Genetic analysis of large-sized RNA 2 species of a TCM-like tobacco rattle virus source from spinach

Summary

RNA 2 of a tobacco rattle virus isolate from spinach (TRV SP) resembles that of a recently described isolate from onion (TRV ON), but its ORF 3 is much larger. Naturally infected spinach apparently contains a second TRV SP RNA 2 species with a partially deleted ORF 3 and an RNA 1-like 3′-end which consists of c. 1500 nts and thus is much longer than in any other tobravirus RNA 2 sequenced so far. RNAs 2 of TRV SP and ON are closely related to that of TRV TCM from tulip, but besides the additional ORF 3 they have longer 5′-UTRs with two GCAUA motifs and different coat protein C-termini. The high percentage of amino acid sequence identity in the coat proteins of the TCM-like tobraviruses suggests that they may be considered as strains of a distinct virus species. Possible pitfalls in the use of serology in tobravirus classification are discussed.