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Occurrence of grapevine leafroll-associated virus complex in Napa Valley.

Sharma AM, Wang J, Duffy S, Zhang S, Wong MK, Rashed A, Cooper ML, Daane KM, Almeida RP - PLoS ONE (2011)

Bottom Line: Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples.Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley.Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America.

ABSTRACT
Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n = 36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n = 134) were GLRaV positive. Of the positives, 81% (n = 109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n = 5), while the remaining samples (15%, n = 20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n = 306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.

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Maximum likelihood tree of a 428 bp segment of the CP gene of GLRaV-3 isolates from Napa Valley.Representative global isolates are in bold for reference. Individual sample number is listed in front of its respective block number (first number, before the dash), numbers after successive commas represent samples from the same block; longer spaces between blocks in the same line were occasionally used due to space limitations, and represent samples from other blocks. Phylogenetic clades were labeled based on Wang et al. (20) and this work. The tree is midpoint rooted for clarity of presentation and ≥70% branch support values are presented; non-supported branches were collapsed for clarity.
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pone-0026227-g002: Maximum likelihood tree of a 428 bp segment of the CP gene of GLRaV-3 isolates from Napa Valley.Representative global isolates are in bold for reference. Individual sample number is listed in front of its respective block number (first number, before the dash), numbers after successive commas represent samples from the same block; longer spaces between blocks in the same line were occasionally used due to space limitations, and represent samples from other blocks. Phylogenetic clades were labeled based on Wang et al. (20) and this work. The tree is midpoint rooted for clarity of presentation and ≥70% branch support values are presented; non-supported branches were collapsed for clarity.

Mentions: Seven well-supported GLRaV-3 phylogenetic clades were found in Napa Valley, in addition to isolate NZ-1 from New Zealand, which remained as the sole representative of that genetic clade (Figure 2). No evidence of recombination was found in the dataset, as previously observed for a larger fragment in the 3′ end of GLRaV-3 isolates (Wang et al. 2011). The grouping of isolates based on sequence data matched typing performed at the variant level, as mentioned above. GLRaV-3 variants may be divided into two major clades, one for which available diagnostic primer sets function well (-3a, -3c, -3d, -3b and -3g) and another for which a novel primer set (CP gene) was necessary (-3e and -3f and NZ-1; NZ-1 based on in silico analysis). Only one isolate of GLRaV-3f clade was found in this study, the same occurred with -3g, although that isolate grouped closely with a sequence from Chile (Cl817), which Engel et al. [24] and Wang et al. [20] found previously to belong to an independent and well supported clade. Variant -3d was previously found infecting plants in the Napa Valley [20]. Variants -3a, -3b and -3c correspond to groups I, II and III, respectively, according to Jooste et al. [25]. Additionally, for single infection plants, there was 100% concurrence between the results for the variant level typing and the results obtained from the sequencing data.


Occurrence of grapevine leafroll-associated virus complex in Napa Valley.

Sharma AM, Wang J, Duffy S, Zhang S, Wong MK, Rashed A, Cooper ML, Daane KM, Almeida RP - PLoS ONE (2011)

Maximum likelihood tree of a 428 bp segment of the CP gene of GLRaV-3 isolates from Napa Valley.Representative global isolates are in bold for reference. Individual sample number is listed in front of its respective block number (first number, before the dash), numbers after successive commas represent samples from the same block; longer spaces between blocks in the same line were occasionally used due to space limitations, and represent samples from other blocks. Phylogenetic clades were labeled based on Wang et al. (20) and this work. The tree is midpoint rooted for clarity of presentation and ≥70% branch support values are presented; non-supported branches were collapsed for clarity.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198396&req=5

pone-0026227-g002: Maximum likelihood tree of a 428 bp segment of the CP gene of GLRaV-3 isolates from Napa Valley.Representative global isolates are in bold for reference. Individual sample number is listed in front of its respective block number (first number, before the dash), numbers after successive commas represent samples from the same block; longer spaces between blocks in the same line were occasionally used due to space limitations, and represent samples from other blocks. Phylogenetic clades were labeled based on Wang et al. (20) and this work. The tree is midpoint rooted for clarity of presentation and ≥70% branch support values are presented; non-supported branches were collapsed for clarity.
Mentions: Seven well-supported GLRaV-3 phylogenetic clades were found in Napa Valley, in addition to isolate NZ-1 from New Zealand, which remained as the sole representative of that genetic clade (Figure 2). No evidence of recombination was found in the dataset, as previously observed for a larger fragment in the 3′ end of GLRaV-3 isolates (Wang et al. 2011). The grouping of isolates based on sequence data matched typing performed at the variant level, as mentioned above. GLRaV-3 variants may be divided into two major clades, one for which available diagnostic primer sets function well (-3a, -3c, -3d, -3b and -3g) and another for which a novel primer set (CP gene) was necessary (-3e and -3f and NZ-1; NZ-1 based on in silico analysis). Only one isolate of GLRaV-3f clade was found in this study, the same occurred with -3g, although that isolate grouped closely with a sequence from Chile (Cl817), which Engel et al. [24] and Wang et al. [20] found previously to belong to an independent and well supported clade. Variant -3d was previously found infecting plants in the Napa Valley [20]. Variants -3a, -3b and -3c correspond to groups I, II and III, respectively, according to Jooste et al. [25]. Additionally, for single infection plants, there was 100% concurrence between the results for the variant level typing and the results obtained from the sequencing data.

Bottom Line: Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples.Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley.Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America.

ABSTRACT
Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n = 36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n = 134) were GLRaV positive. Of the positives, 81% (n = 109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n = 5), while the remaining samples (15%, n = 20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n = 306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.

Show MeSH
Related in: MedlinePlus