Occurrence of grapevine leafroll-associated virus complex in Napa Valley.
Identifieur interne : 000675 ( Main/Exploration ); précédent : 000674; suivant : 000676Occurrence of grapevine leafroll-associated virus complex in Napa Valley.
Auteurs : Abhineet M. Sharma [États-Unis] ; Jinbo Wang ; Siobain Duffy ; Siming Zhang ; Michelle K. Wong ; Arash Rashed ; Monica L. Cooper ; Kent M. Daane ; Rodrigo P P. AlmeidaSource :
- PloS one [ 1932-6203 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- isolement et purification : Virus à ARN.
- virologie : Vitis.
- Californie, Fonctions de vraisemblance, Phylogenèse, Virus à ARN.
English descriptors
- KwdEn :
- MESH :
- geographic : California.
- classification : RNA Viruses.
- isolation & purification : RNA Viruses.
- virology : Vitis.
- Likelihood Functions, Phylogeny.
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.
DOI: 10.1371/journal.pone.0026227
PubMed: 22039446
PubMed Central: PMC3198396
Affiliations:
Links toward previous steps (curation, corpus...)
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Sharma</name><affiliation wicri:level="2"><nlm:affiliation>Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Environmental Science, Policy and Management, University of California, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Wang, Jinbo" sort="Wang, Jinbo" uniqKey="Wang J" first="Jinbo" last="Wang">Jinbo Wang</name></author><author><name sortKey="Duffy, Siobain" sort="Duffy, Siobain" uniqKey="Duffy S" first="Siobain" last="Duffy">Siobain Duffy</name></author><author><name sortKey="Zhang, Siming" sort="Zhang, Siming" uniqKey="Zhang S" first="Siming" last="Zhang">Siming Zhang</name></author><author><name sortKey="Wong, Michelle K" sort="Wong, Michelle K" uniqKey="Wong M" first="Michelle K" last="Wong">Michelle K. Wong</name></author><author><name sortKey="Rashed, Arash" sort="Rashed, Arash" uniqKey="Rashed A" first="Arash" last="Rashed">Arash Rashed</name></author><author><name sortKey="Cooper, Monica L" sort="Cooper, Monica L" uniqKey="Cooper M" first="Monica L" last="Cooper">Monica L. Cooper</name></author><author><name sortKey="Daane, Kent M" sort="Daane, Kent M" uniqKey="Daane K" first="Kent M" last="Daane">Kent M. Daane</name></author><author><name sortKey="Almeida, Rodrigo P P" sort="Almeida, Rodrigo P P" uniqKey="Almeida R" first="Rodrigo P P" last="Almeida">Rodrigo P P. 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Sharma</name><affiliation wicri:level="2"><nlm:affiliation>Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Environmental Science, Policy and Management, University of California, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Wang, Jinbo" sort="Wang, Jinbo" uniqKey="Wang J" first="Jinbo" last="Wang">Jinbo Wang</name></author><author><name sortKey="Duffy, Siobain" sort="Duffy, Siobain" uniqKey="Duffy S" first="Siobain" last="Duffy">Siobain Duffy</name></author><author><name sortKey="Zhang, Siming" sort="Zhang, Siming" uniqKey="Zhang S" first="Siming" last="Zhang">Siming Zhang</name></author><author><name sortKey="Wong, Michelle K" sort="Wong, Michelle K" uniqKey="Wong M" first="Michelle K" last="Wong">Michelle K. Wong</name></author><author><name sortKey="Rashed, Arash" sort="Rashed, Arash" uniqKey="Rashed A" first="Arash" last="Rashed">Arash Rashed</name></author><author><name sortKey="Cooper, Monica L" sort="Cooper, Monica L" uniqKey="Cooper M" first="Monica L" last="Cooper">Monica L. Cooper</name></author><author><name sortKey="Daane, Kent M" sort="Daane, Kent M" uniqKey="Daane K" first="Kent M" last="Daane">Kent M. Daane</name></author><author><name sortKey="Almeida, Rodrigo P P" sort="Almeida, Rodrigo P P" uniqKey="Almeida R" first="Rodrigo P P" last="Almeida">Rodrigo P P. Almeida</name></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>California (MeSH)</term><term>Likelihood Functions (MeSH)</term><term>Phylogeny (MeSH)</term><term>RNA Viruses (classification)</term><term>RNA Viruses (isolation & purification)</term><term>Vitis (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Californie (MeSH)</term><term>Fonctions de vraisemblance (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Virus à ARN (classification)</term><term>Virus à ARN (isolement et purification)</term><term>Vitis (virologie)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>California</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>RNA Viruses</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>RNA Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus à ARN</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Likelihood Functions</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Californie</term><term>Fonctions de vraisemblance</term><term>Phylogenèse</term><term>Virus à ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22039446</PMID><DateCompleted><Year>2012</Year><Month>02</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>10</Issue><PubDate><Year>2011</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Occurrence of grapevine leafroll-associated virus complex in Napa Valley.</ArticleTitle><Pagination><MedlinePgn>e26227</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0026227</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sharma</LastName><ForeName>Abhineet M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jinbo</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Duffy</LastName><ForeName>Siobain</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Siming</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Michelle K</ForeName><Initials>MK</Initials></Author><Author ValidYN="Y"><LastName>Rashed</LastName><ForeName>Arash</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Cooper</LastName><ForeName>Monica L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Daane</LastName><ForeName>Kent M</ForeName><Initials>KM</Initials></Author><Author ValidYN="Y"><LastName>Almeida</LastName><ForeName>Rodrigo P P</ForeName><Initials>RP</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>10</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS 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IdType="pubmed">21391825</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Almeida, Rodrigo P P" sort="Almeida, Rodrigo P P" uniqKey="Almeida R" first="Rodrigo P P" last="Almeida">Rodrigo P P. Almeida</name><name sortKey="Cooper, Monica L" sort="Cooper, Monica L" uniqKey="Cooper M" first="Monica L" last="Cooper">Monica L. Cooper</name><name sortKey="Daane, Kent M" sort="Daane, Kent M" uniqKey="Daane K" first="Kent M" last="Daane">Kent M. Daane</name><name sortKey="Duffy, Siobain" sort="Duffy, Siobain" uniqKey="Duffy S" first="Siobain" last="Duffy">Siobain Duffy</name><name sortKey="Rashed, Arash" sort="Rashed, Arash" uniqKey="Rashed A" first="Arash" last="Rashed">Arash Rashed</name><name sortKey="Wang, Jinbo" sort="Wang, Jinbo" uniqKey="Wang J" first="Jinbo" last="Wang">Jinbo Wang</name><name sortKey="Wong, Michelle K" sort="Wong, Michelle K" uniqKey="Wong M" first="Michelle K" last="Wong">Michelle K. Wong</name><name sortKey="Zhang, Siming" sort="Zhang, Siming" uniqKey="Zhang S" first="Siming" last="Zhang">Siming Zhang</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Sharma, Abhineet M" sort="Sharma, Abhineet M" uniqKey="Sharma A" first="Abhineet M" last="Sharma">Abhineet M. Sharma</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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