Characterization and comparison of the full 3' and 5' untranslated genomic regions of diverse isolates of infectious salmon anaemia virus by using a rapid and universal method.
Identifieur interne : 000543 ( Main/Exploration ); précédent : 000542; suivant : 000544Characterization and comparison of the full 3' and 5' untranslated genomic regions of diverse isolates of infectious salmon anaemia virus by using a rapid and universal method.
Auteurs : Mickael Fourrier [Royaume-Uni] ; Sandra Heuser ; Eann Munro ; Mike SnowSource :
- Journal of virological methods [ 1879-0984 ] ; 2011.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Amorces ADN (génétique), Analyse de séquence d'ADN, Animaux, Canada, Données de séquences moléculaires, Isavirus (génétique), Isavirus (isolement et purification), Norvège, Réaction de polymérisation en chaîne (), Régions 3' non traduites, Régions 5' non traduites, Saumon (virologie), Similitude de séquences d'acides nucléiques, Séquence conservée, Séquence nucléotidique, Écosse.
- MESH :
- génétique : ARN viral, Amorces ADN, Isavirus.
- isolement et purification : Isavirus.
- virologie : Saumon.
- Analyse de séquence d'ADN, Animaux, Canada, Données de séquences moléculaires, Norvège, Réaction de polymérisation en chaîne, Régions 3' non traduites, Régions 5' non traduites, Similitude de séquences d'acides nucléiques, Séquence conservée, Séquence nucléotidique, Écosse.
- Wicri :
English descriptors
- KwdEn :
- 3' Untranslated Regions, 5' Untranslated Regions, Animals, Base Sequence, Canada, Conserved Sequence, DNA Primers (genetics), Isavirus (genetics), Isavirus (isolation & purification), Molecular Sequence Data, Norway, Polymerase Chain Reaction (methods), RNA, Viral (genetics), Salmon (virology), Scotland, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid.
- MESH :
- chemical , genetics : DNA Primers, RNA, Viral.
- chemical : 3' Untranslated Regions, 5' Untranslated Regions.
- geographic : Canada, Norway, Scotland.
- genetics : Isavirus.
- isolation & purification : Isavirus.
- methods : Polymerase Chain Reaction.
- virology : Salmon.
- Animals, Base Sequence, Conserved Sequence, Molecular Sequence Data, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid.
Abstract
The 3' and 5' untranslated regions (UTRs) of the gene segments of orthomyxoviruses interact closely with the polymerase complex and are important for viral replication and transcription regulation. Despite this, the 3' and 5' RNA UTRs of the infectious salmon anaemia virus (ISAV) genome have only been partially characterized and little is known about the level of conservation between different virus subtypes. This report details for the first time, the adaptation of a rapid method for the simultaneous characterization of the 3' and 5' UTRs of each viral segment of ISAV. This was achieved through self circularization of segments using T4 RNA ligase, followed by PCR and sequencing. Dephosphorylation of 5' ends using tobacco acid pyrophosphatase (TAP) proved to be a specific requirement for ligation of ISAV ends which was not essential for characterization of influenza virus in a similar manner. The development of universal primers facilitated the characterization of 4 genetically distinct ISAV isolates from Canada, Norway and Scotland. Comparison of the UTR regions revealed a similarity in organization and presence of conserved terminal sequences as reported for other orthomyxoviruses. Interestingly, the 3' ends of ISAV segments including segments 1, 5 and 6, were shorter and 5' UTRs generally longer than in their influenza counterparts.
DOI: 10.1016/j.jviromet.2011.03.023
PubMed: 21458495
Affiliations:
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Le document en format XML
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qualifier="isolation & purification" xml:lang="en"><term>Isavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Isavirus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Saumon</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Salmon</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Conserved Sequence</term><term>Molecular Sequence Data</term><term>Sequence Analysis, DNA</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Canada</term><term>Données de séquences moléculaires</term><term>Norvège</term><term>Réaction de polymérisation en chaîne</term><term>Régions 3' non traduites</term><term>Régions 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Despite this, the 3' and 5' RNA UTRs of the infectious salmon anaemia virus (ISAV) genome have only been partially characterized and little is known about the level of conservation between different virus subtypes. This report details for the first time, the adaptation of a rapid method for the simultaneous characterization of the 3' and 5' UTRs of each viral segment of ISAV. This was achieved through self circularization of segments using T4 RNA ligase, followed by PCR and sequencing. Dephosphorylation of 5' ends using tobacco acid pyrophosphatase (TAP) proved to be a specific requirement for ligation of ISAV ends which was not essential for characterization of influenza virus in a similar manner. The development of universal primers facilitated the characterization of 4 genetically distinct ISAV isolates from Canada, Norway and Scotland. Comparison of the UTR regions revealed a similarity in organization and presence of conserved terminal sequences as reported for other orthomyxoviruses. Interestingly, the 3' ends of ISAV segments including segments 1, 5 and 6, were shorter and 5' UTRs generally longer than in their influenza counterparts.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21458495</PMID><DateCompleted><Year>2011</Year><Month>08</Month><Day>23</Day></DateCompleted><DateRevised><Year>2011</Year><Month>05</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0984</ISSN><JournalIssue CitedMedium="Internet"><Volume>174</Volume><Issue>1-2</Issue><PubDate><Year>2011</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Journal of virological methods</Title><ISOAbbreviation>J. Virol. Methods</ISOAbbreviation></Journal><ArticleTitle>Characterization and comparison of the full 3' and 5' untranslated genomic regions of diverse isolates of infectious salmon anaemia virus by using a rapid and universal method.</ArticleTitle><Pagination><MedlinePgn>136-43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jviromet.2011.03.023</ELocationID><Abstract><AbstractText>The 3' and 5' untranslated regions (UTRs) of the gene segments of orthomyxoviruses interact closely with the polymerase complex and are important for viral replication and transcription regulation. Despite this, the 3' and 5' RNA UTRs of the infectious salmon anaemia virus (ISAV) genome have only been partially characterized and little is known about the level of conservation between different virus subtypes. This report details for the first time, the adaptation of a rapid method for the simultaneous characterization of the 3' and 5' UTRs of each viral segment of ISAV. This was achieved through self circularization of segments using T4 RNA ligase, followed by PCR and sequencing. Dephosphorylation of 5' ends using tobacco acid pyrophosphatase (TAP) proved to be a specific requirement for ligation of ISAV ends which was not essential for characterization of influenza virus in a similar manner. The development of universal primers facilitated the characterization of 4 genetically distinct ISAV isolates from Canada, Norway and Scotland. Comparison of the UTR regions revealed a similarity in organization and presence of conserved terminal sequences as reported for other orthomyxoviruses. Interestingly, the 3' ends of ISAV segments including segments 1, 5 and 6, were shorter and 5' UTRs generally longer than in their influenza counterparts.</AbstractText><CopyrightInformation>Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fourrier</LastName><ForeName>Mickael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Marine Scotland, Marine Laboratory, Aberdeen, Scotland, UK. m.fourrier@marlab.ac.uk</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heuser</LastName><ForeName>Sandra</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Munro</LastName><ForeName>Eann</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Snow</LastName><ForeName>Mike</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>03</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Virol 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PubStatus="received"><Year>2010</Year><Month>10</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2011</Year><Month>03</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>03</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>8</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21458495</ArticleId><ArticleId IdType="pii">S0166-0934(11)00114-5</ArticleId><ArticleId IdType="doi">10.1016/j.jviromet.2011.03.023</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><noCountry><name sortKey="Heuser, Sandra" sort="Heuser, Sandra" uniqKey="Heuser S" first="Sandra" last="Heuser">Sandra Heuser</name><name sortKey="Munro, Eann" sort="Munro, Eann" uniqKey="Munro E" first="Eann" last="Munro">Eann Munro</name><name sortKey="Snow, Mike" sort="Snow, Mike" uniqKey="Snow M" first="Mike" last="Snow">Mike Snow</name></noCountry><country name="Royaume-Uni"><noRegion><name sortKey="Fourrier, Mickael" sort="Fourrier, Mickael" uniqKey="Fourrier M" first="Mickael" last="Fourrier">Mickael Fourrier</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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