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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. / Alquezar Planas, David Eugenio; Mourier, Tobias; Bruhn, Christian Anders Wathne; Hansen, Anders Johannes; Vitcetz, Sarah Nathalie; Mørk, Søren; Gorodkin, Jan; Nielsen, Hanne Abel; Guo, Yan; Sethuraman, Anand; Paxinos, Ellen E.; Shan, Tongling; Delwart, Eric L.; Nielsen, Lars Peter.

In: Scientific Reports, Vol. 3, 2468, 03.09.2013.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Alquezar Planas, DE, Mourier, T, Bruhn, CAW, Hansen, AJ, Vitcetz, SN, Mørk, S, Gorodkin, J, Nielsen, HA, Guo, Y, Sethuraman, A, Paxinos, EE, Shan, T, Delwart, EL & Nielsen, LP 2013, 'Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing', Scientific Reports, vol. 3, 2468. https://doi.org/10.1038/srep02468

APA

Alquezar Planas, D. E., Mourier, T., Bruhn, C. A. W., Hansen, A. J., Vitcetz, S. N., Mørk, S., Gorodkin, J., Nielsen, H. A., Guo, Y., Sethuraman, A., Paxinos, E. E., Shan, T., Delwart, E. L., & Nielsen, L. P. (2013). Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. Scientific Reports, 3, [2468]. https://doi.org/10.1038/srep02468

Vancouver

Alquezar Planas DE, Mourier T, Bruhn CAW, Hansen AJ, Vitcetz SN, Mørk S et al. Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. Scientific Reports. 2013 Sep 3;3. 2468. https://doi.org/10.1038/srep02468

Author

Alquezar Planas, David Eugenio ; Mourier, Tobias ; Bruhn, Christian Anders Wathne ; Hansen, Anders Johannes ; Vitcetz, Sarah Nathalie ; Mørk, Søren ; Gorodkin, Jan ; Nielsen, Hanne Abel ; Guo, Yan ; Sethuraman, Anand ; Paxinos, Ellen E. ; Shan, Tongling ; Delwart, Eric L. ; Nielsen, Lars Peter. / Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing. In: Scientific Reports. 2013 ; Vol. 3.

Bibtex

@article{c10d239d1a9441be87aa7eac15e0e67f,
title = "Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing",
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.",
author = "{Alquezar Planas}, {David Eugenio} and Tobias Mourier and Bruhn, {Christian Anders Wathne} and Hansen, {Anders Johannes} and Vitcetz, {Sarah Nathalie} and S{\o}ren M{\o}rk and Jan Gorodkin and Nielsen, {Hanne Abel} and Yan Guo and Anand Sethuraman and Paxinos, {Ellen E.} and Tongling Shan and Delwart, {Eric L.} and Nielsen, {Lars Peter}",
year = "2013",
month = sep,
day = "3",
doi = "10.1038/srep02468",
language = "English",
volume = "3",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "nature publishing group",

}

RIS

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

VL - 3

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 2468

ER -

ID: 97253541