Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines
A comparison of 15 field isolates of grapevine leafroll-associated virus 5 (GLRaV-5) was conducted, based on the analysis of nucleotide sequences of two viral ORFs: the coat protein (CP) and the heat shock protein 90 homolog (HSP90h). After amplification and cloning, the population of viral sequence...
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| Veröffentlicht in: | Archives of virology 2012-09, Vol.157 (9), p.1747-1765 |
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| creator | Esteves, Filipa Teixeira Santos, Margarida Eiras-Dias, José Eduardo Fonseca, Filomena |
| description | A comparison of 15 field isolates of grapevine leafroll-associated virus 5 (GLRaV-5) was conducted, based on the analysis of nucleotide sequences of two viral ORFs: the coat protein (CP) and the heat shock protein 90 homolog (HSP90h). After amplification and cloning, the population of viral sequences was analyzed for each isolate, revealing the within-isolate presence of sequence variants for both genes, with one or more major CP variants. Phylogenetic analysis showed the gene sequence variants detected to be exclusive for each isolate. These data, together with estimates of genetic diversity and positive selection, did not reveal evidence of vector-mediated transfer of GLRaV-5. Conversely, a strong effect of host vegetative propagation on divergence dynamics of GLRaV-5 variants was suggested by the isolates from this work The phylogeny of the CP gene further revealed clustering of GLRaV-5 isolates into eight lineages, four of which were detected in our study, revealing a higher diversity than previously described. The information gathered also contributes to firmly establishing GLRaV-5 as a cohesive taxonomic group within the ampeloviruses. |
| doi_str_mv | 10.1007/s00705-012-1371-2 |
| format | Article |
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After amplification and cloning, the population of viral sequences was analyzed for each isolate, revealing the within-isolate presence of sequence variants for both genes, with one or more major CP variants. Phylogenetic analysis showed the gene sequence variants detected to be exclusive for each isolate. These data, together with estimates of genetic diversity and positive selection, did not reveal evidence of vector-mediated transfer of GLRaV-5. Conversely, a strong effect of host vegetative propagation on divergence dynamics of GLRaV-5 variants was suggested by the isolates from this work The phylogeny of the CP gene further revealed clustering of GLRaV-5 isolates into eight lineages, four of which were detected in our study, revealing a higher diversity than previously described. The information gathered also contributes to firmly establishing GLRaV-5 as a cohesive taxonomic group within the ampeloviruses.</description><identifier>ISSN: 0304-8608</identifier><identifier>EISSN: 1432-8798</identifier><identifier>DOI: 10.1007/s00705-012-1371-2</identifier><identifier>PMID: 22692680</identifier><language>eng</language><publisher>Vienna: Springer Vienna</publisher><subject>Biological and medical sciences ; Biomedical and Life Sciences ; Biomedicine ; Cloning ; Closteroviridae - classification ; Closteroviridae - genetics ; Closteroviridae - isolation & purification ; Cluster Analysis ; Disease ; Fundamental and applied biological sciences. Psychology ; Genes ; Genetic Variation ; Genomes ; Grapevine leafroll-associated virus 5 ; Heat shock proteins ; Infectious Diseases ; Medical Microbiology ; Microbiology ; Miscellaneous ; Molecular Sequence Data ; Original Article ; Phylogenetics ; Phylogeny ; Portugal ; RNA polymerase ; RNA, Viral - genetics ; Sequence Analysis, DNA ; Sequence Homology ; Viral Proteins - genetics ; Virology ; Viruses ; Vitaceae ; Vitis - virology</subject><ispartof>Archives of virology, 2012-09, Vol.157 (9), p.1747-1765</ispartof><rights>Springer-Verlag 2012</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c435t-73c19f406da1c9c55c494a2c0b7bf34eb4b36ab126a8556c960fa8b980c1d3663</citedby><cites>FETCH-LOGICAL-c435t-73c19f406da1c9c55c494a2c0b7bf34eb4b36ab126a8556c960fa8b980c1d3663</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00705-012-1371-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00705-012-1371-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26300234$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22692680$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Esteves, Filipa</creatorcontrib><creatorcontrib>Teixeira Santos, Margarida</creatorcontrib><creatorcontrib>Eiras-Dias, José Eduardo</creatorcontrib><creatorcontrib>Fonseca, Filomena</creatorcontrib><title>Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines</title><title>Archives of virology</title><addtitle>Arch Virol</addtitle><addtitle>Arch Virol</addtitle><description>A comparison of 15 field isolates of grapevine leafroll-associated virus 5 (GLRaV-5) was conducted, based on the analysis of nucleotide sequences of two viral ORFs: the coat protein (CP) and the heat shock protein 90 homolog (HSP90h). After amplification and cloning, the population of viral sequences was analyzed for each isolate, revealing the within-isolate presence of sequence variants for both genes, with one or more major CP variants. Phylogenetic analysis showed the gene sequence variants detected to be exclusive for each isolate. These data, together with estimates of genetic diversity and positive selection, did not reveal evidence of vector-mediated transfer of GLRaV-5. Conversely, a strong effect of host vegetative propagation on divergence dynamics of GLRaV-5 variants was suggested by the isolates from this work The phylogeny of the CP gene further revealed clustering of GLRaV-5 isolates into eight lineages, four of which were detected in our study, revealing a higher diversity than previously described. The information gathered also contributes to firmly establishing GLRaV-5 as a cohesive taxonomic group within the ampeloviruses.</description><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cloning</subject><subject>Closteroviridae - classification</subject><subject>Closteroviridae - genetics</subject><subject>Closteroviridae - isolation & purification</subject><subject>Cluster Analysis</subject><subject>Disease</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>Grapevine leafroll-associated virus 5</subject><subject>Heat shock proteins</subject><subject>Infectious Diseases</subject><subject>Medical Microbiology</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Molecular Sequence Data</subject><subject>Original Article</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Portugal</subject><subject>RNA polymerase</subject><subject>RNA, Viral - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology</subject><subject>Viral Proteins - genetics</subject><subject>Virology</subject><subject>Viruses</subject><subject>Vitaceae</subject><subject>Vitis - virology</subject><issn>0304-8608</issn><issn>1432-8798</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqNkc-KFDEQxoMo7jj6AF4kIMJeovnX6W5vsrgqLKwHPTfV6aTJkknapDPLPoGvbcYZXREEL1VQ-X31VfgQes7oa0Zp-ybXQhtCGSdMtIzwB2jDpOCka_vuIdpQQSXpFO3O0JOcbyitA9E8Rmecq56rjm7Q92utS0omaIOjxXOCxexdMNgbsCl6TyDnqB2sZsJ7l0rGDXYBf45pLTP4t3g2waxO4z0kB6Pzbr3DECa8xKV4WF0MOK-p6LUkc1BaZ_xE5hRvw71dfooeWfDZPDv1Lfp6-f7LxUdydf3h08W7K6KlaFbSCs16K6magOleN42WvQSu6diOVkgzylEoGBlX0DWN0r2iFrqx76hmk1BKbNH5ce-S4rdi8jrsXNbGewgmljwwqnpWcfk_qGiV4qz2LXr5F3oTSwr1Iz8pwXjXy0qxI6VTzDkZOyzJ7SDdVWg4BDocAx1qoMMh0IFXzYvT5jLuzPRb8SvBCrw6AZA1eJsgaJfvOSUo5eJgzo9crk9hNunPE__l_gMNQbk0</recordid><startdate>20120901</startdate><enddate>20120901</enddate><creator>Esteves, Filipa</creator><creator>Teixeira Santos, Margarida</creator><creator>Eiras-Dias, José Eduardo</creator><creator>Fonseca, Filomena</creator><general>Springer Vienna</general><general>Springer</general><general>Springer Nature B.V</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20120901</creationdate><title>Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines</title><author>Esteves, Filipa ; Teixeira Santos, Margarida ; Eiras-Dias, José Eduardo ; Fonseca, Filomena</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c435t-73c19f406da1c9c55c494a2c0b7bf34eb4b36ab126a8556c960fa8b980c1d3663</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Cloning</topic><topic>Closteroviridae - classification</topic><topic>Closteroviridae - genetics</topic><topic>Closteroviridae - isolation & purification</topic><topic>Cluster Analysis</topic><topic>Disease</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes</topic><topic>Genetic Variation</topic><topic>Genomes</topic><topic>Grapevine leafroll-associated virus 5</topic><topic>Heat shock proteins</topic><topic>Infectious Diseases</topic><topic>Medical Microbiology</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Molecular Sequence Data</topic><topic>Original Article</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Portugal</topic><topic>RNA polymerase</topic><topic>RNA, Viral - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology</topic><topic>Viral Proteins - genetics</topic><topic>Virology</topic><topic>Viruses</topic><topic>Vitaceae</topic><topic>Vitis - virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Esteves, Filipa</creatorcontrib><creatorcontrib>Teixeira Santos, Margarida</creatorcontrib><creatorcontrib>Eiras-Dias, José Eduardo</creatorcontrib><creatorcontrib>Fonseca, Filomena</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Archives of virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Esteves, Filipa</au><au>Teixeira Santos, Margarida</au><au>Eiras-Dias, José Eduardo</au><au>Fonseca, Filomena</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines</atitle><jtitle>Archives of virology</jtitle><stitle>Arch Virol</stitle><addtitle>Arch Virol</addtitle><date>2012-09-01</date><risdate>2012</risdate><volume>157</volume><issue>9</issue><spage>1747</spage><epage>1765</epage><pages>1747-1765</pages><issn>0304-8608</issn><eissn>1432-8798</eissn><abstract>A comparison of 15 field isolates of grapevine leafroll-associated virus 5 (GLRaV-5) was conducted, based on the analysis of nucleotide sequences of two viral ORFs: the coat protein (CP) and the heat shock protein 90 homolog (HSP90h). After amplification and cloning, the population of viral sequences was analyzed for each isolate, revealing the within-isolate presence of sequence variants for both genes, with one or more major CP variants. Phylogenetic analysis showed the gene sequence variants detected to be exclusive for each isolate. These data, together with estimates of genetic diversity and positive selection, did not reveal evidence of vector-mediated transfer of GLRaV-5. Conversely, a strong effect of host vegetative propagation on divergence dynamics of GLRaV-5 variants was suggested by the isolates from this work The phylogeny of the CP gene further revealed clustering of GLRaV-5 isolates into eight lineages, four of which were detected in our study, revealing a higher diversity than previously described. The information gathered also contributes to firmly establishing GLRaV-5 as a cohesive taxonomic group within the ampeloviruses.</abstract><cop>Vienna</cop><pub>Springer Vienna</pub><pmid>22692680</pmid><doi>10.1007/s00705-012-1371-2</doi><tpages>19</tpages></addata></record> |
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| subjects | Biological and medical sciences Biomedical and Life Sciences Biomedicine Cloning Closteroviridae - classification Closteroviridae - genetics Closteroviridae - isolation & purification Cluster Analysis Disease Fundamental and applied biological sciences. Psychology Genes Genetic Variation Genomes Grapevine leafroll-associated virus 5 Heat shock proteins Infectious Diseases Medical Microbiology Microbiology Miscellaneous Molecular Sequence Data Original Article Phylogenetics Phylogeny Portugal RNA polymerase RNA, Viral - genetics Sequence Analysis, DNA Sequence Homology Viral Proteins - genetics Virology Viruses Vitaceae Vitis - virology |
| title | Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines |
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