Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus.
BACKGROUND
Norovirus is a major cause of gastroenteritis, causing yearly epidemics and hospital outbreaks resulting in a high burden on health care. Detection and characterization of norovirus directly from clinical samples could provide a powerful tool in infection control and norovirus epidemiology.


OBJECTIVE
To determine whether next-generation sequencing directly on fecal samples can accurately detect and characterize norovirus.


METHODS
Whole genome sequencing was performed on fecal samples from 10 patients with gastro-enteritis. Norovirus infection had previously been confirmed by RT-PCR. Genotyping was performed using phylogenetic analysis.


RESULTS
From all clinical samples sufficient amounts of RNA were retrieved to perform whole-transcriptome sequencing for the detection of RNA-viruses. Complete genomic norovirus sequences were obtained from all clinical samples, permitting accurate genotyping by phylogenetic analysis. In addition, a complete coxsackie B1 virus genome was isolated.


CONCLUSIONS
Detailed information on viral content can be obtained from fecal samples in a single-step approach, supporting clinical and epidemiological purposes. Next-generation sequencing performed directly on clinical samples can become a powerful tool in patient care and infection control.
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address: Herjan.Bavelaar@radboudumc.nl.
Herjan H J
HH
Bavelaar
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
Janette
J
Rahamat-Langendoen
Department of Medical Microbiology, Division of Clinical Virology, The University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Hubert G M
HG
Niesters
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
Jan
J
Zoll
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
Willem J G
WJ
Melchers
D017250:Caliciviridae Infections / Q000175:diagnosis / Q000821:virology*; D005243:Feces / Q000821:virology*; D005759:Gastroenteritis / Q000175:diagnosis / Q000821:virology; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058889:Molecular Typing; D029322:Norovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000379:methods
D012367:RNA, Viral
Next generation sequencing; Norovirus; Outbreak management