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

Abstract 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. Objectives To determine whether next-generation sequencing directly on fecal samples can accurately detect and characterize norovirus. Study design 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. Conclusion 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.