title: Application of next generation sequencing for the detection of human viral pathogens in clinical specimens.
abstract: Next generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis.
  
  
  
  To investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods.
  
  
  
  Illumina MiSeq system was used to detect viral pathogens alongside other conventional virology methods using typical clinical specimen matrices. Sixteen clinical specimens and two CDC proficiency panels containing seventeen specimens were analyzed.
  
  
  
  Known pathogenic viral nucleic acid was positively identified in all clinical specimens, correlating and building upon results obtained by more conventional laboratory methods. Sequencing depths ranged from 0.008X to 319 and genome coverage ranged from 0.6% to 99.9%. To substantiate the described methods used to analyze data derived from clinical specimens, the results of a clinical proficiency panel are also presented.
  
  
  
  Our results reveal true scarcity of known pathogenic viral nucleic acids in clinical specimens. NGS outperforms more conventional detection methods in this study by turnaround time as well as the improved depth of knowledge in regards to serotyping and drug resistance.
authors.affiliation: Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA.
authors.forename: Jayme
authors.initials: J
authors.lastname: Parker
authors.affiliation: Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA. Electronic address: j.chen@alaska.edu.
authors.forename: Jack
authors.initials: J
authors.lastname: Chen
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology*; D014780:Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
keywords: Human pathogen; Infectious disease diagnostics; Next-generation sequencing (NGS); Public health laboratory; Virus detection