Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-12

AUTHORS

David E. Alquezar-Planas, Tobias Mourier, Christian A. W. Bruhn, Anders J. Hansen, Sarah Nathalie Vitcetz, Søren Mørk, Jan Gorodkin, Hanne Abel Nielsen, Yan Guo, Anand Sethuraman, Ellen E. Paxinos, Tongling Shan, Eric L. Delwart, Lars P. Nielsen

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. More... »

PAGES

2468

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/srep02468

DOI

http://dx.doi.org/10.1038/srep02468

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022682422

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24002378


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