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

TY - JOUR

T1 - Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

AU - Alquezar Planas, David Eugenio

AU - Mourier, Tobias

AU - Bruhn, Christian Anders Wathne

AU - Hansen, Anders Johannes

AU - Vitcetz, Sarah Nathalie

AU - Mørk, Søren

AU - Gorodkin, Jan

AU - Nielsen, Hanne Abel

AU - Guo, Yan

AU - Sethuraman, Anand

AU - Paxinos, Ellen E.

AU - Shan, Tongling

AU - Delwart, Eric L.

AU - Nielsen, Lars Peter

PY - 2013/9/3

Y1 - 2013/9/3

N2 - 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.

AB - 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.

U2 - 10.1038/srep02468

DO - 10.1038/srep02468

M3 - Journal article

C2 - 24002378

SN - 2045-2322

VL - 3

JO - Scientific Reports

JF - Scientific Reports

M1 - 2468

ER -