Genetic Diversity ofGrapevine virus Ain Washington and California Vineyards

Abstract

Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.

Prevalence and RT/RNase H Genealogy of Sugarcane Bacilliform Virus Isolates from China

“…Because the mealybug vector of SCBV is largely sedentary by nature, the only plausible explanation for the widespread nature of the virus in China is that they occurred mainly via the movement of contaminated vegetative materials. Similar modes of spread have been reported for viruses infecting other vegetatively propagated crops including grapevine (Alabi et al 2011(Alabi et al , 2014, banana and plantain (Thomas et al 2003). …”

“…For instance, the eight SCBV isolates from Fuzhou (Fujian Province) and Liuzhou (Guangxi Province) resulted in 12 'unique' sequences, while the two isolates from Yacheng (Hainan Province) and the two isolates from Mile (Yunnan Province) resulted in three and four 'unique' sequences (100% nt identity), respectively (Table 1). In contrast, all three independent clones sequenced from isolates derived from various loca- Alabi et al 2011Alabi et al , 2014Glouzon et al 2014).…”

Phylogenetic analysis and recombination events in full genome sequences of apple stem grooving virus

“…Though no recombination hotspot was found, recombination events play an important role in ASGV evolution as reported recombination in cp gene (Negi et al, 2010). Moreover, recombination might be common in members of Betaflexiviridae as detected in a few reports (Singh et al, 2007(Singh et al, , 2008(Singh et al, , 2012Komorowska et al, 2011;Singh et al, 2012;Dhir et al, 2013;Pramesh and Baranwal, 2013;Alabi et al, 2014;Chen et al, 2014). As no vector is known for ASGV and it can be transmitted by grafting, recombinant events among isolates from different host species and countries, and phylogenetic clusters with no correlation to host or geographical origins are likely to be the result of vegetative propagation and exchanges of propagation materials between countries.…”

Grapevine Biotechnology: Molecular Approaches Underlying Abiotic and Biotic Stress Responses

“…GVA is related with the Kober stem grooving symptom, where severe grooving on the grafted stems occurs [86,87], while GVB is associated with the corky bark syndrome consisting of soft, rubbery and abnormal swelling of the basal internodes of the canes, longitudinal cracks and cork forming, typical of the rugose wood complex [88]. Vitivirus genus has other species less ubiquitous, named GVD, GVE, and the most recently discovered GVF [89], causing similar symptoms to the corky rugose wood but its role is still unclear [90].…”