Association of a Novel DNA Virus with the Grapevine Vein-Clearing and Vine Decline Syndrome

Abstract

A severe vein-clearing and vine decline syndrome has emerged on grapevines (Vitis vinifera) and hybrid grape cultivars in the Midwest region of the United States. The typical symptoms are translucent vein-clearing on young leaves, short internodes and decline of vine vigor. Known viral pathogens of grapevines were not closely associated with the syndrome. To obtain a comprehensive profile of viruses in a diseased grapevine, small RNAs were enriched and two cDNA libraries were constructed from a symptomatic grapevine and a symptomless grapevine, respectively. Deep sequencing of the two cDNA libraries showed that the most abundant viral small RNAs align with the genomes of viruses in the genus Badnavirus, the family Caulimoviridae. Amplification of the viral DNA by polymerase chain reaction allowed the assembly of the whole genome sequence of a grapevine DNA virus, which shared the highest homology with the Badnavirus sequences. This is the first report of a DNA virus in grapevines. The new DNA virus is closely associated with the vein-clearing symptom, and thus has been given a provisional name Grapevine vein clearing virus (GVCV). GVCV was detected in six grapevine cultivars showing vein-clearing and vine decline syndrome in Missouri, Illinois, and Indiana, suggesting its wide distribution in the Midwest region of the United States. Discovery of DNA viruses in grapevines merits further studies on their epidemics and economic impact on grape production worldwide.

Grapevine Virus Diseases:economic Impact and Current Advances in Viral Prospection and Management

“…Several metagenomics studies were developed aiming to know the virome and causal agents of economically important grapevine diseases (al RWahNIh et al, 2009(al RWahNIh et al, , 2013b(al RWahNIh et al, and 2015cOeTZee et al, 2010;FaJaRDO et al, 2015c;GIaMPeTRuZZI et al, 2012;JO et al, 2015;POOJaRI et al, 2013;ZhaNG et al, 2011). In addition, several new viral species or strains of known viruses, mycoviruses, viroids and phytoplasmas were identified using NGS of total RNas, siRNas or dsRNas isolated from specific tissues.…”

“…Grapevine vein clearing virus (GVcV) was found associated with vein-clearing symptom, shortening of the internodes, crinkled leaves, misshapen and smaller grape berries, with irregular shape and abnormal texture (GuO et al, 2014;ZhaNG et al, 2011). GVcV has no known insect vector and its economic importance is not clearly defined.…”

“…Grapevine viruses associated with these diseases have a RNa genome. Recently, DNA viral agents have been identified, such as a geminivirus associated with Red blotch disease in the USA (AL RWAHNIH et al, 2013b;KRENZ et al, 2012 andPOOJaRI et al, 2013), two badnaviruses associated with Grapevine vein-clearing and vine decline syndrome in the uSa (ZhaNG et al, 2011) and with Roditis leaf discoloration disease in Greece (MALIOGKA et al, 2015b), and a unclassified virus associated with fruit tree decline syndrome in the Brazilian orchards and vineyards (BaSSO et al, 2015).…”

Advances in Propagation of Grapevine in the World

“…However, recently, some new viruses have been discovered in grapevines and quickly became known as "emerging viruses" for the expression and relevance they have acquired in the world . Some examples are Grapevine Syrah virus 1 (GSyV-1) ADVANCES IN PROPAGATION OF GRAPEVINE IN THE WORLD... associated with the Syrah decline (AL RWAHNIH et al, 2009); Grapevine red blotch-associated virus (GRBaV), which causes the red blotch disease (SUDARSHANA et al, 2015); Grapevine vein clearing virus (GVCV), which causes "vein clearing" (ZHANG et al, 2011) and Grapevine Pinot gris virus (GPGV), which causes chlorotic mottling and leaf deformation .…”

Current status of viroid taxonomy

“…Therefore, besides being molecular markers of ongoing viroid infections, overlapping vd-sRNAs can be assembled in silico into viroid contigs to subsequently search for similar sequences in databanks (as previously shown for plant viruses). Several viroids have been detected by this approach in the last few years [1,5,26,36,48,68]. In 2012, an algorithm was developed to assemble circular RNA genomes from small RNAs resulting from NGS, thus allowing identification of viroid-like RNAs independent of any homology with previously reported sequences [67].…”