Limited Genetic Variability Among American Isolates of Grapevine virus E from Vitis spp

Pest categorisation of non-EU viruses and viroids of Vitis L

Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of grapevine virus 101-14.N.23.9.1/South Africa/2009 for which very limited information exists, the pest categorisation was completed for 30 viruses or viroids having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for potential entry. Depending on the virus, additional pathway(s) can also be seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Grapevine yellow speckle viroid 2, blueberry leaf mottle virus, grapevine Ajinashika virus, grapevine Anatolian ringspot virus, grapevine berry inner necrosis virus, grapevine deformation virus, grapevine fabavirus, grapevine red blotch virus, grapevine stunt virus, grapevine Tunisian ringspot virus, grapevine vein-clearing virus, temperate fruit decay-associated virus, peach rosette mosaic virus, tobacco ringspot virus, tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact for the EU territory, on which the Panel was unable to conclude, blackberry virus S, grapevine geminivirus A, grapevine leafroll-associated virus 7, grapevine leafroll-associated virus 13, grapevine satellite virus, grapevine virus E, grapevine virus I, grapevine virus J, grapevine virus S, summer grape enamovirus, summer grape latent virus satisfy all the other criteria to be considered as potential Union QPs. Australian grapevine viroid, grapevine cryptic virus 1, grapevine endophyte endornavirus and wild vitis virus 1 do not meet all the criteria evaluated by EFSA to be regarded as potential Union QPs because they are not known to cause an impact on Vitis. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non-quarantine pests.

Development of RT-PCR assays for the detection and the resultant phylogenetic analysis of four grapevine vitiviruses based on the coat protein sequences

Four sets of primers were designed based on the alignment of the complete coat protein (CP) gene sequences of several isolates of four different vitiviruses, i.e. grapevine virus B (GVB), GVD, GVE and GVF, and tested for their efficiency in RT-PCR assays to detect vitiviruses infections in grapevine. The resultant RT-PCR amplicons were sequenced and analyzed for their genetic variability and phylogenetic studies. The results of the RT-PCR assays showed that these primers were highly efficient in detecting different vitivirus isolates in grapevine material originating from ten different Mediterranean countries. In particular, 76 out of 218 tested samples (ca. 35%) were infected with at least one vitivirus. GVE was the most detected (14.7%), followed by GVF (11.5%), GVB (6.9%), and GVD (2.8%). Nucleotide (nt) sequence analysis of the CP genes from this study and Genbank showed that the sequence identity matrixes among isolates of GVB and GVE were the most variable, with nt identity ranging from 77% to 100%, whereas isolates of GVD and GVF showed more conserved nt identities ranging between 82% to 100% and 86.4% to 99.8%, respectively. The phylogenetic trees constructed based on the CP sequences distinguished two main groups of isolates for each vitivirus species, except for the GVD isolates, which did not show any particular subdivision. In general, the distributions of the isolates in the phylogenetic tree were associated with their geographical origin, thus suggesting limited movement of grapevine materials between the different countries. This study reported for the first time: (i) the development of primers based on the complete CP gene sequences for RT-PCR assays for the universal detection of vitivirus species, (ii) the high genetic variability among Mediterranean isolates of vitiviruses and (iii) the presence of GVD in Jordanian vines, of GVE in grapevines from Hungary, Italy, Jordan, Malta and Palestine, and of GVF in grapevines from Afghanistan, Bulgaria, China, France, Hungary, Italy, Jordan, Lebanon and Malta.