Genetic variability within the Polish tomato torrado virus Kra isolate caused by deletions in the 3′-untranslated region of genomic RNA1

• Kra isolate of Tomato torrado virus consists of the pool of genomic RNAs differing in lengths.
• The genetic variability within the ToTV isolates results from large deletions in the 3′UTR region of RNA1.
• The deletions in 3′UTR of RNA1 affect the predicted in silico secondary structure of viral RNA.
• The extensive variability in the length of the 3′UTR seems to be very atypical phenomenon among plant viruses.

Tomato torrado virus (ToTV) is in the genus Torradovirus in the family Secoviridae. ToTV contains a single-stranded, positive-sense, bipartite RNA genome encapsidated in icosahedral particles. It is a serious tomato pathogen causing significant crop reductions. Its occurrence has been reported from many countries worldwide. However, the state of knowledge of ToTV epidemiology, sequences and phylogeny is still rather poor. In this study we found that the Polish ToTV isolates are characterized by significant genetic variability of the 3′-untranslated region (UTR) of RNA1. The high resolution melting real-time PCR approach showed the presence of genetic variants within Polish ToTV isolates purified from Nicotiana benthamiana. Further sequencing of Kra ToTV revealed five genetic variants of RNA1 within the isolate differing in the 3′-untranslated region length resulting from deletions ranging from 6 to 163 nucleotides. In light of the published studies, the genetic variability of ToTV associated with large deletions within an isolate may not necessarily be rare and may influence the virus evolution and adaptation.