Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3

Chooi, Kar Mun; Cohen, Daniel; Pearson, M. N.

doi:10.1016/j.jviromet.2012.12.018

Cited by 22 publications

(32 citation statements)

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“…The detection of GLRaV‐3 isolates was carried out by combining a multiplex RT‐PCR protocol with the partial sequencing of two genomic regions, and allowed the identification in Galicia of viral variants from four of the main six currently recognized phylogenetic groups (groups I to VI; Bester et al ., ; Chooi et al ., ,b). The distribution of the GLRaV‐3 isolates in the five selected vineyards is differential, reflecting the different vines and the cultivation history at each particular vineyard.…”

Section: Discussionmentioning

confidence: 99%

“…In another survey in New Zealand, groups I and VI were predominant in germplasm banks and in commercial vineyards (Chooi et al ., ). Phylogenetic analysis of the CP region from the set of 185 GenBank isolates showed that group I variants are the most frequent (57·8%), followed by group II (24·3%) and group III (14%), although the representation of GLRaV‐3 variants in the databases could be biased as the tools to detect group VI variants were only recently developed (Sharma et al ., ; Bester et al ., ; Chooi et al ., ,b) and divergent variants are probably underrepresented (Seah et al ., ; Goszczynski, ). Groups I and II were the most common in Galicia, as apparently is the case in the rest of the world.…”

Section: Discussionmentioning

confidence: 99%

“…After extraction, RNA was eluted in 50 lL RNase-free water and stored at À70°C until further use. For the GLRaV-3 variant specific analysis in the set of 98 samples, 80-100 mg of plant tissue (leaf petioles) were homogenized using TissueLyser II (QIAGEN) and processed according to the method described by Chooi et al (2013b). The quality and yield of all RNA extractions were determined using the ND-1000 spectrophotometer (NanoDrop Technologies).…”

Section: Total Rna Extractionmentioning

confidence: 99%

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Genetic analysis of Grapevine leafroll‐associated virus 3 population from Galicia, Spain

2015

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Grapevine leafroll‐associated virus 3 (GLRaV‐3; Ampelovirus, Closteroviridae) isolates from Galicia in northwestern Spain were selected to characterize their genetic diversity according to different factors (age, origin, location, variety, etc.). The vines belonged either to local white and red varieties autochthonous to Galicia or to varieties from other Spanish regions but widely used in Galicia. These GLRaV‐3 isolates came from different vineyards in Galicia located in coastal or inner areas. Multiplex RT‐PCR allowed the detection of isolates belonging to groups I, II, III–V and VI. Two genomic regions were studied in the isolates, the HSP70h and the capsid protein, using specific primers that allow the detection of variants from groups I to V. Some possible recombinants could be detected; however, multiple infections with different variants indicated that they were not genuine recombinants. No differences were found in the population structure considering variety or geographical factors. Isolates belonging to four groups were found in the distinct areas surveyed: groups I and II were the most common, followed by groups VI and III, as is the case in the rest of the world. In the same surveys, the presence of insect vectors for GLRaV‐3 was investigated and found lacking in inland areas but present in those with milder climate. Genetic analysis did not support isolation of the GLRaV‐3 isolates in Galicia, suggesting that the uncontrolled exchange of infected vines and/or rootstocks has been a major agent of virus spread.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Total Rna Extractionmentioning

confidence: 99%

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Genetic analysis of Grapevine leafroll‐associated virus 3 population from Galicia, Spain

2015

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“…Group I genetic variants were found to be dominant in a Chinese survey (Farooq et al, 2012), while in Portugal groups I and II were the most common (Gouveia et al, 2009). In a New Zealand study, group I and VI-like (similar to NZ2) variants occurred predominantly in a germplasm and commercial vineyard block, while the group VI variant was only found in high numbers in the germplasm block (Chooi et al, 2013b). …”

Section: Genetic Variants Of Glrav-3mentioning

confidence: 99%

“…The genomic RNA of GLRaV-3 is found to be heterogeneous and up to date six genetic variants of the virus have been reported (Jooste et al, 2010; Gouveia et al, 2011; Wang et al, 2011; Kumar et al, 2012). Due to this genomic variability, two different multiplex PCRs were described for the detection and differentiation of four and five of the genetic variant groups of GLRaV-3, respectively (Bester et al, 2012b; Chooi et al, 2012). Another approach to PCR is called immunocapture PCR (IC-PCR).…”

Section: Detectionmentioning

confidence: 99%

Grapevine leafroll-associated virus 3

Maree¹,

Almeida²,

Bester³

et al. 2013

Front. Microbiol.

Self Cite

203

187

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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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Grapevine leafroll-associated virus 7

Rwahnih

Saldarelli

Rowhani

2017

Grapevine Viruses: Molecular Biology, Diagnostics and Management

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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.

show abstract

Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3

Cited by 22 publications

References 50 publications

Genetic analysis of Grapevine leafroll‐associated virus 3 population from Galicia, Spain

Genetic analysis of Grapevine leafroll‐associated virus 3 population from Galicia, Spain

Grapevine leafroll-associated virus 3

Grapevine leafroll-associated virus 7

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