Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer
Identifieur interne : 000F00 ( Main/Exploration ); précédent : 000E99; suivant : 000F01Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer
Auteurs : Makoto Kuroda [Japon] ; Harutaka Katano [Japon] ; Noriko Nakajima [Japon] ; Minoru Tobiume [Japon] ; Akira Ainai [Japon] ; Tsuyoshi Sekizuka [Japon] ; Hideki Hasegawa [Japon] ; Masato Tashiro [Japon] ; Yuko Sasaki [Japon] ; Yoshichika Arakawa [Japon] ; Satoru Hata [Japon] ; Masahide Watanabe [Japon] ; Tetsutaro Sata [Japon]Source :
- PLoS ONE [ 1932-6203 ] ; 2010.
Abstract
Pandemic 2009 influenza A virus (A/H1N1/2009) has emerged globally. In this study, we performed a comprehensive detection of potential pathogens by
Url:
DOI: 10.1371/journal.pone.0010256
PubMed: 20428231
PubMed Central: 2859049
Affiliations:
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Kantō</region></placeName></affiliation></author><author><name sortKey="Tobiume, Minoru" sort="Tobiume, Minoru" uniqKey="Tobiume M" first="Minoru" last="Tobiume">Minoru Tobiume</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Ainai, Akira" sort="Ainai, Akira" uniqKey="Ainai A" first="Akira" last="Ainai">Akira Ainai</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National 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Hasegawa</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Tashiro, Masato" sort="Tashiro, Masato" uniqKey="Tashiro M" first="Masato" last="Tashiro">Masato Tashiro</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Sasaki, Yuko" sort="Sasaki, Yuko" uniqKey="Sasaki Y" first="Yuko" last="Sasaki">Yuko Sasaki</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Arakawa, Yoshichika" sort="Arakawa, Yoshichika" uniqKey="Arakawa Y" first="Yoshichika" last="Arakawa">Yoshichika Arakawa</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Hata, Satoru" sort="Hata, Satoru" uniqKey="Hata S" first="Satoru" last="Hata">Satoru Hata</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano</wicri:regionArea><wicri:noRegion>Nagano</wicri:noRegion></affiliation></author><author><name sortKey="Watanabe, Masahide" sort="Watanabe, Masahide" uniqKey="Watanabe M" first="Masahide" last="Watanabe">Masahide 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type="wicri:Area/Main/Exploration">000F00</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by <italic>De Novo</italic> Sequencing Using a Next-Generation DNA Sequencer</title><author><name sortKey="Kuroda, Makoto" sort="Kuroda, Makoto" uniqKey="Kuroda M" first="Makoto" last="Kuroda">Makoto Kuroda</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Katano, Harutaka" sort="Katano, Harutaka" uniqKey="Katano H" first="Harutaka" last="Katano">Harutaka Katano</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Nakajima, Noriko" sort="Nakajima, Noriko" uniqKey="Nakajima N" first="Noriko" last="Nakajima">Noriko Nakajima</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Tobiume, Minoru" sort="Tobiume, Minoru" uniqKey="Tobiume M" first="Minoru" last="Tobiume">Minoru Tobiume</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Ainai, Akira" sort="Ainai, Akira" uniqKey="Ainai A" first="Akira" last="Ainai">Akira Ainai</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Sekizuka, Tsuyoshi" sort="Sekizuka, Tsuyoshi" uniqKey="Sekizuka T" first="Tsuyoshi" last="Sekizuka">Tsuyoshi Sekizuka</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Hasegawa, Hideki" sort="Hasegawa, Hideki" uniqKey="Hasegawa H" first="Hideki" last="Hasegawa">Hideki Hasegawa</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Tashiro, Masato" sort="Tashiro, Masato" uniqKey="Tashiro M" first="Masato" last="Tashiro">Masato Tashiro</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Sasaki, Yuko" sort="Sasaki, Yuko" uniqKey="Sasaki Y" first="Yuko" last="Sasaki">Yuko Sasaki</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Arakawa, Yoshichika" sort="Arakawa, Yoshichika" uniqKey="Arakawa Y" first="Yoshichika" last="Arakawa">Yoshichika Arakawa</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Hata, Satoru" sort="Hata, Satoru" uniqKey="Hata S" first="Satoru" last="Hata">Satoru Hata</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano</wicri:regionArea><wicri:noRegion>Nagano</wicri:noRegion></affiliation></author><author><name sortKey="Watanabe, Masahide" sort="Watanabe, Masahide" uniqKey="Watanabe M" first="Masahide" last="Watanabe">Masahide Watanabe</name><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Pathology, Nagano Red Cross Hospital, Nagano, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, Nagano Red Cross Hospital, Nagano</wicri:regionArea><wicri:noRegion>Nagano</wicri:noRegion></affiliation></author><author><name sortKey="Sata, Tetsutaro" sort="Sata, Tetsutaro" uniqKey="Sata T" first="Tetsutaro" last="Sata">Tetsutaro Sata</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Pathology, National Institute of Infectious Diseases, Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Pandemic 2009 influenza A virus (A/H1N1/2009) has emerged globally. In this study, we performed a comprehensive detection of potential pathogens by <italic>de novo</italic> sequencing using a next-generation DNA sequencer on total RNAs extracted from an autopsy lung of a patient who died of viral pneumonia with A/H1N1/2009. Among a total of 9.4×10<sup>6</sup> 40-mer short reads, more than 98% appeared to be human, while 0.85% were identified as A/H1N1/2009 (A/Nagano/RC1-L/2009(H1N1)). Suspected bacterial reads such as <italic>Streptococcus pneumoniae</italic> and other oral bacteria flora were very low at 0.005%, and a significant bacterial infection was not histologically observed. <italic>De novo</italic> assembly and read mapping analysis of A/Nagano/RC1-L/2009(H1N1) showed more than ×200 coverage on average, and revealed nucleotide heterogeneity on hemagglutinin as quasispecies, specifically at two amino acids (Gly<sub>172</sub>Glu and Gly<sub>239</sub>Asn of HA) located on the Sa and Ca2 antigenic sites, respectively. Gly239 and Asn239 on antigenic site Ca2 appeared to be minor amino acids compared with the highly distributed Asp239 in H1N1 HAs. This study demonstrated that <italic>de novo</italic> sequencing can comprehensively detect pathogens, and such in-depth investigation facilitates the identification of influenza A viral heterogeneity. To better characterize the A/H1N1/2009 virus, unbiased comprehensive techniques will be indispensable for the primary investigations of emerging infectious diseases.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Dawood, Fs" uniqKey="Dawood F">FS Dawood</name></author><author><name sortKey="Jain, S" uniqKey="Jain S">S Jain</name></author><author><name sortKey="Finelli, L" uniqKey="Finelli L">L Finelli</name></author><author><name sortKey="Shaw, Mw" uniqKey="Shaw M">MW Shaw</name></author><author><name sortKey="Lindstrom, S" uniqKey="Lindstrom S">S Lindstrom</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gill, Jr" uniqKey="Gill J">JR Gill</name></author><author><name sortKey="Sheng, Zm" uniqKey="Sheng Z">ZM Sheng</name></author><author><name sortKey="Ely, Sf" uniqKey="Ely S">SF Ely</name></author><author><name sortKey="Guinee, Dg" uniqKey="Guinee D">DG Guinee</name></author><author><name 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Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bao, H" uniqKey="Bao H">H Bao</name></author><author><name sortKey="Guo, H" uniqKey="Guo H">H Guo</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Zhou, R" uniqKey="Zhou R">R Zhou</name></author><author><name sortKey="Lu, X" uniqKey="Lu X">X Lu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement></list><tree><country name="Japon"><region name="Région de Kantō"><name sortKey="Kuroda, Makoto" sort="Kuroda, Makoto" uniqKey="Kuroda M" first="Makoto" last="Kuroda">Makoto Kuroda</name></region><name sortKey="Ainai, Akira" sort="Ainai, Akira" uniqKey="Ainai A" first="Akira" last="Ainai">Akira Ainai</name><name sortKey="Arakawa, Yoshichika" sort="Arakawa, Yoshichika" uniqKey="Arakawa Y" first="Yoshichika" last="Arakawa">Yoshichika Arakawa</name><name sortKey="Hasegawa, Hideki" sort="Hasegawa, Hideki" uniqKey="Hasegawa H" first="Hideki" last="Hasegawa">Hideki Hasegawa</name><name sortKey="Hata, Satoru" sort="Hata, Satoru" uniqKey="Hata S" first="Satoru" last="Hata">Satoru Hata</name><name sortKey="Katano, Harutaka" sort="Katano, Harutaka" uniqKey="Katano H" first="Harutaka" last="Katano">Harutaka Katano</name><name sortKey="Nakajima, Noriko" sort="Nakajima, Noriko" uniqKey="Nakajima N" first="Noriko" last="Nakajima">Noriko Nakajima</name><name sortKey="Sasaki, Yuko" sort="Sasaki, Yuko" uniqKey="Sasaki Y" first="Yuko" last="Sasaki">Yuko Sasaki</name><name sortKey="Sata, Tetsutaro" sort="Sata, Tetsutaro" uniqKey="Sata T" first="Tetsutaro" last="Sata">Tetsutaro Sata</name><name sortKey="Sekizuka, Tsuyoshi" sort="Sekizuka, Tsuyoshi" uniqKey="Sekizuka T" first="Tsuyoshi" last="Sekizuka">Tsuyoshi Sekizuka</name><name sortKey="Tashiro, Masato" sort="Tashiro, Masato" uniqKey="Tashiro M" first="Masato" last="Tashiro">Masato Tashiro</name><name sortKey="Tobiume, Minoru" sort="Tobiume, Minoru" uniqKey="Tobiume M" first="Minoru" last="Tobiume">Minoru Tobiume</name><name sortKey="Watanabe, Masahide" sort="Watanabe, Masahide" uniqKey="Watanabe M" first="Masahide" last="Watanabe">Masahide Watanabe</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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