Phylogenetic analysis of viruses in Tuscan Vitis vinifera sylvestris (Gmeli) Hegi

Abstract

The health status of the native grapevine Vitis vinifera subsp. sylvestris (Gmeli) Hegi in natural areas in Europe has received little attention. A survey was carried out on wild grapevines in Tuscany (Italy), where isolates of the Grapevine rupestris stem pitting virus (GRSPaV), Grapevine leafroll-associated virus 1 and 3 (GLRaV-1 and GLRaV-3) and Grapevine virus A (GVA) were detected. The complete coat protein (CP) region of these isolates was sequenced to investigate the relationship of the viral variants from Tuscan wild grapevines with isolates from different geographical origins. According to the phylogenetic analyses, GLRaV-1 and GLRaV-3 isolates from Tuscan wild grapevines clustered with isolates from cultivated grapevines with nucleotide sequence identities ranging from 66% to 87% and from 72.5% to 99% respectively, without any correlation between the distribution and geographical origin. Conversely, GRSPaV and GVA isolates clustered together with other Italian isolates from V. vinifera with nucleotide sequence identities ranging from 71.14% to 96.12% and from 73.5% to 92%, respectively. Our analysis of the whole amino acid sequences revealed a high conservation level for the studied proteins explained by a selective pressure on this genomic region, probably due to functional constraints imposed on CP, such as specific interactions with cellular receptors in the insect vectors necessary for successful transmission. In addition, analyses of genetic recombination suggest no significant point mutations that might play a significant role in genetic diversification. The dN/dS ratio also estimated a low number of non-silent mutations, highlighting the purifying selective pressure. The widespread distribution of the Rugose wood complex (GRSPaV and GVA associated disease) in comparison with the Grapevine Leafroll associated viruses (GLRaV-1 and -3) could explain the major geographical correlation found for the viral variants detected in Tuscany.

Survey of five major grapevine viruses infecting Blatina and Žilavka cultivars in Bosnia and Herzegovina

“…The explanation for the prevalence of GLRaV-3 I variants over the other groups is possibly related to a higher fitness of these variants or their more efficient transmission by vectors relative to the other variants [ 79 ]. Like the previous studies [ 25 , 78 , 80 ], we were unable to find any association of the phylogenetic group with the geographic origin or the grapevine cultivar. Although the genetic diversity of the GLRaV-3 BiH isolates of the CP region (0.010) was lower than that found in other similar studies (0.058 in Spain [ 78 ]; 0.063 in Portugal [ 79 ]), it is noteworthy that we considered only two cultivars, while previous reports were conducted on a higher number of cultivars.…”

“…Considering GLRaV-1, the phylogenetic analyses assigned four of the studied isolates into three groups. This may indicate a lack of geographical distribution, as already reported [ 25 , 83 – 85 ] and the impact of using infected propagation material in the spread of this virus within the country. Although one GFLV and ArMv isolate from BiH were characterized, the phylogenetic analyses clustered each of them within the phylogenetic groups containing the isolates from different countries, i.e.…”

“…Grapevines may also be infected with viruses without displaying any noticeable symptoms (latent infection) [ 20 , 24 , 25 ]. Therefore, it is recommended to take samples from both symptomatic and asymptomatic plants to perform virus testing [ 24 ].…”

Somatic embryogenesis as a tool for virus elimination in Croatian indigenous grapevine cultivars

“…The clearly visible phenotypic characteristics of infection were a darker area around the leaf veins and downward-twisted leaf edges (Martelli 1993, Andret-Link et al 2004, Meng et al 2017. Both symptoms are characteristic of red varieties infected with the most widespread and damaging viruses (Alliaume et al 2018, Sabella et al 2018 of the leafroll complex (Meng et al 2017). In the advanced phase of infection, the viruses of the leafroll complex cause anthocyanin accumulation.…”

The occurrence of grapevine rugose wood disease in Algeria

“…For example, in Tunisia, this mixed infection was found to occur with an infection rate of 56.8% (Selmi et al, 2017). In Italy and Spain mixed infections between these two viruses were also reported (Fiore et al, 2016;Sabella et al, 2018). These results showed that there is a positive correlation of prevalence between these two viruses.…”