Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information

Jan Zoll, Janette Rahamat-Langendoen, Inge Ahout, Marien I de Jonge, Jop Jans, Martijn A Huijnen, Gerben Ferwerda, Adilia Warris, Willem J G Melchers

Research output: Contribution to journalArticle

18 Citations (Scopus)

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.

OBJECTIVES: 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.

STUDY DESIGN: 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.

Original languageEnglish
Pages (from-to)6-11
Number of pages6
JournalJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology
Volume66
Early online date18 Feb 2015
DOIs
Publication statusPublished - May 2015

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Respiratory System
Respiratory Tract Infections
Genome
Pediatrics
Rhinovirus
Virus Diseases
Infection Control
Polymerase Chain Reaction
Metapneumovirus
Viruses
High-Throughput Nucleotide Sequencing
Virology
Respiratory Syncytial Viruses
Molecular Pathology
Viral Genome
Sputum
Nucleic Acids
Communicable Diseases
Epidemiologic Studies
Morbidity

Keywords

  • Female
  • Genome, Viral
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Infant
  • Male
  • Metagenome
  • Molecular Diagnostic Techniques
  • Nasopharynx
  • Respiratory Tract Infections
  • Sputum
  • Virus Diseases
  • Viruses
  • Case Reports
  • Journal Article
  • Research Support, Non-U.S. Gov't

Cite this

Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information. / Zoll, Jan; Rahamat-Langendoen, Janette; Ahout, Inge; de Jonge, Marien I; Jans, Jop; Huijnen, Martijn A; Ferwerda, Gerben; Warris, Adilia; Melchers, Willem J G.

In: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, Vol. 66, 05.2015, p. 6-11.

Research output: Contribution to journalArticle

Zoll, Jan ; Rahamat-Langendoen, Janette ; Ahout, Inge ; de Jonge, Marien I ; Jans, Jop ; Huijnen, Martijn A ; Ferwerda, Gerben ; Warris, Adilia ; Melchers, Willem J G. / Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information. In: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology. 2015 ; Vol. 66. pp. 6-11.
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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.OBJECTIVES: 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.STUDY DESIGN: 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.",
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author = "Jan Zoll and Janette Rahamat-Langendoen and Inge Ahout and {de Jonge}, {Marien I} and Jop Jans and Huijnen, {Martijn A} and Gerben Ferwerda and Adilia Warris and Melchers, {Willem J G}",
note = "This research was funded by Agentschap NL, LSH, grant FES0908 (VIRGO project), Technology Foundation STW (FES0901 and FES HTSM), Netherlands Genomics Initiative Project No. 050-060-452, and EU (FP7).",
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T1 - Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information

AU - Zoll, Jan

AU - Rahamat-Langendoen, Janette

AU - Ahout, Inge

AU - de Jonge, Marien I

AU - Jans, Jop

AU - Huijnen, Martijn A

AU - Ferwerda, Gerben

AU - Warris, Adilia

AU - Melchers, Willem J G

N1 - This research was funded by Agentschap NL, LSH, grant FES0908 (VIRGO project), Technology Foundation STW (FES0901 and FES HTSM), Netherlands Genomics Initiative Project No. 050-060-452, and EU (FP7).

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N2 - 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.OBJECTIVES: 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.STUDY DESIGN: 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.

AB - 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.OBJECTIVES: 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.STUDY DESIGN: 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.

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KW - Case Reports

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