A divergent variant of Grapevine leafroll-associated virus 3is present in California

Seah, Yee Mey; Sharma, Abhineet M.; Zhang, Siming; Almeida, Rodrigo P. P.; Duffy, Siobain

doi:10.1186/1743-422x-9-235

Cited by 21 publications

(23 citation statements)

References 16 publications

(25 reference statements)

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“…Phylogenetic analysis of the HSP70h gene showed at least five possible variant groups (Fuchs et al, 2009). Subsequent studies using phylogenetic analysis of various genome regions, predominantly the CP but also HSP70h, CPm, p55, and RdRp, also confirmed five variant groups as well as identified diverse isolates currently grouped in group VI and more distantly related isolates suggesting a group VII (Chooi et al, 2009, 2013a; Gouveia et al, 2011; Sharma et al, 2011; Wang et al, 2011; Bester et al, 2012a; Seah et al, 2012). Due to limited sequence information and for the purpose of this review all isolates related to group VI, but divergent, will be referred to as group VI-like.…”

Section: Genetic Variants Of Glrav-3mentioning

confidence: 91%

“…There is also a large, GC-rich intergenic region between ORFs 2 and 3 that is atypical of members of the family Closteroviridae . The genomes of isolates in variant group VI that have been characterized so far lack ORF2 (Bester et al, 2012a; Seah et al, 2012). Isolates from groups IV and V have yet to be fully sequenced.…”

Section: Glrav-3 Genome Organization and Functions Of Encoded Proteinsmentioning

confidence: 99%

“…The expression of this ORF is uncertain; as mentioned above, it is also missing in GLRaV-3 group VI isolates and seems unlikely to carry an essential function (Bester et al, 2012a; Seah et al, 2012). In contrast, the following five ORFs 3–7 comprise a quintuple gene module that is a conserved hallmark of the family Closteroviridae (Dolja et al, 2006).…”

Section: Glrav-3 Genome Organization and Functions Of Encoded Proteinsmentioning

confidence: 99%

“…Another full-length sequence of a representative of group III, isolate LN (GenBank: JQ423939), contained a much longer 5′UTR compared to PL-20. The recent full-length sequences of group VI variants from South Africa (Isolates: GH11 and GH30), and the USA (Isolate: CA7246) revealed 5′UTRs of 737 nt for isolates GH11 and CA7246, and a shorter length 5′UTR for isolate GH30 (Bester et al, 2012a; Seah et al, 2012). To determine if there are sequence or structural conservation within the 5′UTR it will be important to also have sequence information from groups IV and V.…”

Section: Genetic Variants Of Glrav-3mentioning

confidence: 99%

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Grapevine leafroll-associated virus 3

Maree¹,

Almeida²,

Bester³

et al. 2013

Front. Microbiol.

197

186

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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.

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Section: Genetic Variants Of Glrav-3mentioning

confidence: 91%

Section: Glrav-3 Genome Organization and Functions Of Encoded Proteinsmentioning

confidence: 99%

Section: Glrav-3 Genome Organization and Functions Of Encoded Proteinsmentioning

confidence: 99%

Section: Genetic Variants Of Glrav-3mentioning

confidence: 99%

See 2 more Smart Citations

Grapevine leafroll-associated virus 3

Maree¹,

Almeida²,

Bester³

et al. 2013

Front. Microbiol.

197

186

View full text Add to dashboard Cite

show abstract

“…Peculiarly, GLRaV-1 possesses two divergent copies of CPm, whereas, in contrast, CPm is absent in the GLRaV-4-like viruses. Another unique feature of some variants of GLRaV-3 is the presence of a small ORF (ORF 2) that potentially encodes a 6-kDa protein, the function of which still needs to be resolved (21,125). GLRaV-3 also has a large, GC-rich intergenic region between p6 (ORF 2) and p5 (ORF 3) that is not characteristic of members of the family Closteroviridae.…”

Section: Figurementioning

confidence: 99%

Grapevine Leafroll Disease and Associated Viruses: A Unique Pathosystem

Naidu

Maree

Burger

2015

Annu. Rev. Phytopathol.

101

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Grapevine leafroll is the most complex and intriguing viral disease of grapevine (Vitis spp.). Several monopartite closteroviruses (family Closteroviridae) from grapevines have been molecularly characterized, yet their role in disease etiology is not completely resolved. Hence, these viruses are currently designated under the umbrella term of Grapevine leafroll-associated viruses (GLRaVs). This review examines our current understanding of the genetically divergent GLRaVs and highlights the emerging picture of several unique aspects of the leafroll disease pathosystem. A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease. In addition, grapevine-infecting closteroviruses have a great potential as designer viruses to pursue functional genomics and for the rational design of novel disease intervention strategies in this agriculturally important perennial fruit crop.

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Grapevine leafroll-associated virus 7

Rwahnih

Saldarelli

Rowhani

2017

Grapevine Viruses: Molecular Biology, Diagnostics and Management

View full text Add to dashboard Cite

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.

show abstract

A divergent variant of Grapevine leafroll-associated virus 3is present in California

Cited by 21 publications

References 16 publications

Grapevine leafroll-associated virus 3

Grapevine leafroll-associated virus 3

Grapevine Leafroll Disease and Associated Viruses: A Unique Pathosystem

Grapevine leafroll-associated virus 7

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