Genus: Torradovirus


Genus: Torradovirus

Distinguishing features

Similar to cheraviruses, torradoviruses have a bipartite genome and three capsid proteins. The genome  RNAs are polyadenylated. Presence of a VPg at the 5ʹ end of the RNAs has not been tested experimentally. The genomic organization is similar to that of other members of the family with a bipartite genome. The replication block is found in the polyprotein encoded by RNA-1 while the structural proteins are present in the C-terminal region of the polyprotein encoded by RNA-2. A putative movement protein upstream of the CP domains shares little sequence similarity with that of other bipartite members of the family with the exception of the small LPL motif (van der Vlugt et al., 2015). A distinguishing feature of the torradovirus genome is the presence of a second open reading frame upstream and partially overlapping with the large ORF2 in RNA-2 (Figure 3.Secoviridae). This reading frame encodes a putative protein of unknown function, with no apparent homology to known proteins, which exhibits a large degree of sequence diversity (61-74% identity) among tomato-infecting torradoviruses and non-tomato infecting torradoviruses but a significantly higher level of diversity (21%-31% identity) between these two groups. 3ʹ-UTR sequences differ substantially between members of species but for most torradoviruses the 3ʹ-UTRs of RNA-1 and RNA-2 are nearly identical (>99%) with only a relatively short 5ʹ-terminal variable region showing clear differences in length as well as in sequence. 3ʹ-UTRs of a given torradovirus also show extensive sequence duplications while significant stretches of homologous conserved regions in the 3ʹ-UTRs occur between members of distinct virus species. RNA secondary structure analyses has identified several conserved stem loop structures in both 5ʹ- UTRs and 3ʹ-UTRs of RNA-1 and RNA-2 (van der Vlugt et al., 2015).

Tomato torrado virus, tomato marchitez virus and squash chlorotic leaf spot virus were demonstrated to be transmitted by whiteflies in a semi-persistent manner (Lecoq et al., 2016). Carrot torrado virus 1 was demonstrated to be transmitted by at least three different species of aphids (Rozado-Aguirre et al., 2016). Vector and specificity remains to be determined for the other torradoviruses.

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 abbreviationIsolate abbreviation
Carrot torradovirus 1carrot torradovirus 1CaTV1/H6RNA-1: KF533719; RNA-2: KF533720RNA-1: NC_025479; RNA-2: NC_025480Complete genomeCaTV1
Lettuce necrotic leaf curl viruslettuce necrotic leaf curl virus5317015RNA-1: KC855266; RNA-2: KC855267Complete genomeLNLCV
Motherwort yellow mottle virusmotherwort yellow mottle virusAD01RNA-1: KM229700; RNA-2: KM229701Complete genomeMYMoV
Squash chlorotic leaf spot virussquash chlorotic leaf spot virusSu12/10RNA-1: KU052530; RNA-2: KU052531Complete genomeSCLSV
Tomato marchitez virustomato marchitez virusPRI/0601RNA-1: EF681764; RNA-2: EF681765RNA-1: NC_010987; RNA-2: NC_010988Complete genomeToMarV
Tomato torrado virustomato torrado virusPRI/0301RNA-1: DQ388879; RNA-2: DQ388880RNA-1: NC_009013; RNA-2: NC_009032Complete genomeToTV

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

tomato chocolàte virus

RNA-1: FJ560489; RNA-2: FJ560490

ToChV

tomato chocolate spot virus

RNA-1: GQ305131; RNA-2: GQ305132

ToChSV

tomato necrotic dwarf virus

RNA-1: KC999058; RNA-2: KC999059

ToTV 

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.

Tomato chocolàte virus (ToChV), tomato chocolate spot virus (ToChSV) and tomato necrotic dwarf virus (ToNDV) are related to tomato marchitez virus (ToMarV) and to a lesser degree to tomato torrado virus (ToTV). All viruses infect tomato and cause similar symptoms (Batuman et al., 2010, Larsen et al., 1984, Verbeek et al., 2010). Comparison of the aa sequence of the Pro-Pol and combined CP regions would suggest that ToChV, ToChSV and ToNDV are distant strains of ToMarV (82-92% aa sequence identity for the Pro-Pol region and 79-89% aa sequence identity in the combined CP region among the three viruses). However, other regions of the genome (RNA-2-encoded ORF1 and the 3ʹ UTR) show significant sequence variation. In addition the length of the 3ʹ UTR varies significantly among these viruses. It is not known whether reassortment between the RNAs of ToMarV, ToChV, ToChSV and/or ToNDV is possible. Therefore, the taxonomic position of ToChV, ToChSV, ToNDV as either three distinct species in the genus Torradovirus, three strains of a single new species in the genus Torradovirus or three distant strains of the species Tomato marchitez virus remains unclear.