Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760282/
https://www.ncbi.nlm.nih.gov/pubmed/24002378
http://dx.doi.org/10.1038/srep02468
_version_ 1782282750016880640
author 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.
author_facet 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.
author_sort Alquezar-Planas, David E.
collection PubMed
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.
format Online
Article
Text
id pubmed-3760282
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Nature Publishing Group
record_format MEDLINE/PubMed
spelling pubmed-37602822013-09-03 Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing 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. Sci Rep Article 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. Nature Publishing Group 2013-09-03 /pmc/articles/PMC3760282/ /pubmed/24002378 http://dx.doi.org/10.1038/srep02468 Text en Copyright © 2013, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-nd/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
spellingShingle Article
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.
Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title_full Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title_fullStr Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title_full_unstemmed Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title_short Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
title_sort discovery of a divergent hpiv4 from respiratory secretions using second and third generation metagenomic sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760282/
https://www.ncbi.nlm.nih.gov/pubmed/24002378
http://dx.doi.org/10.1038/srep02468
work_keys_str_mv AT alquezarplanasdavide discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT mouriertobias discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT bruhnchristianaw discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT hansenandersj discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT vitcetzsarahnathalie discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT mørksøren discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT gorodkinjan discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT nielsenhanneabel discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT guoyan discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT sethuramananand discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT paxinosellene discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT shantongling discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT delwartericl discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing
AT nielsenlarsp discoveryofadivergenthpiv4fromrespiratorysecretionsusingsecondandthirdgenerationmetagenomicsequencing