Evolutionary Aspects of Grapevine Virology

Dolja, Valerian V.; Meng, Bin; Martelli, G. P.

doi:10.1007/978-3-319-57706-7_32

Cited by 18 publications

(14 citation statements)

References 76 publications

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“…The genome of GLRaV-4 strains 4, 5, and 9 possesses two large gene modules, similar to other viruses in the family Closteroviridae (Fig. 1a) [1, 2]. The replication gene module (RGB), located towards 5′ end of the viral genome, consists of ORF 1a and ORF1b and occupies bulk of the virus genome of all three GLRaV-4 strains.…”

Section: Resultsmentioning

confidence: 99%

“…The replication gene module (RGB), located towards 5′ end of the viral genome, consists of ORF 1a and ORF1b and occupies bulk of the virus genome of all three GLRaV-4 strains. ORF1a encoding a polyprotein of ~ 260 kDa contained signature domains conserved in all closteroviruses [1, 2, 7, 10–13]. These domains are arranged in the polyprotein from N-terminus to C-terminus as follows: a papain-like leader protease (L-Pro) with conserved catalytic residues cysteine (C 444 ) and histidine (H 487 ) and a predicted cleavage site after glycine (G 504 ) [11, 32], a methyltransferase (MET, Pfam 01660, Pfam database 27.0) [33] and helicase (HEL, Pfam 01443).…”

Section: Resultsmentioning

confidence: 99%

“…( a ) Graphical representation (not drawn to scale) of the generalized genome map of GLRaV-4. Individual open reading frames (ORFs) are shown as boxes with associated protein designations used for closteroviruses [2] and numbered 1 to 6 above the diagram. Abbreviations of ORFs: L-Pro , papain-like leader protease; MET , methyltransferase domain; HEL , RNA helicase domain; AlkB , the AlkB domain; RdRp , RNA-dependent RNA polymerase; p5, 5 kDa protein; Hsp70h , heat shock protein 70 homolog; CP , coat protein; p23, 23 kDa protein.…”

Section: Resultsmentioning

confidence: 99%

“…Grapevine leafroll-associated viruses (GLRaVs, family Closteroviridae ) represent a group of highly complex and genetically distinct viruses infecting an agriculturally important perennial fruit crop [1]. Among the six distinct species of GLRaVs, GLRaV-1, − 3, − 4, and − 13 belong to the genus Ampelovirus , whereas GLRaV-2 and -7 belong, respectively, to the genus Closterovirus and genus Velarivirus [2]. Thus, the genus Ampelovirus contains higher number of GLRaVs compared to other genera in the family Closteroviridae .…”

Section: Introductionmentioning

confidence: 99%

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Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4

Adiputra

Jarugula

Naidu

2019

Virol J

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BackgroundGrapevine leafroll disease is one of the most economically important viral diseases affecting grape production worldwide. Grapevine leafroll-associated virus 4 (GLRaV-4, genus Ampelovirus, family Closteroviridae) is one of the six GLRaV species documented in grapevines (Vitis spp.). GLRaV-4 is made up of several distinct strains that were previously considered as putative species. Currently known strains of GLRaV-4 stand apart from other GLRaV species in lacking the minor coat protein.MethodsIn this study, the complete genome sequence of three strains of GLRaV-4 from Washington State vineyards was determined using a combination of high-throughput sequencing, Sanger sequencing and RACE. The genome sequence of these three strains was compared with corresponding sequences of GLRaV-4 strains reported from other grapevine-growing regions. Phylogenetic analysis and SimPlot and Recombination Detection Program (RDP) were used to identify putative recombination events among GLRaV-4 strains.ResultsThe genome size of GLRaV-4 strain 4 (isolate WAMR-4), strain 5 (isolate WASB-5) and strain 9 (isolate WALA-9) from Washington State vineyards was determined to be 13,824 nucleotides (nt), 13,820 nt, and 13,850 nt, respectively. Multiple sequence alignments showed that a 11-nt sequence (5′-GTAATCTTTTG-3′) towards 5′ terminus of the 5′ non-translated region (NTR) and a 10-nt sequence (5′-ATCCAGGACC-3′) towards 3′ end of the 3′ NTR are conserved among the currently known GLRaV-4 strains. LR-106 isolate of strain 4 and Estellat isolate of strain 6 were identified as recombinants due to putative recombination events involving divergent sequences in the ORF1a from strain 5 and strain Pr.ConclusionGenome-wide analyses showed for the first time that recombinantion can occur between distinct strains of GLRaV-4 resulting in the emergence of genetically stable and biologically successful chimeric viruses. Although the origin of recombinant strains of GLRaV-4 remains elusive, intra-species recombination could be playing an important role in shaping genetic diversity and evolution of the virus and modulating the biology and epidemiology of GLRaV-4 strains.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4

Adiputra

Jarugula

Naidu

2019

Virol J

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“…(); Dolja et al. () Blackberry virus X BVXXNot reported to be present in the EUVirus characterised in 2008, present in the US. It might be present but not reported in the EUTzanetakis et al.…”

Section: Appendix a – Viruses And Viroids Of Cydonia Mill Fragaria mentioning

confidence: 99%

List of non‐EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L.

Bragard¹,

Dehnen‐Schmutz²,

Gonthier³

et al. 2019

EFS2

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The Panel on Plant Health performed a listing of non-EU viruses and viroids (reported hereinafter as viruses) of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review identified 197 viruses infecting one or more of the host genera under consideration. Viruses were allocated into three categories (i) 86 non-EU viruses, known to occur only outside the EU or having only limited presence in the EU (i.e. reported in only one or few Member States (MSs), known to have restricted distribution, outbreaks), (ii) 97 viruses excluded at this stage from further categorisation efforts because they have significant presence in the EU (i.e. only reported so far from the EU or known to occur or be widespread in some MSs or frequently reported in the EU), (iii) 14 viruses with undetermined standing for which available information did not readily allow to allocate to one or the other of the two above groups. Comments provided by MSs during consultation phases were integrated in the opinion. The main knowledge gaps and uncertainties of this listing concern (i) the geographic distribution and prevalence of the viruses analysed, in particular when they were recently described; (ii) the taxonomy and biological status of a number of poorly characterised viruses; (iii) the host status of particular plant genera in relation to some viruses. The viruses considered as non-EU and those with undetermined standing will be categorised in the next steps to answer a specific mandate from the Commission to develop pest categorisations for non-EU viruses. This list does not imply a prejudice on future needs for a pest categorisation for other viruses which are excluded from the current categorisation efforts.

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Grapevine virus I, a putative new vitivirus detected in co-infection with grapevine virus G in New Zealand

et al. 2018

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A novel virus, with characteristics of viruses classified within the genus Vitivirus, was identified from a sample of Vitis vinifera cv. Chardonnay in New Zealand. The virus was detected with high throughput sequencing (small RNA and total RNA) and its sequence was confirmed by Sanger sequencing. Its genome is 7507 nt long (excluding the polyA tail) with an organisation similar to that described for other classifiable members of the genus Vitivirus. The closest relative of the virus is grapevine virus E (GVE) with 65% aa identity in ORF1 (65% nt identity) and 63% aa identity in the coat protein (66% nt identity). The relationship with GVE was confirmed with phylogenetic analysis, showing the new virus branching with GVE, Agave tequilina leaf virus and grapevine virus G (GVG). A limited survey revealed the presence of this virus in multiple plants from the same location where the newly described GVG was discovered, and in most cases both viruses were detected as co-infections. The genetic characteristics of this virus suggest it represents an isolate of a new species within the genus Vitivirus and following the current nomenclature, we propose the name "Grapevine virus I".

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Evolutionary Aspects of Grapevine Virology

Cited by 18 publications

References 76 publications

Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4

Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4

List of non‐EU viruses and viroids of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L.

Grapevine virus I, a putative new vitivirus detected in co-infection with grapevine virus G in New Zealand

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