title: Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information.
abstract: BACKGROUND
  Acute respiratory tract infections (RTI) cause substantial morbidity during childhood, and are responsible for the majority of pediatric infectious diseases. Although most acute RTI are thought to be of viral origin, viral etiology is still unknown in a significant number of cases.
  
  
  OBJECTIVE
  Multiplexed whole genome sequencing (WGS) was used for virome determination directly on clinical samples as proof of principle for the use of deep sequencing techniques in clinical diagnosis of viral infections.
  
  
  METHODS
  WGS was performed with nucleic acids from sputum and nasopharyngeal aspirates from four pediatric patients with known respiratory tract infections (two patients with human rhinovirus, one patient with human metapneumovirus and one patient with respiratory syncytial virus), and from four pediatric patients with PCR-negative RTI, and two control samples.
  
  
  RESULTS
  Viral infections detected by routine molecular diagnostic methods were confirmed by WGS; in addition, typing information of the different viruses was generated. In three out of four samples from pediatric patients with PCR-negative respiratory tract infections and the two control samples, no causative viral pathogens could be detected. In one sample from a patient with PCR-negative RTI, rhinovirus type-C was detected. Almost complete viral genomes could be assembled and in all cases virus species could be determined.
  
  
  CONCLUSIONS
  Our study shows that, in a single run, viral pathogens can be detected and characterized, providing information for clinical assessment and epidemiological studies. We conclude that WGS is a powerful tool in clinical virology that delivers comprehensive information on the viral content of clinical samples.
authors: Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands. Electronic address: jan.zoll@radboudumc.nl.
authors: Jan
authors: J
authors: Zoll
authors: Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
authors: Janette
authors: J
authors: Rahamat-Langendoen
authors: Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, Nijmegen, The Netherlands.
authors: Inge
authors: I
authors: Ahout
authors: Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, Nijmegen, The Netherlands.
authors: Marien I
authors: MI
authors: de Jonge
authors: Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, Nijmegen, The Netherlands.
authors: Jop
authors: J
authors: Jans
authors: Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands.
authors: Martijn A
authors: MA
authors: Huijnen
authors: Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, Nijmegen, The Netherlands.
authors: Gerben
authors: G
authors: Ferwerda
authors: Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, Nijmegen, The Netherlands.
authors: Adilia
authors: A
authors: Warris
authors: Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
authors: Willem J G
authors: WJ
authors: Melchers
mesh_terms: D005260:Female; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D054892:Metagenome; D025202:Molecular Diagnostic Techniques / Q000379:methods; D009305:Nasopharynx / Q000821:virology; D012141:Respiratory Tract Infections / Q000175:diagnosis / Q000821:virology*; D013183:Sputum / Q000821:virology; D014777:Virus Diseases / Q000175:diagnosis / Q000821:virology*; D014780:Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
keywords: Infection; Respiratory tract; Virus; Whole genome sequencing