Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato

Abstract

Summary. A new virus was isolated from tomato plants from the Murcia region in Spain which showed symptoms of ‘torrado disease’ very distinct necrotic, almost burn-like symptoms on leaves of infected plants. The virus particles are isometric with a diameter of approximately 28 nm. The viral genome consists of two (+)ssRNA molecules of 7793 (RNA1) and 5389 nts (RNA2). RNA1 contains one open reading frame (ORF) encoding a predicted polyprotein of 241 kDa that shows conserved regions with motifs typical for a protease-cofactor, a helicase, a protease and an RNA-dependent RNA polymerase. RNA2 contains two, partially overlapping ORFs potentially encoding proteins of 20 and 134 kDa. These viral RNAs are encapsidated by three proteins with estimated sizes of 35, 26 and 23 kDa. Direct protein sequencing mapped these coat proteins to ORF2 on RNA2. Phylogenetic analyses of nucleotide and derived amino acid sequences showed that the virus is related to but distinct from viruses belonging to the genera Sequivirus , Sadwavirus and Cheravirus . This new virus, for which the name tomato torrado virus is proposed, most likely represents a member of a new plant virus genus.

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

“…For example, the presence of two domains upstream of the helicase domain on the RNA1-encoded polyprotein has been suggested to be a common feature of nepoviruses that distinguishes them from comoviruses or fabaviruses [47]. Second, the presence of additional open reading frames has been reported for members of the proposed genus Torradovirus [44] (see below) and for waikaviruses [11,38], although additional studies will be required to confirm that these predicted ORFs are functional. Third, in the case of a waikavirus and a nepovirus, possible subgenomic RNAs that correspond to the long 3 0 untranslated region have been detected in infected cells, although it is not clear whether these RNAs encode a protein and what their biological function may be [3,35].…”

“…Tomato torrado virus shares many characteristics with members of the proposed family Secoviridae, including similar virion structure and genome organization, with the typical Hel-Pro-Pol domains at the C-terminus of the RNA1-encoded polyprotein [44]. The RNA2-encoded polyprotein contains the domains for three CPs and a putative movement protein [44].…”

“…The RNA2-encoded polyprotein contains the domains for three CPs and a putative movement protein [44]. Phylogenetic studies using the Pro-Pol region reveal that ToTV branches with members of the proposed family Secoviridae when it is compared to other picornavirales [23].…”

“…Phylogenetic studies using the Pro-Pol region reveal that ToTV branches with members of the proposed family Secoviridae when it is compared to other picornavirales [23]. A putative movement protein was identified in the genome of ToTV (the proposed type species for the new genus Torradovirus), but it has no homology with the movement proteins of members of the family Comoviridae, except for a very small motif (LxxPxL motif) [44]. It is not known whether ToTV or related viruses induce tubular structures to enable their movement from cell to cell.…”

“…For example, strawberry latent ringspot virus (SLRSV), a founder member of the nepovirus ''group'' is currently considered a tentative sadwavirus because it encodes two CP subunits, but it clusters with cheraviruses in phylogenetic analysis using the amino acid sequence of replication proteins and has other characteristics typical of cheraviruses [22]. Recently, the elucidation of the complete genomic sequence of tomato torrado virus (ToTV) and tomato marchitez virus (ToMarV), two plant ''picorna-like viruses'' of a new type, also suggests that they do not belong to any of the existing genera and that a new genus should be created within the order Picornavirales [44,45]. The ''plant picornavirales'' ICTV study group reevaluated the taxonomy of this group of viruses and proposed to create a new family that would encompass all plant viruses that currently belong to the order Picornavirales (these viruses will be referred to as plant picornavirales in the remainder of this paper).…”