Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus

•Whole genome sequencing was performed on fecal samples from patients with norovirus.•Complete norovirus sequences were obtained from all clinical samples.•Whole genome sequencing permitted characterization of different norovirus genotypes.•WGS directly on clinical samples benefits patient management and infection control.

BackgroundNorovirus 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.ObjectivesTo determine whether next-generation sequencing directly on fecal samples can accurately detect and characterize norovirus.Study designWhole 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.ResultsFrom 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.ConclusionDetailed 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.