The length of the 3′ UTR of the tomato torrado virus (ToTV) RNA1 affects virus accumulation in Solanum lycopersicum during mechanical passages from plant to plant

Tomato torrado virus (ToTV), a member of the Torradovirus genus, primarily infects tomatoes. Previous analyses revealed high heterogeneity in the 3′ untranslated region (3′ UTR) of RNA1 of isolate ToTV-Kra. In addition to the full-length 3′ UTR RNA1 (a wild-type, wt), four truncated versions (var2, var3, var4 and var5) were identified. Here, we investigated the biological importance of this phenomenon by assessing whether such defective genomes are infectious individually, and how the length of the 3′ UTR influences disease symptoms, virus transmission and viral RNA accumulation. Using the ToTV_pJL-Kra infectious clone, we introduced deletions corresponding to the known RNA1 defective variants and examined their impact on ToTV virulence and sap transmission ability. Viral RNA accumulation was assessed in agroinfiltrated tomatoes, as well as during serial passages. We found that all defective genomes were infectious and the length of the 3′ UTR of RNA1 influenced viral RNA accumulation. Tomatoes agroinfiltrated with var2, var3 or var5 showed the highest copy numbers of genomic RNAs. However, during serial passages, ToTV_pJL-Kra-var1 and -var2 (six nucleotides shorter) showed limited sap transmission ability compared to the other variants, which persisted and replicated well in tomatoes. Plants treated with ToTV_pJL-Kra-var3, -var4 and a mixture of var1–var5 showed the highest viral RNA accumulation, which was not associated with increased symptom severity in comparison to the other variants. Additionally, we identified a further sequence insertion in the 3′ UTR of var3 RNA1. This insertion could have occurred spontaneously or as a result of virus adaptation to the mode of transmission.