A putative new ampelovirus associated with grapevine leafroll disease

Abstract

A putative new ampelovirus was detected in Vitis vinifera cv. Carnelian showing mild leafroll symptoms and molecularly characterized. The complete genome consisted of 13,625 nt and had a structure similar to that of members of subgroup I in the genus Ampelovirus (fam. Closteroviridae). In-depth analyses showed that the virus from cv. Carnelian is the most distinct member of the "GLRaV-4 lineage" of ampeloviruses, which comprises GLRaV-4, -5, -6, -9, and the recently characterized GLRaV-Pr, and GLRaV-De. This virus appears to be a new member of the family Closteroviridae, for which the provisional name grapevine leafroll-associated Carnelian virus is proposed.

Fig. 1

a Mild leafroll symptoms induced by GLRaCV on indicator Vitis vinifera cv. Cabernet Franc. b Electrophoretic patterns of dsRNAs extracted from cv. Carnelian (lane 1) compared to dsRNAs extracted from grapevine infected with grapevine rupestris stem pitting-associated virus (lane 2) and from GLRaV-2-infected Nicotiana benthamiana (lane 3)

Fig. 2

Diagrammatic representation of the GLRaCV genome to scale. Boxes depict putative ORFs. PRO protease; MTR methyltransferase; HEL helicase; RdRp RNA-dependent RNA polymerase; p5 hydrophobic 5 K protein; HSP70h heat shock 70 protein homologue; p60 60 K protein; CP coat protein; p23 23 K protein with unknown function

Fig. 3

Phylogenetic tree constructed using HSP70h amino acid sequences of members of some definitive and tentative species in the family Closteroviridae. Bootstrap values are indicated on the nodes. Sequences used to construct the tree and their accession numbers are as follows: beet yellows virus (BYV, NC_001598), beet yellow stunt virus (BYSV, U51931), blackberry yellow vein associated virus (BYVaV, NC_006963), carnation necrotic fleck virus (CNFV, EU884443), carrot yellow leaf virus (CYLV, NC_013007), citrus tristeza virus (CTV, NC_001661), cucurbit yellow stunting disorder virus (CYSDV, NC_004810), grapevine leafroll-associated virus 1 (GLRaV-1, AF195822), 2 (GLRaV-2, NC_007448), 3 (GLRaV-3, NC_004667), 4 (GLRaV-4, AM162280), 5 (GLRaV-5, AF233934), 7 (GLRaV-7, Y15987), 9 (GLRaV-9, AY297819), De (GLRaV-De, AM494935), Pr (GLRaV-Pr, NC_011702), grapevine leafroll-associated Carnelian virus (GLRaCV, FJ907331), little cherry virus 1 (LChV-1, NC_001836), little cherry virus 2 (LChV-2, NC_005065), lettuce infectious yellows virus (LIYV, NC_003618), mint virus-1 (MV-1, NC_006944), pineapple mealybug wilt-associated virus 1 (PMWaV-1, NC_010178), pineapple mealybug wilt-associated virus 2 (PMWaV-2, AF283103), pineapple mealybug wilt-associated virus 3 (PMWaV-3, DQ399259), plum bark necrosis stem pitting associated virus (PBNSPaV, NC_009992), potato yellow vein virus (PYVV, NC_006063), raspberry leaf mottle virus (RLMoV, NC_008585), sweet potato chlorotic stunt virus (SPCSV, NC_004124) and tomato infectious chlorosis virus (TICV, NC_013259). Outgroup: putative heat shock protein 70 of Arabidopsis thaliana (AAN71949)