title: Exploring the potential of next-generation sequencing in detection of respiratory viruses.
abstract: Efficient detection of human respiratory viral pathogens is crucial in the management of patients with acute respiratory tract infection. Sequence-independent amplification of nucleic acids combined with next-generation sequencing technology and bioinformatics analyses is a promising strategy for identifying pathogens in clinical and public health settings. It allows the characterization of hundreds of different known pathogens simultaneously and of novel pathogens that elude conventional testing. However, major hurdles for its routine use exist, including cost, turnaround time, and especially sensitivity of the assay, as the detection limit is dependent on viral load, host genetic material, and sequencing depth. To obtain insights into these aspects, we analyzed nasopharyngeal aspirates from a cohort of 81 Thai children with respiratory disease for the presence of respiratory viruses using a sequence-independent next-generation sequencing approach and routinely used diagnostic real-time reverse transcriptase PCR (real-time RT-PCR) assays. With respect to the detection of rhinovirus and human metapneumovirus, the next-generation sequencing approach was at least as sensitive as diagnostic real-time RT-PCR in this small cohort, whereas for bocavirus and enterovirus, next-generation sequencing was less sensitive than real-time RT-PCR. The advantage of the sequencing approach over real-time RT-PCR was the immediate availability of virus-typing information. Considering the development of platforms capable of generating more output data at declining costs, next-generation sequencing remains of interest for future virus diagnosis in clinical and public health settings and certainly as an additional tool when screening results from real-time RT-PCR are negative.
authors.affiliation: Center of Excellence in Clinical Virology, Department of Pediatrics, Chulalongkorn University and Hospital, Bangkok, Thailand.
authors.forename: Slinporn
authors.initials: S
authors.lastname: Prachayangprecha
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Claudia M E
authors.initials: CM
authors.lastname: Schapendonk
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands Virology Division, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
authors.forename: Marion P
authors.initials: MP
authors.lastname: Koopmans
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands Viroclinics Biosciences, Rotterdam, the Netherlands.
authors.forename: Albert D M E
authors.initials: AD
authors.lastname: Osterhaus
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Anita C
authors.initials: AC
authors.lastname: Schürch
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Suzan D
authors.initials: SD
authors.lastname: Pas
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Annemiek A
authors.initials: AA
authors.lastname: van der Eijk
authors.affiliation: Center of Excellence in Clinical Virology, Department of Pediatrics, Chulalongkorn University and Hospital, Bangkok, Thailand.
authors.forename: Yong
authors.initials: Y
authors.lastname: Poovorawan
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Bart L
authors.initials: BL
authors.lastname: Haagmans
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands Viroclinics Biosciences, Rotterdam, the Netherlands s.smits@erasmusmc.nl.
authors.forename: Saskia L
authors.initials: SL
authors.lastname: Smits
mesh_terms: D000293:Adolescent; D002648:Child; D002675:Child, Preschool; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D009305:Nasopharynx / Q000821:virology; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000821:virology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013785:Thailand; D014773:Virology / Q000379:methods; D014777:Virus Diseases / Q000175:diagnosis* / Q000821:virology; D014780:Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
references.citation: J Clin Microbiol. 2010 May;48(5):1787-94
references.pmid: 20335418
references.citation: J Clin Microbiol. 2010 Nov;48(11):4044-50
references.pmid: 20844210
references.citation: Curr Opin Virol. 2012 Feb;2(1):63-77
references.pmid: 22440968
references.citation: PLoS One. 2011 Mar 01;6(3):e17427
references.pmid: 21390255
references.citation: Emerg Infect Dis. 2012 May;18(5):821-4
references.pmid: 22516379
references.citation: PLoS One. 2012;7(5):e35190
references.pmid: 22586446
references.citation: J Virol Methods. 2008 Sep;152(1-2):25-31
references.pmid: 18598722
references.citation: Clin Microbiol Infect. 2013 Jan;19(1):15-22
references.pmid: 23279287
references.citation: J Virol. 2012 Feb;86(4):2360-5
references.pmid: 22171250
references.citation: J Gen Virol. 2013 Aug;94(Pt 8):1791-1806
references.pmid: 23677786
references.citation: PLoS One. 2009 Dec 30;4(12):e8518
references.pmid: 20041158
references.citation: mBio. 2012 Nov 20;3(6):
references.pmid: 23170002
references.citation: BMC Infect Dis. 2007 Feb 15;7:6
references.pmid: 17300736
references.citation: Emerg Infect Dis. 2011 Aug;17(8):1494-7
references.pmid: 21801632
references.citation: PLoS One. 2012;7(6):e27735
references.pmid: 22719819
references.citation: Arch Virol. 2010 Dec;155(12):2023-8
references.pmid: 20686798
references.citation: Emerg Infect Dis. 2011 Aug;17(8):1430-5
references.pmid: 21801620
references.citation: J Clin Virol. 2011 Oct;52(2):103-6
references.pmid: 21802981
references.citation: Virol J. 2008 Oct 14;5:117
references.pmid: 18854035
references.citation: Scand J Infect Dis. 2013 Jan;45(1):65-9
references.pmid: 22992129
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Arch Virol. 2014 Mar;159(3):499-507
references.pmid: 24068580
references.citation: Pediatr Infect Dis J. 2012 Mar;31(3):309-12
references.pmid: 22315004
references.citation: Virol J. 2013 Jun 13;10:193
references.pmid: 23758792
references.citation: J Infect Dis. 2012 Jun 15;205(12):1877-84
references.pmid: 22492851
references.citation: Rev Med Virol. 2010 Nov;20(6):392-407
references.pmid: 20925048
references.citation: J Infect. 2009 Aug;59(2):115-21
references.pmid: 19556008
references.citation: Front Cell Infect Microbiol. 2014 Mar 06;4:25
references.pmid: 24639952
references.citation: J Virol. 2013 Jul;87(13):7758-64
references.pmid: 23616657
references.citation: Science. 2009 Apr 3;324(5923):55-9
references.pmid: 19213880
references.citation: Neuropsychol Rehabil. 2007 Aug-Oct;17(4-5):406-28
references.pmid: 17676528
references.citation: Microbiol Mol Biol Rev. 2010 Sep;74(3):363-77
references.pmid: 20805403
references.citation: Curr Opin Virol. 2013 Apr;3(2):e1-e6
references.pmid: 23578938
references.citation: Southeast Asian J Trop Med Public Health. 2014 May;45(3):610-21
references.pmid: 24974645
references.citation: J Med Virol. 2001 Oct;65(2):296-300
references.pmid: 11536236
references.citation: Viruses. 2012 Aug;4(8):1328-34
references.pmid: 23012629
references.citation: Pediatr Infect Dis J. 2000 Apr;19(4):293-8
references.pmid: 10783017