Characterization of the partial RNA1 and RNA2 3′ untranslated region of Tomato ringspot virus isolates from North America

Abstract

The 3′ untranslated regions (UTRs) of RNA1 and RNA2 of Tomato ringspot virus (ToRSV) are 1.3 kb in size and virtually identical. In this study, sequences containing most of the 3′ UTRs (1168–1265 bp) were determined from 18 ToRSV isolates collected from fruit trees, small fruits and grapevines in North America. Pairwise nucleotide sequence comparisons with sequences of two isolates available in GenBank showed identities ranging from 95.1 to 100% for the majority of ToRSV isolates. Most genetic variation occurs as point mutations and single insertions and/or deletions. Phylogenetic analysis showed that 17 of the 20 isolates grouped together into a major cluster and three isolates grouped into two minor clusters, with genetic divergence rates among the three clusters of 11.8% to 23.8%. No correlation was found between the 3′ UTR sequences and symptom expression on Nicotiana benthamiana, host plant or geographic origin of ToRSV isolates. RT-PCR using primers designed within the highly conserved 3′ UTR regions detected all 18 ToRSV isolates as well as two isolates from a vineyard. This assay can serve as a practical methodology for the sensitive detection of varied ToRSV isolates as it is more sensitive than a RT-PCR assay based on previously reported U1/D1 primers.