Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The...
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| Veröffentlicht in: | Scientific reports 2013-09, Vol.3 (1), p.2468-2468, Article 2468 |
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| creator | Alquezar-Planas, David E. Mourier, Tobias Bruhn, Christian A. W. Hansen, Anders J. Vitcetz, Sarah Nathalie Mørk, Søren Gorodkin, Jan Nielsen, Hanne Abel Guo, Yan Sethuraman, Anand Paxinos, Ellen E. Shan, Tongling Delwart, Eric L. Nielsen, Lars P. |
| description | Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT®) sequencing. Subsequent “primer walking” combined with Sanger sequencing validated the
RS
platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described. |
| doi_str_mv | 10.1038/srep02468 |
| format | Article |
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RS
platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep02468</identifier><identifier>PMID: 24002378</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/1647/2163 ; 631/181/757 ; 631/208/182 ; 631/326/596/2142 ; Base Sequence ; Children ; DNA sequencing ; Gene mapping ; Genetic Variation ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humanities and Social Sciences ; Humans ; Metagenomics - methods ; Molecular Sequence Data ; multidisciplinary ; Next-generation sequencing ; Open Reading Frames ; Parainfluenza ; Parainfluenza Virus 4, Human - classification ; Parainfluenza Virus 4, Human - genetics ; Parainfluenza Virus 4, Human - isolation & purification ; Phylogeny ; Polymerase chain reaction ; Prevalence ; Respiratory tract ; Respiratory tract diseases ; Respiratory Tract Infections - epidemiology ; Respiratory Tract Infections - virology ; Science ; Secretions ; Sequence Alignment ; Strains (organisms) ; Viruses</subject><ispartof>Scientific reports, 2013-09, Vol.3 (1), p.2468-2468, Article 2468</ispartof><rights>The Author(s) 2013</rights><rights>Copyright Nature Publishing Group Sep 2013</rights><rights>Copyright © 2013, Macmillan Publishers Limited. All rights reserved 2013 Macmillan Publishers Limited. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c504t-84b6fbee1547ea07aba8b174846e4ad321c009633beac37eb893b07942bd6c123</citedby><cites>FETCH-LOGICAL-c504t-84b6fbee1547ea07aba8b174846e4ad321c009633beac37eb893b07942bd6c123</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760282/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760282/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24002378$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alquezar-Planas, David E.</creatorcontrib><creatorcontrib>Mourier, Tobias</creatorcontrib><creatorcontrib>Bruhn, Christian A. W.</creatorcontrib><creatorcontrib>Hansen, Anders J.</creatorcontrib><creatorcontrib>Vitcetz, Sarah Nathalie</creatorcontrib><creatorcontrib>Mørk, Søren</creatorcontrib><creatorcontrib>Gorodkin, Jan</creatorcontrib><creatorcontrib>Nielsen, Hanne Abel</creatorcontrib><creatorcontrib>Guo, Yan</creatorcontrib><creatorcontrib>Sethuraman, Anand</creatorcontrib><creatorcontrib>Paxinos, Ellen E.</creatorcontrib><creatorcontrib>Shan, Tongling</creatorcontrib><creatorcontrib>Delwart, Eric L.</creatorcontrib><creatorcontrib>Nielsen, Lars P.</creatorcontrib><title>Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT®) sequencing. Subsequent “primer walking” combined with Sanger sequencing validated the
RS
platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described.</description><subject>631/1647/2163</subject><subject>631/181/757</subject><subject>631/208/182</subject><subject>631/326/596/2142</subject><subject>Base Sequence</subject><subject>Children</subject><subject>DNA sequencing</subject><subject>Gene mapping</subject><subject>Genetic Variation</subject><subject>Genome, Viral</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Metagenomics - methods</subject><subject>Molecular Sequence Data</subject><subject>multidisciplinary</subject><subject>Next-generation sequencing</subject><subject>Open Reading Frames</subject><subject>Parainfluenza</subject><subject>Parainfluenza Virus 4, Human - classification</subject><subject>Parainfluenza Virus 4, Human - genetics</subject><subject>Parainfluenza Virus 4, Human - isolation & purification</subject><subject>Phylogeny</subject><subject>Polymerase chain reaction</subject><subject>Prevalence</subject><subject>Respiratory tract</subject><subject>Respiratory tract diseases</subject><subject>Respiratory Tract Infections - epidemiology</subject><subject>Respiratory Tract Infections - virology</subject><subject>Science</subject><subject>Secretions</subject><subject>Sequence Alignment</subject><subject>Strains (organisms)</subject><subject>Viruses</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkV1LHDEUhoNYqlgv-gck4I0K2-ZrZjI3gtj6AUJ70fY2JJkza2QnWZOZBf99z7K6bG0g5CR5zptz8hLymbMvnEn9tWRYMqFqvUcOBVPVTEgh9nfiA3JcyhPDUYlW8fYjORCKMSEbfUjKt1B8WkF-oamnlnYB4znEkd79vP-jaJ_TQDOUZch2TEgV8BnGkGKhUwlxvj5IsaMW5_gYckcxGxBGhA4wWtymIXjknieIHlM-kQ-9XRQ4fl2PyO-b77-u72YPP27vr68eZr5iapxp5ereAfBKNWBZY53VjjdKqxqU7aTgnrG2ltKB9bIBp1vpWNMq4bracyGPyOVGdzm5ATqPXWW7MMscBptfTLLB_HsTw6OZp5WRTc2EXgucvQrkhMWX0Qz4W7BY2AhpKoYryWRbK10hevoOfUpTjtie4bptlGK81kidbyifU0Hj-m0xnJm1m2brJrInu9VvyTfvELjYAAWv4hzyzpP_qf0FAQSrVA</recordid><startdate>20130902</startdate><enddate>20130902</enddate><creator>Alquezar-Planas, David E.</creator><creator>Mourier, Tobias</creator><creator>Bruhn, Christian A. 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W. ; Hansen, Anders J. ; Vitcetz, Sarah Nathalie ; Mørk, Søren ; Gorodkin, Jan ; Nielsen, Hanne Abel ; Guo, Yan ; Sethuraman, Anand ; Paxinos, Ellen E. ; Shan, Tongling ; Delwart, Eric L. ; Nielsen, Lars P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c504t-84b6fbee1547ea07aba8b174846e4ad321c009633beac37eb893b07942bd6c123</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>631/1647/2163</topic><topic>631/181/757</topic><topic>631/208/182</topic><topic>631/326/596/2142</topic><topic>Base Sequence</topic><topic>Children</topic><topic>DNA sequencing</topic><topic>Gene mapping</topic><topic>Genetic Variation</topic><topic>Genome, Viral</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Metagenomics - methods</topic><topic>Molecular Sequence Data</topic><topic>multidisciplinary</topic><topic>Next-generation sequencing</topic><topic>Open Reading Frames</topic><topic>Parainfluenza</topic><topic>Parainfluenza Virus 4, Human - classification</topic><topic>Parainfluenza Virus 4, Human - genetics</topic><topic>Parainfluenza Virus 4, Human - isolation & purification</topic><topic>Phylogeny</topic><topic>Polymerase chain reaction</topic><topic>Prevalence</topic><topic>Respiratory tract</topic><topic>Respiratory tract diseases</topic><topic>Respiratory Tract Infections - epidemiology</topic><topic>Respiratory Tract Infections - virology</topic><topic>Science</topic><topic>Secretions</topic><topic>Sequence Alignment</topic><topic>Strains (organisms)</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alquezar-Planas, David E.</creatorcontrib><creatorcontrib>Mourier, Tobias</creatorcontrib><creatorcontrib>Bruhn, Christian A. 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W.</au><au>Hansen, Anders J.</au><au>Vitcetz, Sarah Nathalie</au><au>Mørk, Søren</au><au>Gorodkin, Jan</au><au>Nielsen, Hanne Abel</au><au>Guo, Yan</au><au>Sethuraman, Anand</au><au>Paxinos, Ellen E.</au><au>Shan, Tongling</au><au>Delwart, Eric L.</au><au>Nielsen, Lars P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2013-09-02</date><risdate>2013</risdate><volume>3</volume><issue>1</issue><spage>2468</spage><epage>2468</epage><pages>2468-2468</pages><artnum>2468</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Molecular detection of viruses has been aided by high-throughput sequencing, permitting the genomic characterization of emerging strains. In this study, we comprehensively screened 500 respiratory secretions from children with upper and/or lower respiratory tract infections for viral pathogens. The viruses detected are described, including a divergent human parainfluenza virus type 4 from GS FLX pyrosequencing of 92 specimens. Complete full-genome characterization of the virus followed, using Single Molecule, Real-Time (SMRT®) sequencing. Subsequent “primer walking” combined with Sanger sequencing validated the
RS
platform's utility in viral sequencing from complex clinical samples. Comparative genomics reveals the divergent strain clusters with the only completely sequenced HPIV4a subtype. However, it also exhibits various structural features present in one of the HPIV4b reference strains, opening questions regarding their lifecycle and evolutionary relationships among these viruses. Clinical data from patients infected with the strain, as well as viral prevalence estimates using real-time PCR, is also described.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>24002378</pmid><doi>10.1038/srep02468</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/1647/2163 631/181/757 631/208/182 631/326/596/2142 Base Sequence Children DNA sequencing Gene mapping Genetic Variation Genome, Viral High-Throughput Nucleotide Sequencing Humanities and Social Sciences Humans Metagenomics - methods Molecular Sequence Data multidisciplinary Next-generation sequencing Open Reading Frames Parainfluenza Parainfluenza Virus 4, Human - classification Parainfluenza Virus 4, Human - genetics Parainfluenza Virus 4, Human - isolation & purification Phylogeny Polymerase chain reaction Prevalence Respiratory tract Respiratory tract diseases Respiratory Tract Infections - epidemiology Respiratory Tract Infections - virology Science Secretions Sequence Alignment Strains (organisms) Viruses |
| title | Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing |
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