High‐throughput sequencing allowed the completion of the genome of grapevine Red Globe virus and revealed recurring co‐infection with other tymoviruses in grapevine

Abstract

Grapevine Red Globe virus (GRGV) is a member of family Tymoviridae tentatively assigned to genus Maculavirus. There is evidence that the distribution of this virus may be widespread. In a recent report, the authors of the present study described the presence of GRGV in Spain. To further estimate its incidence, a survey was carried out that allowed the detection of the virus using RT‐PCR in a germplasm collection in northern Spain. In the present study, three isolates were selected to obtain full‐length genome sequences using high‐throughput sequencing (HTS) of RNA combined with Sanger sequencing. The GRGV complete genome consists of 6850 nucleotides, excluding the polyA tail. Two ORFs could be identified as the putative replicase and coat protein. Although comparison of the complete genomes provided no evidence for the presence of the additional ORF previously described, another ORF was identified within the coat protein ORF, but it probably lacks functional significance. Phylogenetic analysis supported the ascription of GRGV to genus Maculavirus. The profile of vsiRNA (virus‐derived small interfering RNA) distribution along the GRGV genomes suggested the presence of a subgenomic RNA corresponding to the coat protein ORF. To improve detection of GRGV, new primer sets were designed based on consensus sequences. HTS revealed a frequent co‐infection of GRGV and grapevine rupestris vein feathering virus (GRVFV). Biological indexing by grafting two GRGV‐infected vines on indicator plants and the visual inspection of symptoms in other infected plants revealed that the virus has a negligible impact on grapevine.