Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing
| Autor: | Anand Sethuraman, David E. Alquezar-Planas, Sarah Nathalie Vitcetz, Yan-Yan Guo, Anders J. Hansen, Lars Peter Nielsen, Eric Delwart, Søren Mørk, Tongling Shan, Ellen E. Paxinos, Tobias Mourier, Christian A. W. Bruhn, Hanne Abel Nielsen, Jan Gorodkin |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
viruses
Molecular Sequence Data Genome Viral Biology Genome Article symbols.namesake Open Reading Frames Primer walking Prevalence Humans Respiratory Tract Infections Exome sequencing Phylogeny Genetics Sanger sequencing Comparative genomics Multidisciplinary Base Sequence Genetic Variation High-Throughput Nucleotide Sequencing Parainfluenza Virus 4 Human Single cell sequencing Metagenomics symbols Pyrosequencing Sequence Alignment |
| Zdroj: | 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, vol. 3, 2468 . https://doi.org/10.1038/srep02468 Scientific Reports 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, vol. 3, 2468 . https://doi.org/10.1038/srep02468 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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