellink, Olivier Gall, Alexander Karasev, René Vlugt, Thierry WetzelAbstract:The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus , Fabavirus and Nepovirus ) and Sequiviridae (genera Sequivirus and Waikavirus ) and into the unassigned genera Cheravirus and Sadwavirus . These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus , Fabavirus , Nepovirus , Cheravirus , Sadwavirus , Sequivirus and Waikavirus . Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae.
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Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)
Archives of Virology, 2007Co-Authors: O. Gall, Alexander Karasev, Joan Wellink, K Lehto, M. Ikegami, T. Iwanami, T. Jones, T. Wetzel, N. YoshikawaAbstract: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 ).