Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development.
Identifieur interne : 000B72 ( PubMed/Curation ); précédent : 000B71; suivant : 000B73Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development.
Auteurs : Natalia Go I [Uruguay] ; Andrés Iriarte ; Victoria Comas ; Martín So Ora ; Pilar Moreno ; Gonzalo Moratorio ; Héctor Musto ; Juan CristinaSource :
- Virology journal [ 1743-422X ] ; 2012.
Descripteurs français
- KwdFr :
- Adaptation biologique, Codon, Grippe humaine (), Grippe humaine (virologie), Grippe humaine (épidémiologie), Humains, Mutation, Sous-type H1N1 du virus de la grippe A (génétique), Sous-type H1N1 du virus de la grippe A (immunologie), Sélection génétique, Vaccins antigrippaux (génétique), Vaccins antigrippaux (immunologie), Évolution moléculaire.
- MESH :
- génétique : Sous-type H1N1 du virus de la grippe A, Vaccins antigrippaux.
- immunologie : Sous-type H1N1 du virus de la grippe A, Vaccins antigrippaux.
- virologie : Grippe humaine.
- épidémiologie : Grippe humaine.
- Adaptation biologique, Codon, Grippe humaine, Humains, Mutation, Sélection génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Adaptation, Biological, Codon, Evolution, Molecular, Humans, Influenza A Virus, H1N1 Subtype (genetics), Influenza A Virus, H1N1 Subtype (immunology), Influenza Vaccines (genetics), Influenza Vaccines (immunology), Influenza, Human (epidemiology), Influenza, Human (prevention & control), Influenza, Human (virology), Mutation, Selection, Genetic.
- MESH :
- chemical , genetics : Influenza Vaccines.
- chemical , immunology : Influenza Vaccines.
- chemical : Codon.
- epidemiology : Influenza, Human.
- genetics : Influenza A Virus, H1N1 Subtype.
- immunology : Influenza A Virus, H1N1 Subtype.
- prevention & control : Influenza, Human.
- virology : Influenza, Human.
- Adaptation, Biological, Evolution, Molecular, Humans, Mutation, Selection, Genetic.
Abstract
Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed.
DOI: 10.1186/1743-422X-9-263
PubMed: 23134595
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Musto</name></author><author><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name></author></analytic><series><title level="j">Virology journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Biological</term><term>Codon</term><term>Evolution, Molecular</term><term>Humans</term><term>Influenza A Virus, H1N1 Subtype (genetics)</term><term>Influenza A Virus, H1N1 Subtype (immunology)</term><term>Influenza Vaccines (genetics)</term><term>Influenza Vaccines (immunology)</term><term>Influenza, Human (epidemiology)</term><term>Influenza, Human (prevention & control)</term><term>Influenza, Human (virology)</term><term>Mutation</term><term>Selection, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation biologique</term><term>Codon</term><term>Grippe humaine ()</term><term>Grippe humaine (virologie)</term><term>Grippe humaine (épidémiologie)</term><term>Humains</term><term>Mutation</term><term>Sous-type H1N1 du virus de la grippe A (génétique)</term><term>Sous-type H1N1 du virus de la grippe A (immunologie)</term><term>Sélection génétique</term><term>Vaccins antigrippaux (génétique)</term><term>Vaccins antigrippaux (immunologie)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Influenza Vaccines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="immunology" xml:lang="en"><term>Influenza Vaccines</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Sous-type H1N1 du virus de la grippe A</term><term>Vaccins antigrippaux</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Sous-type H1N1 du virus de la grippe A</term><term>Vaccins antigrippaux</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term></keywords><keywords scheme="MESH" qualifier="prevention & control" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Grippe humaine</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Grippe humaine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adaptation, Biological</term><term>Evolution, Molecular</term><term>Humans</term><term>Mutation</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adaptation biologique</term><term>Codon</term><term>Grippe humaine</term><term>Humains</term><term>Mutation</term><term>Sélection génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23134595</PMID><DateCompleted><Year>2013</Year><Month>06</Month><Day>19</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1743-422X</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><PubDate><Year>2012</Year><Month>Nov</Month><Day>08</Day></PubDate></JournalIssue><Title>Virology journal</Title><ISOAbbreviation>Virol. J.</ISOAbbreviation></Journal><ArticleTitle>Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development.</ArticleTitle><Pagination><MedlinePgn>263</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1743-422X-9-263</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Goñi</LastName><ForeName>Natalia</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iriarte</LastName><ForeName>Andrés</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Comas</LastName><ForeName>Victoria</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Soñora</LastName><ForeName>Martín</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Moreno</LastName><ForeName>Pilar</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Moratorio</LastName><ForeName>Gonzalo</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Musto</LastName><ForeName>Héctor</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Cristina</LastName><ForeName>Juan</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>11</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Virol J</MedlineTA><NlmUniqueID>101231645</NlmUniqueID><ISSNLinking>1743-422X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003062">Codon</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007252">Influenza Vaccines</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000220" MajorTopicYN="N">Adaptation, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003062" MajorTopicYN="N">Codon</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053118" MajorTopicYN="N">Influenza A Virus, H1N1 Subtype</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="Y">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007252" MajorTopicYN="N">Influenza Vaccines</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000276" MajorTopicYN="Y">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007251" MajorTopicYN="N">Influenza, Human</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000517" MajorTopicYN="Y">prevention & control</QualifierName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>02</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>11</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>11</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:23134595" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \
| NlmPubMed2Wicri -a PandemieGrippaleV1
| This area was generated with Dilib version V0.6.34. |  |