Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties

Abstract

The genetic variability and population structure of grapevine leafroll-associated virus 3 (GLRaV-3) variants were updated by examining the diversity within the viral coat protein (CP) gene among 174 isolates belonging to a collection of Vitis vinifera representing most of the Portuguese varieties. Phylogenetic analysis revealed the existence of five well-defined clusters. Three of these correspond to previously defined groups, another corresponds to variants from Chile for which only one sequence has been previously identified, and an additional new group includes only Portuguese variants. A typing tool based on asymmetric PCR-ELISA (APET) was developed within the frame of this population structure. This tool was used to assess the prevalence of each phylogenetic group among the infected grapevine varieties. Although most of the isolates harbour variants from groups 1 and 2, variants from the remaining three groups exist in a number of varieties, reinforcing the notion that they are genuine genomic variants and are not isolated, atypical cases.

Viral Diversity in Autochthonous Croatian Grapevine Cultivars

“…Prevalence of variant group II is reported from South Africa (Jooste et al 2011), Spain (Pesqueira et al 2016), and Hungary (Cseh et al 2013), while Napa Valley (Sharma et al 2011), China (Farooq et al 2012), and New Zealand ) are dominated by group I. Mixed infections with both variants were present in 20 GLRaV-3 positive vines (45.5%), significantly more than the 25.3% reported from Portugal (Gouveia et al 2011) or 22% from Napa Valley (Sharma et al 2011). Our study had a much smaller sample size than studies in Portugal and Napa Valley; therefore, reliable comparisons are difficult to make.…”

“…The same groups were dominant in Portugal (Gouveia et al 2011). Prevalence of variant group II is reported from South Africa (Jooste et al 2011), Spain (Pesqueira et al 2016), and Hungary (Cseh et al 2013), while Napa Valley (Sharma et al 2011), China (Farooq et al 2012), and New Zealand ) are dominated by group I.…”

Identification of an RNA silencing suppressor encoded by Grapevine leafroll-associated virus 3

“…GLRaV-3 clones of the candidate genes were obtained from the Portuguese isolate "Touriga Franca", a Group 1 isolate described in Gouveia et al (2011). The methods used to obtain the candidate genes are the same described in that paper except that the primers used were those indicated in Table 1 Tomato aspermy virus, used as suppressing positive control in the initial assays, was a gift from Dr. GarciaArenal (Universidad Politécnica de Madrid, Spain).…”

Simultaneous detection of Brazilian isolates of grapevine viruses by TaqMan real-time RT-PCR

“…The genetic diversity of GLRaV-3 has been demonstrated (Gouveia et al, 2011), based on the analysis of the capsid protein or heat shock 70 (HSP70) genes, which revealed the existence of three to five phylogenetic groups in the populations of this virus.…”