GrippeAllemagneV4, Main, Exploration, bibRecord, 000032

Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.

Identifieur interne : 000032 ( Main/Exploration ); précédent : 000031; suivant : 000033

Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.

Auteurs : Dominik M. Meinel [Allemagne] ; Susanne Heinzinger [Allemagne] ; Ute Eberle [Allemagne] ; Nikolaus Ackermann [Allemagne] ; Katharina Schönberger [Allemagne] ; Andreas Sing [Allemagne]

Source :

Infection [ 1439-0973 ] ; 2018.

RBID : pubmed:29086356

Descripteurs français

KwdFr :
- Allemagne (MeSH), Grippe humaine (diagnostic), Grippe humaine (virologie), Génome viral (MeSH), Humains (MeSH), Sous-type H3N2 du virus de la grippe A (génétique), Sous-type H3N2 du virus de la grippe A (isolement et purification), Sous-type H3N2 du virus de la grippe A (physiologie), Séquençage du génome entier (méthodes), Séquençage du génome entier (économie).
MESH :
- diagnostic : Grippe humaine.
- génétique : Sous-type H3N2 du virus de la grippe A.
- isolement et purification : Sous-type H3N2 du virus de la grippe A.
- méthodes : Séquençage du génome entier.
- physiologie : Sous-type H3N2 du virus de la grippe A.
- virologie : Grippe humaine.
- économie : Séquençage du génome entier.
- Allemagne, Génome viral, Humains.

English descriptors

KwdEn :
- Genome, Viral (MeSH), Germany (MeSH), Humans (MeSH), Influenza A Virus, H3N2 Subtype (genetics), Influenza A Virus, H3N2 Subtype (isolation & purification), Influenza A Virus, H3N2 Subtype (physiology), Influenza, Human (diagnosis), Influenza, Human (virology), Whole Genome Sequencing (economics), Whole Genome Sequencing (methods).
MESH :
- diagnosis : Influenza, Human.
- economics : Whole Genome Sequencing.
- genetics : Influenza A Virus, H3N2 Subtype.
- isolation & purification : Influenza A Virus, H3N2 Subtype.
- methods : Whole Genome Sequencing.
- physiology : Influenza A Virus, H3N2 Subtype.
- virology : Influenza, Human.
- Genome, Viral, Germany, Humans.

Abstract

OBJECTIVES

Influenza with its annual epidemic waves is a major cause of morbidity and mortality worldwide. However, only little whole genome data are available regarding the molecular epidemiology promoting our understanding of viral spread in human populations.

METHODS

We implemented a RT-PCR strategy starting from patient material to generate influenza A whole genome sequences for molecular epidemiological surveillance. Samples were obtained within the Bavarian Influenza Sentinel. The complete influenza virus genome was amplified by a one-tube multiplex RT-PCR and sequenced on an Illumina MiSeq.

RESULTS

We report whole genomic sequences for 50 influenza A H3N2 viruses, which was the predominating virus in the season 2014/15, directly from patient specimens. The dataset included random samples from Bavaria (Germany) throughout the influenza season and samples from three suspected transmission clusters. We identified the outbreak samples based on sequence identity. Whole genome sequencing (WGS) was superior in resolution compared to analysis of single segments or partial segment analysis. Additionally, we detected manifestation of substantial amounts of viral quasispecies in several patients, carrying mutations varying from the dominant virus in each patient.

CONCLUSION

Our rapid whole genome sequencing approach for influenza A virus shows that WGS can effectively be used to detect and understand outbreaks in large communities. Additionally, the genomic data provide in-depth details about the circulating virus within one season.

DOI: 10.1007/s15010-017-1091-3
PubMed: 29086356

Affiliations:

Allemagne

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 000047
to stream Main, to step Curation: 000047

Le document en format XML

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<series><title level="j">Infection</title>
<idno type="eISSN">1439-0973</idno>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Viral (MeSH)</term>
<term>Germany (MeSH)</term>
<term>Humans (MeSH)</term>
<term>Influenza A Virus, H3N2 Subtype (genetics)</term>
<term>Influenza A Virus, H3N2 Subtype (isolation & purification)</term>
<term>Influenza A Virus, H3N2 Subtype (physiology)</term>
<term>Influenza, Human (diagnosis)</term>
<term>Influenza, Human (virology)</term>
<term>Whole Genome Sequencing (economics)</term>
<term>Whole Genome Sequencing (methods)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Allemagne (MeSH)</term>
<term>Grippe humaine (diagnostic)</term>
<term>Grippe humaine (virologie)</term>
<term>Génome viral (MeSH)</term>
<term>Humains (MeSH)</term>
<term>Sous-type H3N2 du virus de la grippe A (génétique)</term>
<term>Sous-type H3N2 du virus de la grippe A (isolement et purification)</term>
<term>Sous-type H3N2 du virus de la grippe A (physiologie)</term>
<term>Séquençage du génome entier (méthodes)</term>
<term>Séquençage du génome entier (économie)</term>
</keywords>
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</keywords>
<keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Grippe humaine</term>
</keywords>
<keywords scheme="MESH" qualifier="economics" xml:lang="en"><term>Whole Genome Sequencing</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Whole Genome Sequencing</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Séquençage du génome entier</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Sous-type H3N2 du virus de la grippe A</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Grippe humaine</term>
</keywords>
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</keywords>
<keywords scheme="MESH" qualifier="économie" xml:lang="fr"><term>Séquençage du génome entier</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genome, Viral</term>
<term>Germany</term>
<term>Humans</term>
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<front><div type="abstract" xml:lang="en"><p><b>OBJECTIVES</b>
</p>
<p>Influenza with its annual epidemic waves is a major cause of morbidity and mortality worldwide. However, only little whole genome data are available regarding the molecular epidemiology promoting our understanding of viral spread in human populations.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>METHODS</b>
</p>
<p>We implemented a RT-PCR strategy starting from patient material to generate influenza A whole genome sequences for molecular epidemiological surveillance. Samples were obtained within the Bavarian Influenza Sentinel. The complete influenza virus genome was amplified by a one-tube multiplex RT-PCR and sequenced on an Illumina MiSeq.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>We report whole genomic sequences for 50 influenza A H3N2 viruses, which was the predominating virus in the season 2014/15, directly from patient specimens. The dataset included random samples from Bavaria (Germany) throughout the influenza season and samples from three suspected transmission clusters. We identified the outbreak samples based on sequence identity. Whole genome sequencing (WGS) was superior in resolution compared to analysis of single segments or partial segment analysis. Additionally, we detected manifestation of substantial amounts of viral quasispecies in several patients, carrying mutations varying from the dominant virus in each patient.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSION</b>
</p>
<p>Our rapid whole genome sequencing approach for influenza A virus shows that WGS can effectively be used to detect and understand outbreaks in large communities. Additionally, the genomic data provide in-depth details about the circulating virus within one season.</p>
</div>
</front>
</TEI>
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<DateCompleted><Year>2018</Year>
<Month>07</Month>
<Day>31</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
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<Month>Feb</Month>
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<Title>Infection</Title>
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<ArticleTitle>Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.</ArticleTitle>
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<Abstract><AbstractText Label="OBJECTIVES" NlmCategory="OBJECTIVE">Influenza with its annual epidemic waves is a major cause of morbidity and mortality worldwide. However, only little whole genome data are available regarding the molecular epidemiology promoting our understanding of viral spread in human populations.</AbstractText>
<AbstractText Label="METHODS" NlmCategory="METHODS">We implemented a RT-PCR strategy starting from patient material to generate influenza A whole genome sequences for molecular epidemiological surveillance. Samples were obtained within the Bavarian Influenza Sentinel. The complete influenza virus genome was amplified by a one-tube multiplex RT-PCR and sequenced on an Illumina MiSeq.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We report whole genomic sequences for 50 influenza A H3N2 viruses, which was the predominating virus in the season 2014/15, directly from patient specimens. The dataset included random samples from Bavaria (Germany) throughout the influenza season and samples from three suspected transmission clusters. We identified the outbreak samples based on sequence identity. Whole genome sequencing (WGS) was superior in resolution compared to analysis of single segments or partial segment analysis. Additionally, we detected manifestation of substantial amounts of viral quasispecies in several patients, carrying mutations varying from the dominant virus in each patient.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Our rapid whole genome sequencing approach for influenza A virus shows that WGS can effectively be used to detect and understand outbreaks in large communities. Additionally, the genomic data provide in-depth details about the circulating virus within one season.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Meinel</LastName>
<ForeName>Dominik M</ForeName>
<Initials>DM</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Heinzinger</LastName>
<ForeName>Susanne</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
</AffiliationInfo>
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<ForeName>Ute</ForeName>
<Initials>U</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Ackermann</LastName>
<ForeName>Nikolaus</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Schönberger</LastName>
<ForeName>Katharina</ForeName>
<Initials>K</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Sing</LastName>
<ForeName>Andreas</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany. andreas.sing@lgl.bayern.de.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>13-30</GrantID>
<Agency>Bavarian State Ministry of Health and Care</Agency>
<Country></Country>
</Grant>
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<ArticleDate DateType="Electronic"><Year>2017</Year>
<Month>10</Month>
<Day>31</Day>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005858" MajorTopicYN="N">Germany</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D053122" MajorTopicYN="N">Influenza A Virus, H3N2 Subtype</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName>
<QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName>
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<MeshHeading><DescriptorName UI="D007251" MajorTopicYN="N">Influenza, Human</DescriptorName>
<QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName>
<QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="N">Whole Genome Sequencing</DescriptorName>
<QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Epidemiology</Keyword>
<Keyword MajorTopicYN="N">Influenza A</Keyword>
<Keyword MajorTopicYN="N">NGS</Keyword>
<Keyword MajorTopicYN="N">Next-generation sequencing</Keyword>
<Keyword MajorTopicYN="N">Outbreak analysis</Keyword>
<Keyword MajorTopicYN="N">Quasispecies</Keyword>
<Keyword MajorTopicYN="N">Surveillance</Keyword>
<Keyword MajorTopicYN="N">WGS</Keyword>
<Keyword MajorTopicYN="N">Whole genome sequencing</Keyword>
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Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.

Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.

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