Genetic diversity and identification of putative recombination events in Grapevine rupestris stem pitting-associated virus

[摘要] ENGLISH ABSTRACT: Phylogenetic analysis for variant classification plays a key role in the characterisation of theaetiological role of viruses. The genomic regions selected to identify viral variants and the occurrenceof recombination has the potential to influence tree topologies. To investigate the impact of thesefactors on variant classification, and to evaluate the success of certification schemes in eliminatingvirus infection, a diversity study was performed on Grapevine rupestris stem pitting-associated virus(GRSPaV), a ubiquitous virus commonly detected in cultivated vines and reportedly associated withRupestris Stem Pitting disorder. Three surveys were conducted to characterise and compare thegenetic diversity of GRSPaV on a global and local level, using a phylogenetic approach. The firstconstituted a collection of accessions from various countries to represent global virus diversity. Asecond survey was carried out on local mother blocks that previously conformed to certificationrequirements for South Africa. Finally, GRSPaV diversity in South African vineyards establishedprior to the implementation of current sanitary protocols was investigated. Two genomic areas, thecoat protein and replicase domains, were selected for this study as these were used to characterise thesequence diversity of GRSPaV in previous studies. Mixed infections were found to occur withinsingle vines, the genetic diversity of GRSPaV was confirmed with the clustering of sequences intofive of the six distinct, currently recognised lineages, and a seventh, previously unclassified lineagewas detected. Furthermore, the ability of the two domains to detect and classify variants wascompared. Additional evidence for recombination in GRSPaV was provided and a correlationbetween recombinant sequences and inconsistencies between topologies generated by the twogenome regions, was observed. Results indicate that disease control methods were moderatelysuccessful, but less effective at eliminating non-symptomatic variants. The study illustrates the effectof recombination on phylogenetic trees, and emphasises the importance of accounting for such factorsin the characterisation of virus diversity. Increased knowledge of the recombination events within theGRSPaV genome could promote the development of a standardised method for variant classificationand the clarification of the aetiological role of the virus.

[发布机构] Stellenbosch University