High-Throughput Sequencing Assists Studies in Genomic Variability and Epidemiology of Little Cherry Virus 1 and 2 infecting Prunus spp. in Belgium.

Tim Beliën,Kris De Jonghe,Rachid Tahzima,Gertie Peusens,Yoika Foucart,Sébastien Massart

doi:10.3390/v11070592

Abstract

Little cherry disease, caused by little cherry virus 1 (LChV-1) and little cherry virus 2 (LChV-2), which are both members of the family Closteroviridae, severely affects sweet (Prunus avium L.) and sour cherry (P. cerasus L.) orchards lifelong production worldwide. An intensive survey was conducted across different geographic regions of Belgium to study the disease presence on these perennial woody plants and related species. Symptomatic as well as non-symptomatic Prunus spp. trees tested positive via RT-PCR for LChV-1 and -2 in single or mixed infections, with a slightly higher incidence for LChV-1. Both viruses were widespread and highly prevalent in nearly all Prunus production areas as well as in private gardens and urban lane trees. The genetic diversity of Belgian LChV-1 and -2 isolates was assessed by Sanger sequencing of partial genomic regions. A total RNA High-Throughput Sequencing (HTS) approach confirmed the presence of both viruses, and revealed the occurrence of other Prunus-associated viruses, namely cherry virus A (CVA), prune dwarf virus (PDV) and prunus virus F (PrVF). The phylogenetic inference from full-length genomes revealed well-defined evolutionary phylogroups with high genetic variability and diversity for LChV-1 and LChV-2 Belgian isolates, yet with little or no correlation with planting area or cultivated varieties. The global diversity and the prevalence in horticultural areas of LChV-1 and -2 variants, in association with other recently described fruit tree viruses, are of particular concern. Future epidemiological implications as well as new investigation avenues are exhaustively discussed.

Highlights

Little cherry disease (LChD) is an economically important viral disease causing a wide range of phenotypic responses and significant reduction of fruit yield and quality in sweet (Prunus avium L., family Rosaceae) and sour cherry (Prunus cerasus L.) field stock nurseries and commercial orchards.Two distinct (+)ssRNA viruses, found in single or mixed infections, are the associated causal agents of LChD
Many Prunus species are known to host a wide spectrum of viral populations and to frequently harbor mixed infections [8,43]
We demonstrated that the little cherry disease, caused by harbor mixed infections [8,43]

Summary

Introduction

Little cherry disease (LChD) is an economically important viral disease causing a wide range of phenotypic responses and significant reduction of fruit yield and quality in sweet (Prunus avium L., family Rosaceae) and sour cherry (Prunus cerasus L.) field stock nurseries and commercial orchards.Two distinct (+)ssRNA viruses, found in single or mixed infections, are the associated causal agents of LChD. Little cherry disease (LChD) is an economically important viral disease causing a wide range of phenotypic responses and significant reduction of fruit yield and quality in sweet (Prunus avium L., family Rosaceae) and sour cherry (Prunus cerasus L.) field stock nurseries and commercial orchards. Symptoms are highly variable among cherry cultivars and are strongly influenced by season, weather and growing conditions ([8] and references therein), leading to significant yield losses and poor-quality fruit. This variability limits the ability of growers to associate poor fruit development with LChD

Methods

Results

Conclusion