Detection of virus-associated dsRNA from leafroll infected grapevines

Grapevine leafroll-associated virus 3

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.

Genetic diversity analyses reveal novel recombination events in Grapevine leafroll-associated virus 3 in China

Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent causal agent of grapevine leafroll disease (GLD). Of the 75 grapevine samples collected from three regions in China, 46.7% and 94.7% of samples tested positive for GLRaV-3 in reverse transcription-PCR (RT-PCR) and reverse transcription nested PCR (RT-nPCR), respectively. The SSCP analysis for the clones of complete CP gene from 16 GLRaV-3 isolates showed that 15 isolates contained one predominant haplotype and one isolate had no predominant haplotype. The sequences of the CP genes showed 89.9-100% identities at the nucleotide level. Phylogenetic analysis of the CP gene sequences revealed the existence of four well defined variant groups, which corresponded to previously reported phylogenetic groups (1, 2, 3, and 5). Two new sub-groups designated as sub-group 1B and sub-group 3B in groups 1 and 3, respectively, were identified in the Chinese GLRaV-3 population. Recombination analyses illustrated that those two new sub-groups (1B and 3B) were emerged as a result of recombination events between variants in groups 1 and 2, and variants in groups 1 and 3, respectively. These results further indicated that the variants in those new sub-groups are viable and evolutionary successful. Recombinants with highly similar coat protein structure to variants of group 1 were abundantly found in the viral population. In addition, these analyses provided evidence about CP gene as one of the recombination hotspots in GLRaV-3 genome. The population genetic parameters of all available CP sequences suggested that the recombinants might have emerged due to population bottlenecks during transmission. The results provide new insights into the variability and evolution of GLRaV-3.

Mapping of the 5' terminal nucleotides of Grapevine leafroll-associated virus 3 sgRNAs

Grapevine leafroll-associated virus 3 (GLRaV-3) is a positive sense, single stranded RNA virus that has a detrimental effect on wine and table grapes worldwide. Previous studies have shown that GLRaV-3, like other closteroviruses produces subgenomic (sg) RNAs during replication and that these sgRNAs are deployed for the expression of the ORFs on the 3' half of the genome. In this study a dsRNA blot confirmed the presence of three, 3' co-terminal sgRNAs species [sgRNA(ORF3/4), sgRNA(ORF5) and sgRNA(ORF6)] in GLRaV-3-infected plant material when using a probe directed at the coat protein. The specific 5' terminal nucleotides for these sgRNAs as well as four additional sgRNAs [sgRNA(ORF7), sgRNA(ORF8), sgRNA(ORF9) and sgRNA(ORF10-12)] were determined by RLM-RACE for GLRaV-3 isolate GP18.

Single-stranded DNA of Tomato leaf curl virus accumulates in the cytoplasm of phloem cells

Geminiviruses have been reported to replicate in, and localize to, the nuclei of host plant cells. We have investigated the tissue and intracellular distribution of the monopartite Tomato leaf curl virus (TLCV) by in situ hybridization. Contrary to the current understanding of geminiviral localization, single-stranded (ss) DNA of TLCV accumulated in the cytoplasm. TLCV ssDNA was also found in the nucleus, as was lower levels of replicative form double-stranded (ds) DNA. Under the same conditions, Tomato golden mosaic virus (TGMV) ssDNA and dsDNA were found in nuclei. ssDNA of TLCV, TGMV, and Tomato yellow leaf curl Sardinia virus (TYLCSV) was detected in some xylem vessels under specific hybridization conditions. Tissue specificity of TLCV was partially released by co-infection with TGMV. Our observations suggest that the mechanism of TLCV movement may differ from that of bipartite begomoviruses.

Nucleotide sequence and organization of ten open reading frames in the genome of grapevine leafroll-associated virus 1 and identification of three subgenomic RNAs

The genome of Grapevine leafroll-associated virus 1 (GLRaV-1) was cloned and the sequence of 12394 nts determined. It contains 10 major open reading frames (ORFs) and a 3'-non-coding region lacking a poly(A) tract. The first ORF (ORF 1a) encodes a putative RNA helicase at the C-terminal portion of an apparently larger protein. The downstream ORF, 1b, overlaps ORF 1a and lacks an initiation codon. This ORF encodes an RNA-dependent RNA polymerase of M(r) 59276. ORF 2 encodes a small hydrophobic protein of M(r) 6736, and ORF 3 encodes a homologue of the HSP70 family of heat shock proteins and has an M(r) of 59500. ORF 4 encodes a protein with an M(r) of 54648 that shows similarity to the corresponding proteins of other closteroviruses. ORF 5 encodes the viral coat protein (CP) with an M(r) of 35416. The identity of this ORF as the CP gene was confirmed by expression in Escherichia coli and testing with the viral antibody. ORFs 6 and 7 code for two CP-related products with M(r) of 55805 and 50164, respectively. ORFs 8 and 9 encode proteins of M(r) 21558 and 23771 with unknown functions. Using DNA probes to different regions of the GLRaV-1 sequence, three major 3'-coterminal subgenomic RNA species were identified and mapped on the GLRaV-1 genome. Phylogenetic analyses of the individual genes of GLRaV-1 demonstrated a closer relationship between GLRaV-1 and GLRaV-3 than with other closteroviruses.

Efficient cloning of cDNA from grapevine leafroll-associated virus 4 and demonstration of probe specificity by the viral antibody

Using a random-PCR method, a cDNA clone (LR4) was constructed from the replicative form dsRNA of grapevine leafroll-associated virus 4 (GLRaV-4). Northern blot analysis showed hybridization of LR4 to dsRNA in an extract of a Thompson Seedless grapevine clone from which GLRaV-4 was isolated originally by Hu et al. (1990). The cDNA clone was sequenced and shown to be specific to GLRaV-4 by reverse-transcription-PCR using GLRaV-4 particles enriched by the virus antibody coupled to magnetic beads. Reverse-transcription-PCR was used successfully to screen different varieties of grapevines for the virus. Western blot analysis of GLRaV-4 extracts from different varieties of infected grapevines revealed two distinct species of capsid protein with estimated Mr of either 35500 or 38000 depending on the variety used. Both proteins reacted with polyclonal as well as monoclonal antibodies.