Evidence of novel genetic variants of Grapevine rupestris stem pitting-associated virus and intra-host diversity in Indian grapevine cultivars

Grapevine rupestris stem pitting-associated virus (GRSPaV) is a member of the genus Foveavirus in the family Betaflexiviridae exhibiting high genetic variability. In the present study, a total of eleven full length coat protein gene sequences of GRSPaV were characterized from wine grape cultivars grown in the state of Maharashtra (Nashik and Pune) and Imphal (Manipur). Their molecular diversity was compared with corresponding sequences reported from other grape-growing regions globally. In pairwise sequence comparisons, the coat protein (CP) sequences of Indian GRSPaV isolates exhibited the identity in the range of 81–98% at nucleotide level when compared to respective CP sequences of GRSPaV isolates reported across the globe. A maximum likelihood phylogenetic analysis based on CP with the global isolates revealed six major phylogenetic clusters and two putative new clusters. Nine Indian GRSPaV isolates clustered in previously recognized three major lineages (groups II, III, and IV), while two of the isolates GRSPaV-RG14 and -B2 shared the recently identified putative group VIII. Our study also revealed the intra-host diversity exhibiting the presence of genetically distinct variants in the single host and inconsistencies in the placements was observed in their CP-based phylogenetic tree. This study also analyzed the population genetic parameters of GRSPaV isolates that showed the CP sequences were more variable within the isolates of group III (GRSPaV-BS) cluster (π =0.054), while various other factors including Tajima values (D) for group VIII appeared to be deviating from the trend for other GRSPaV lineages.