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Similar to cheraviruses, torradoviruses have a bipartite genome with two open reading frames in RNA-2 and three capsid proteins.
See discussion under family description.
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 capsid protein (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 are transmitted by whiteflies in a semi-persistent manner (Lecoq et al., 2016). Carrot torrado virus 1 is 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.
tomato chocolàte virus
RNA-1: FJ560489; RNA-2: FJ560490
tomato chocolate spot virus
RNA-1: GQ305131; RNA-2: GQ305132
tomato necrotic dwarf virus
RNA-1: KC999058; RNA-2: KC999059
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.
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