Grapevine leafroll-associated virus 3

Abstract

Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management.

Keywords: Closteroviridae; GLRaV-3; ampelovirus; genetic variants; grapevine leafroll disease.

Figure 1

Typical leafroll diseased vines: (A) a red cultivar, Vitis vinifera cv Cabernet Franc; (B) a white cultivar, Vitis vinifera cv Chardonnay.

Figure 2

Diagram of the proposed taxonomic modification that is in process to be examined by the International Committee of Taxonomy of Viruses (Martelli et al., 2012).

Figure 3

Transmission electron micrograph of negatively stained, purified GLRaV-3 particles, using 1% (w/v) aqueous uranyl acetate staining. Picture taken by G. G. F. Kasdorf.

Figure 4

A schematic diagram of the GLRaV-3 genome to scale. Lines above the genome map indicate the positions of the ORFs and their respective corresponding numbers. In the genome map, boxes indicate positions of genes with gene products and domains indicated. Homology between the CP and p55 and CPm is indicated by the same coloring. UTR, Untranslated region; L-Pro, Leader papain-like protease; MET, Methyltransferase; AlkB, AlkB domain; [Fe (II)/2-oxoglutarate-dependent dioxygenase], HEL, Helicase; POL, RNA dependent RNA polymerase; Hsp70h, Heat shock protein 70 homolog; CP, Coat protein; CPm, minor coat protein. Below the genome map the predicted sgRNAs are indicated by lines. ^aNot present in Group VI variants. ^bHighly divergent in Group VI and VI-like variants. ^cPutative sgRNA.

Figure 5

Similarity plot constructed from a multiple alignment of nine full-length sequences representing six well-defined variant groups of GLRaV-3 using SimPlot, PHYLIP (Pylogeny Inference Package) v3.5.1 (Lole et al., 1999).

Figure 6

Phylogenetic tree of full-length CP gene from representative GLRaV-3 isolates (Isolate NZ1, GenBank: EF508151, is a partial sequence). Proposed GLRaV-3 variant groups are shown with roman numerals. Maximum likelihood tree is shown, but analyses with distance and maximum parsimony methods provide similar topology. The tree is midpoint rooted for presentation and asterisks indicate ≥75% branch support with all three methods. Accession number, isolate name, and country where samples were collected are shown; fully sequenced genomes are underlined for reference. The phylogenetic analysis was performed with PAUP* (Swofford, 2003) and image generated with FigTree (Rambaut, 2006).