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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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Geospatial and clustering analyses of GLRaV-3 variants in the Napa Valley.Images A through C illustrate results for GLRaV-3a, -3b and -3c, respectively; spatial distribution patterns for each variant are shown using interpolation data. The colored gradient and the corresponding values for spatial distribution represent the proportion for a given GLRaV-3 variant compared to the total number of GLRaV present in the tested block. The red dots indicate localities with statistically supported high incidence (p<0.01) of a particular variant in relationship to the remaining sample set. Image D shows all blocks positive for at least one GLRaV-3 variant. Each grid box represents 1 km2.
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pone-0026227-g003: Geospatial and clustering analyses of GLRaV-3 variants in the Napa Valley.Images A through C illustrate results for GLRaV-3a, -3b and -3c, respectively; spatial distribution patterns for each variant are shown using interpolation data. The colored gradient and the corresponding values for spatial distribution represent the proportion for a given GLRaV-3 variant compared to the total number of GLRaV present in the tested block. The red dots indicate localities with statistically supported high incidence (p<0.01) of a particular variant in relationship to the remaining sample set. Image D shows all blocks positive for at least one GLRaV-3 variant. Each grid box represents 1 km2.

Mentions: Based on the Hot-Spot Analysis, the distribution of GLRaV-3 variants in Napa Valley was variable. GLRaV-3a was more frequent in blocks in the northern section (Z>2.78, P<0.01), while -3b had higher prevalence in the central areas (Z>2.78, P<0.01). However, there were no statistically supported blocks with high or low -3c, reflecting the high frequency of -3c across the entire sample set. Figure 3 shows the geographical location of the blocks with high frequency. The interpolation data in the same figure helps illustrate the frequency of occurrence for each variant in a given area. Variants -3d and -3e were not widely distributed across the region to run the analysis, -3d was limited to one block and -3e was found in two pairs of neighboring blocks (21/22 and 43/44).


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)

Geospatial and clustering analyses of GLRaV-3 variants in the Napa Valley.Images A through C illustrate results for GLRaV-3a, -3b and -3c, respectively; spatial distribution patterns for each variant are shown using interpolation data. The colored gradient and the corresponding values for spatial distribution represent the proportion for a given GLRaV-3 variant compared to the total number of GLRaV present in the tested block. The red dots indicate localities with statistically supported high incidence (p<0.01) of a particular variant in relationship to the remaining sample set. Image D shows all blocks positive for at least one GLRaV-3 variant. Each grid box represents 1 km2.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0026227-g003: Geospatial and clustering analyses of GLRaV-3 variants in the Napa Valley.Images A through C illustrate results for GLRaV-3a, -3b and -3c, respectively; spatial distribution patterns for each variant are shown using interpolation data. The colored gradient and the corresponding values for spatial distribution represent the proportion for a given GLRaV-3 variant compared to the total number of GLRaV present in the tested block. The red dots indicate localities with statistically supported high incidence (p<0.01) of a particular variant in relationship to the remaining sample set. Image D shows all blocks positive for at least one GLRaV-3 variant. Each grid box represents 1 km2.
Mentions: Based on the Hot-Spot Analysis, the distribution of GLRaV-3 variants in Napa Valley was variable. GLRaV-3a was more frequent in blocks in the northern section (Z>2.78, P<0.01), while -3b had higher prevalence in the central areas (Z>2.78, P<0.01). However, there were no statistically supported blocks with high or low -3c, reflecting the high frequency of -3c across the entire sample set. Figure 3 shows the geographical location of the blocks with high frequency. The interpolation data in the same figure helps illustrate the frequency of occurrence for each variant in a given area. Variants -3d and -3e were not widely distributed across the region to run the analysis, -3d was limited to one block and -3e was found in two pairs of neighboring blocks (21/22 and 43/44).

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