About: Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

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About: Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
Creator	Guo, Yan Mourier, Tobias Delwart, Eric Shan, Tongling Gorodkin, Jan Alquezar-Planas, David Bruhn, Christian Hansen, Anders Mørk, Søren Nielsen, Hanne Nielsen, Lars Paxinos, Ellen Sethuraman, Anand Vitcetz, Sarah
Source	Medline; PMC
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.
has issue date	2013-09-03(xsd:dateTime)
bibo:doi	10.1038/srep02468
bibo:pmid	24002378
has license	cc-by-nc-nd
sha1sum (hex)	e0c0c5277a24320d44e9b356e13c5801dad521af
schema:url	https://doi.org/10.1038/srep02468
resource representing a document's title	Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
has PubMed Central identifier	PMC3760282
has PubMed identifier	24002378
schema:publication	Sci Rep
resource representing a document's body	covid:e0c0c5277a24320d44e9b356e13c5801dad521af#body_text
is schema:about of	named entity 'RESPIRATORY' named entity 'DISCOVERY' named entity 'GENERATION' named entity 'SECRETIONS' named entity 'METAGENOMIC SEQUENCING' named entity 'USING' named entity 'SECOND' named entity 'primers' named entity 'Pacific Biosciences' named entity 'EBI' named entity 'gene' named entity 'genome' named entity 'number of reads' named entity 'Primer3' named entity 'Nucleic acid' named entity 'PacBio' named entity 'proteins expressed' named entity 'Roche Diagnostics' named entity 'RNA' named entity 'Bayesian Information criterion' named entity 'qPCR' named entity 'gene' named entity 'molecule' named entity 'Beckman Coulter' named entity 'PCR' named entity 'New England Biolabs' named entity 'homologous' named entity 'Nucleotide substitution' named entity 'gene' named entity 'Beckman Coulter' named entity 'B. pertussis' named entity 'clinical samples' named entity 'significantly smaller' named entity 'Beta sheet' named entity 'TaqMan' named entity 'GS FLX' named entity 'amino-acid residues' named entity 'crystallographic' named entity 'gene' named entity 'transcriptional' named entity 'Henipavirus' named entity 'RNA' named entity '4.2' named entity 'amino acids' named entity 'leader sequence' named entity 'quantitative PCR' named entity 'DNase' named entity 'Contigs' named entity 'clinical samples' named entity 'case report' named entity 'nucleotides' named entity 'PacBio' named entity 'start codon' named entity 'primers' named entity 'epidemiological data' named entity 'ultracentrifuge' named entity 'PacBio' named entity 'epidemiology' named entity 'nucleotide' named entity 'supernatant' named entity 'gap penalties' named entity '3' end' named entity 'Sanger' named entity 'genome sequence' named entity 'RNA' named entity 'Titanium' named entity 'Fusion protein' named entity 'cDNA'

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