Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.
Identifieur interne : 000551 ( PubMed/Corpus ); précédent : 000550; suivant : 000552Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.
Auteurs : George Gachara ; Samuel Symekher ; Michael Otieno ; Japheth Magana ; Benjamin Opot ; Wallace BulimoSource :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-7257 ] ; 2016.
English descriptors
- KwdEn :
- Evolution, Molecular, Genome, Viral, Humans, Influenza A Virus, H1N1 Subtype (genetics), Influenza A Virus, H1N1 Subtype (isolation & purification), Influenza, Human (epidemiology), Influenza, Human (transmission), Influenza, Human (virology), Kenya (epidemiology), Pandemics, Phylogeny, Sequence Analysis, RNA (methods).
- MESH :
- epidemiology : Influenza, Human, Kenya.
- genetics : Influenza A Virus, H1N1 Subtype.
- isolation & purification : Influenza A Virus, H1N1 Subtype.
- methods : Sequence Analysis, RNA.
- transmission : Influenza, Human.
- virology : Influenza, Human.
- Evolution, Molecular, Genome, Viral, Humans, Pandemics, Phylogeny.
Abstract
An influenza pandemic caused by a novel influenza virus A(H1N1)pdm09 spread worldwide in 2009 and is estimated to have caused between 151,700 and 575,400 deaths globally. While whole genome data on new virus enables a deeper insight in the pathogenesis, epidemiology, and drug sensitivities of the circulating viruses, there are relatively limited complete genetic sequences available for this virus from African countries. We describe herein the full genome analysis of influenza A(H1N1)pdm09 viruses isolated in Kenya between June 2009 and August 2010. A total of 40 influenza A(H1N1)pdm09 viruses isolated during the pandemic were selected. The segments from each isolate were amplified and directly sequenced. The resulting sequences of individual gene segments were concatenated and used for subsequent analysis. These were used to infer phylogenetic relationships and also to reconstruct the time of most recent ancestor, time of introduction into the country, rates of substitution and to estimate a time-resolved phylogeny. The Kenyan complete genome sequences clustered with globally distributed clade 2 and clade 7 sequences but local clade 2 viruses did not circulate beyond the introductory foci while clade 7 viruses disseminated country wide. The time of the most recent common ancestor was estimated between April and June 2009, and distinct clusters circulated during the pandemic. The complete genome had an estimated rate of nucleotide substitution of 4.9×10(-3) substitutions/site/year and greater diversity in surface expressed proteins was observed. We show that two clades of influenza A(H1N1)pdm09 virus were introduced into Kenya from the UK and the pandemic was sustained as a result of importations. Several closely related but distinct clusters co-circulated locally during the peak pandemic phase but only one cluster dominated in the late phase of the pandemic suggesting that it possessed greater adaptability.
DOI: 10.1016/j.meegid.2016.02.029
PubMed: 26921801
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pubmed:26921801Le document en format XML
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Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Magana, Japheth" sort="Magana, Japheth" uniqKey="Magana J" first="Japheth" last="Magana">Japheth Magana</name><affiliation><nlm:affiliation>Centre for Virus Research, KEMRI, Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Opot, Benjamin" sort="Opot, Benjamin" uniqKey="Opot B" first="Benjamin" last="Opot">Benjamin Opot</name><affiliation><nlm:affiliation>United States Army Medical Research Unit-Kenya, Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Bulimo, Wallace" sort="Bulimo, Wallace" uniqKey="Bulimo W" first="Wallace" last="Bulimo">Wallace Bulimo</name><affiliation><nlm:affiliation>United States Army Medical Research Unit-Kenya, Kenya.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:26921801</idno><idno type="pmid">26921801</idno><idno 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uniqKey="Otieno M" first="Michael" last="Otieno">Michael Otieno</name><affiliation><nlm:affiliation>Department of Medical Laboratory Sciences, Kenyatta University, Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Magana, Japheth" sort="Magana, Japheth" uniqKey="Magana J" first="Japheth" last="Magana">Japheth Magana</name><affiliation><nlm:affiliation>Centre for Virus Research, KEMRI, Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Opot, Benjamin" sort="Opot, Benjamin" uniqKey="Opot B" first="Benjamin" last="Opot">Benjamin Opot</name><affiliation><nlm:affiliation>United States Army Medical Research Unit-Kenya, Kenya.</nlm:affiliation></affiliation></author><author><name sortKey="Bulimo, Wallace" sort="Bulimo, Wallace" uniqKey="Bulimo W" first="Wallace" last="Bulimo">Wallace Bulimo</name><affiliation><nlm:affiliation>United States Army Medical Research Unit-Kenya, Kenya.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</title><idno type="eISSN">1567-7257</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Influenza A Virus, H1N1 Subtype (genetics)</term><term>Influenza A Virus, H1N1 Subtype (isolation & purification)</term><term>Influenza, Human (epidemiology)</term><term>Influenza, Human (transmission)</term><term>Influenza, Human (virology)</term><term>Kenya (epidemiology)</term><term>Pandemics</term><term>Phylogeny</term><term>Sequence Analysis, RNA (methods)</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Influenza, Human</term><term>Kenya</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Influenza A Virus, H1N1 Subtype</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Influenza, Human</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Pandemics</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An influenza pandemic caused by a novel influenza virus A(H1N1)pdm09 spread worldwide in 2009 and is estimated to have caused between 151,700 and 575,400 deaths globally. While whole genome data on new virus enables a deeper insight in the pathogenesis, epidemiology, and drug sensitivities of the circulating viruses, there are relatively limited complete genetic sequences available for this virus from African countries. We describe herein the full genome analysis of influenza A(H1N1)pdm09 viruses isolated in Kenya between June 2009 and August 2010. A total of 40 influenza A(H1N1)pdm09 viruses isolated during the pandemic were selected. The segments from each isolate were amplified and directly sequenced. The resulting sequences of individual gene segments were concatenated and used for subsequent analysis. These were used to infer phylogenetic relationships and also to reconstruct the time of most recent ancestor, time of introduction into the country, rates of substitution and to estimate a time-resolved phylogeny. The Kenyan complete genome sequences clustered with globally distributed clade 2 and clade 7 sequences but local clade 2 viruses did not circulate beyond the introductory foci while clade 7 viruses disseminated country wide. The time of the most recent common ancestor was estimated between April and June 2009, and distinct clusters circulated during the pandemic. The complete genome had an estimated rate of nucleotide substitution of 4.9×10(-3) substitutions/site/year and greater diversity in surface expressed proteins was observed. We show that two clades of influenza A(H1N1)pdm09 virus were introduced into Kenya from the UK and the pandemic was sustained as a result of importations. Several closely related but distinct clusters co-circulated locally during the peak pandemic phase but only one cluster dominated in the late phase of the pandemic suggesting that it possessed greater adaptability.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26921801</PMID><DateCompleted><Year>2017</Year><Month>07</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>04</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1567-7257</ISSN><JournalIssue CitedMedium="Internet"><Volume>40</Volume><PubDate><Year>2016</Year><Month>06</Month></PubDate></JournalIssue><Title>Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</Title><ISOAbbreviation>Infect. Genet. Evol.</ISOAbbreviation></Journal><ArticleTitle>Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.</ArticleTitle><Pagination><MedlinePgn>98-103</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1567-1348(16)30060-0</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.meegid.2016.02.029</ELocationID><Abstract><AbstractText>An influenza pandemic caused by a novel influenza virus A(H1N1)pdm09 spread worldwide in 2009 and is estimated to have caused between 151,700 and 575,400 deaths globally. While whole genome data on new virus enables a deeper insight in the pathogenesis, epidemiology, and drug sensitivities of the circulating viruses, there are relatively limited complete genetic sequences available for this virus from African countries. We describe herein the full genome analysis of influenza A(H1N1)pdm09 viruses isolated in Kenya between June 2009 and August 2010. A total of 40 influenza A(H1N1)pdm09 viruses isolated during the pandemic were selected. The segments from each isolate were amplified and directly sequenced. The resulting sequences of individual gene segments were concatenated and used for subsequent analysis. These were used to infer phylogenetic relationships and also to reconstruct the time of most recent ancestor, time of introduction into the country, rates of substitution and to estimate a time-resolved phylogeny. The Kenyan complete genome sequences clustered with globally distributed clade 2 and clade 7 sequences but local clade 2 viruses did not circulate beyond the introductory foci while clade 7 viruses disseminated country wide. The time of the most recent common ancestor was estimated between April and June 2009, and distinct clusters circulated during the pandemic. The complete genome had an estimated rate of nucleotide substitution of 4.9×10(-3) substitutions/site/year and greater diversity in surface expressed proteins was observed. We show that two clades of influenza A(H1N1)pdm09 virus were introduced into Kenya from the UK and the pandemic was sustained as a result of importations. Several closely related but distinct clusters co-circulated locally during the peak pandemic phase but only one cluster dominated in the late phase of the pandemic suggesting that it possessed greater adaptability.</AbstractText><CopyrightInformation>Copyright © 2016 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gachara</LastName><ForeName>George</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Department of Medical Laboratory Sciences, Kenyatta University, Kenya.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Symekher</LastName><ForeName>Samuel</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre for Virus Research, KEMRI, Kenya.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Otieno</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Medical Laboratory Sciences, Kenyatta University, Kenya.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magana</LastName><ForeName>Japheth</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Centre for Virus Research, KEMRI, Kenya.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Opot</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>United States Army Medical Research Unit-Kenya, Kenya.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bulimo</LastName><ForeName>Wallace</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>United States Army Medical Research Unit-Kenya, Kenya.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Infect Genet Evol</MedlineTA><NlmUniqueID>101084138</NlmUniqueID><ISSNLinking>1567-1348</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</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="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007251" MajorTopicYN="N">Influenza, Human</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="Y">epidemiology</QualifierName><QualifierName UI="Q000635" MajorTopicYN="N">transmission</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007630" MajorTopicYN="N">Kenya</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Influenza A(H1N1)pdm09</Keyword><Keyword MajorTopicYN="Y">Kenya</Keyword><Keyword MajorTopicYN="Y">Sequencing</Keyword><Keyword MajorTopicYN="Y">Whole genome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>12</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>02</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>02</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>2</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>7</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26921801</ArticleId><ArticleId IdType="pii">S1567-1348(16)30060-0</ArticleId><ArticleId IdType="doi">10.1016/j.meegid.2016.02.029</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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