Herjan H J Bavelaar1, Janette Rahamat-Langendoen2, Hubert G M Niesters3, Jan Zoll2, Willem J G Melchers2. 1. Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address: Herjan.Bavelaar@radboudumc.nl. 2. Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands. 3. Department of Medical Microbiology, Division of Clinical Virology, The University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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.
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.
Authors: Haziqah Hasan; Nor Ashika Nasirudeen; Muhammad Alif Farhan Ruzlan; Muhammad Aiman Mohd Jamil; Noor Akmal Shareela Ismail; Asrul Abdul Wahab; Adli Ali Journal: Children (Basel) Date: 2021-12-02