""Technical workshop on Plant virus diagnostic application of RNA high throughput sequencing to phytosanitary certification procedures. 7-9 November 2018, IPSP-CNR, Bari, ITALY" 

Abstract: Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed

Abstract: Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches.

Introduction

	Fruit trees and grapevine are propagated vegetatively and are often grafted
	As a result they suffer from a high number of pathogens such as viruses and viroids, with some of them causing severe yield losses and reducing the productive life of the affected plants
	These pathogens cannot be controlled by the application of chemicals therefore the most efficient way to combat them is the production and commercialization of high quality pathogen-tested propagative material

Objectives of VirFree

VirFree brings together participants from both academia and privatecompanies to collaborate through their expertise on the following objectives:
to identify new viral and viroid strains or species affecting fruit trees and grapevine	to optimize existing and develop novel detection methods	to improve propagation and sanitation methods for producing high quality (virus-tested) plant material of fruit trees and grapevine

 Approach

Diagnostic tools currently used in certification schemes will becombined with cutting edge technologies such as NGS and Nanobodies

Virfree Project Virfree Project Virfree Project Virfree Project

 Expected benefits

Training of a new generation of researchers to fulfill the needs of both industrial and academic sectors	Enrich the knowledge on viruses/viroids associated with different diseases	Improve the sensitivity of detection methods	Development of new detection products	Improvement of the disseminated propagative material

""The VirFree Midterm meeting has been performed at the School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece on 4 and 5 June 2018." 

• 5 June 2018

5 June 2018

VirFree brings together participants from both academia and privatecompanies to collaborate through their expertise on the following objectives

rfree, NGS, Nanobodies, Fruit tree viruses, viroids, virus elimination ,http://www.virfree.eu ,virfree,virfree.eu , This email address is being protected from spambots. You need JavaScript enabled to view it.

"The hands-on training School entitled "Bioinformatic analysis of NGS data for plant virus detection", has been performed successfully on 6 and 7 June 2018 at Heraklion, Crete "

• Category Title

Category Title

Category Title

VirFree brings together participants from both academia and privatecompanies to collaborate through their expertise on the following objectives

rfree, NGS, Nanobodies, Fruit tree viruses, viroids, virus elimination ,http://www.virfree.eu ,virfree,virfree.eu , This email address is being protected from spambots. You need JavaScript enabled to view it.

The VirFree project initiated with a kick-off meeting that took place at the School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece on 27th of January 2017.

• Kick-off Meeting

Kick-off Meeting

VirFree brings together participants from both academia and privatecompanies to collaborate through their expertise on the following objectives

rfree, NGS, Nanobodies, Fruit tree viruses, viroids, virus elimination ,http://www.virfree.eu ,virfree,virfree.eu , This email address is being protected from spambots. You need JavaScript enabled to view it.

Felix Moran; Antonio Olmos; Leonidas Lotos; Lukas Predajňa; Nikolaos Katis; Miroslav Glasa; Varvara Maliogka; Ana B. Ruiz-Garcia 

First Report of Grapevine Latent Viroid Infecting Grapevine (Vitis vinifera L.) 1 in Italy
S. Rotunno, A.M. Vaira, D. Marian, A. Schneider and S. Raimondi , Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy; F. Di Serio and B. Navarro, Institute for Sustainable Plant Protection, Bari Unit, via Amendola, 122/D, 70126, Bari, Italy; L. Miozzi*, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, 

Igor Koloniuk; Tatiana Sarkisova; Karel Petrzik; Ondrej Lenz; Jaroslava Pribylová; Jana Fránová; Josef Špak; Leonidas Lotos; Christina Beta; Asimina Katsiani; Thierry Candresse; Varvara I. Maliogka

During their lifetime, perennial woody plants are expected to face multiple infection events. Furthermore, multiple genotypes of individual virus species may co-infect the same host. This may eventually lead to a situation where plants harbor complex communities of viral species/strains. Using high-throughput sequencing, we describe co-infection of sweet and sour cherry trees with diverse genomic variants of two closely related viruses, namely prunus virus F (PrVF) and cherry virus F (CVF).