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

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David Eugenio Alquezar Planas, Tobias Mourier, Christian Anders Wathne Bruhn, Anders Johannes Hansen, Sarah Nathalie Vitcetz, Søren Mørk, Jan Gorodkin, Hanne Abel Nielsen, Yan Guo, Anand Sethuraman, Ellen E. Paxinos, Tongling Shan, Eric L. Delwart, Lars Peter Nielsen

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.
OriginalsprogEngelsk
Artikelnummer2468
TidsskriftScientific Reports
Vol/bind3
Antal sider10
ISSN2045-2322
DOI
StatusUdgivet - 3 sep. 2013

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