Genetic diversity of Raspberry leaf blotch emaravirus in red raspberries from Serbia

Abstract

Raspberry leaf blotch emaravirus (RLBV) is a recently characterised virus infecting raspberries reported in several European countries. RLBV causes yellow blotching, the distortion of leaf margins, and the twisting of raspberry leaves. For a long time, similar symptoms were attributed to the feeding damage caused by raspberry leaf and bud mite (Phyllocoptes gracilis). From 2014-2017, a large-scale survey was conducted in Serbia to investigate the degree of association of the observed symptoms with the RLBV infection. A total of 98 symptomatic and asymptomatic samples were collected from 30 locations. All collected samples were tested on the RLBV presence by reverse transcription and polymerase chain reaction (RT-PCR) using three sets of RNA-specific primers targeting RNA-1, RNA-3, and RNA-5 of the RLBV genome. RT-PCR analysis revealed high incidence of RLBV in tested samples (68.7%). RLBV was confirmed in raspberries 'Fertodi Zamatos', 'Glen Ample', 'Meeker', 'Polana', 'Tulameen' and 'Willamette'. Twenty-one isolates were selected for sequencing the portion of the nucleocapsid (NC) gene. The nucleotide sequences of the isolates showed 93.2-100% identity. Phylogenetic analysis confirmed significant genetic variability of the Serbian RLBV isolates based on the nucleocapsid-encoding sequences and revealed the existence of two main clusters. Phylogenetic analysis of the 45 RLBV sequences from Finland, Slovakia, Scotland, and this study also confirmed the existence of two main clusters of isolates.