Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.
Identifieur interne : 000041 ( Main/Corpus ); précédent : 000040; suivant : 000042Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.
Auteurs : Dominik M. Meinel ; Susanne Heinzinger ; Ute Eberle ; Nikolaus Ackermann ; Katharina Schönberger ; Andreas SingSource :
- Infection [ 1439-0973 ] ; 2018.
English descriptors
- KwdEn :
- Genome, Viral, Germany, Humans, 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
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.
DOI: 10.1007/s15010-017-1091-3
PubMed: 29086356
Links to Exploration step
pubmed:29086356Le document en format XML
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<author><name sortKey="Heinzinger, Susanne" sort="Heinzinger, Susanne" uniqKey="Heinzinger S" first="Susanne" last="Heinzinger">Susanne Heinzinger</name>
<affiliation><nlm:affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</nlm:affiliation>
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<author><name sortKey="Eberle, Ute" sort="Eberle, Ute" uniqKey="Eberle U" first="Ute" last="Eberle">Ute Eberle</name>
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<author><name sortKey="Schonberger, Katharina" sort="Schonberger, Katharina" uniqKey="Schonberger K" first="Katharina" last="Schönberger">Katharina Schönberger</name>
<affiliation><nlm:affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</nlm:affiliation>
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<author><name sortKey="Sing, Andreas" sort="Sing, Andreas" uniqKey="Sing A" first="Andreas" last="Sing">Andreas Sing</name>
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<author><name sortKey="Ackermann, Nikolaus" sort="Ackermann, Nikolaus" uniqKey="Ackermann N" first="Nikolaus" last="Ackermann">Nikolaus Ackermann</name>
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<author><name sortKey="Schonberger, Katharina" sort="Schonberger, Katharina" uniqKey="Schonberger K" first="Katharina" last="Schönberger">Katharina Schönberger</name>
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<series><title level="j">Infection</title>
<idno type="eISSN">1439-0973</idno>
<imprint><date when="2018" type="published">2018</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Viral</term>
<term>Germany</term>
<term>Humans</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="MESH" qualifier="diagnosis" xml:lang="en"><term>Influenza, Human</term>
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<keywords scheme="MESH" qualifier="economics" xml:lang="en"><term>Whole Genome Sequencing</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A Virus, H3N2 Subtype</term>
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<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Influenza A Virus, H3N2 Subtype</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Whole Genome Sequencing</term>
</keywords>
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<keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Influenza, Human</term>
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<front><div type="abstract" xml:lang="en">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.</div>
</front>
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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>
</DateRevised>
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<JournalIssue CitedMedium="Internet"><Volume>46</Volume>
<Issue>1</Issue>
<PubDate><Year>2018</Year>
<Month>Feb</Month>
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<Title>Infection</Title>
<ISOAbbreviation>Infection</ISOAbbreviation>
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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>
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<ForeName>Susanne</ForeName>
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<AffiliationInfo><Affiliation>Bavarian Health and Food Safety Authority, Veterinärstraße 2, 85764, Oberschleißheim, Germany.</Affiliation>
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<Language>eng</Language>
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<Agency>Bavarian State Ministry of Health and Care</Agency>
<Country></Country>
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<MeshHeading><DescriptorName UI="D053122" MajorTopicYN="N">Influenza A Virus, H3N2 Subtype</DescriptorName>
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<Keyword MajorTopicYN="N">Next-generation sequencing</Keyword>
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