Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus
| Autor: | Jan Zoll, Willem J. G. Melchers, Hubert G. M. Niesters, Janette Rahamat-Langendoen, Herjan Bavelaar |
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| Přispěvatelé: | Microbes in Health and Disease (MHD) |
| Rok vydání: | 2015 |
| Předmět: |
INFORMATION
Genotype viruses OUTBREAK Genome Viral medicine.disease_cause Genome Virus Specimen Handling Outbreak management Feces fluids and secretions Virology Next generation sequencing Medicine Infection control Humans Genotyping Phylogeny Caliciviridae Infections Whole genome sequencing Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] Phylogenetic tree business.industry Norovirus Outbreak High-Throughput Nucleotide Sequencing Sequence Analysis DNA Gastroenteritis Molecular Typing Infectious Diseases lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4] RNA Viral business |
| Zdroj: | Journal of Clinical Virology, 72, 122-5 Journal of Clinical Virology, 72, pp. 122-5 Journal of Clinical Virology, 72, 122-125. ELSEVIER SCIENCE BV |
| ISSN: | 1873-5967 1386-6532 |
| Popis: | 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 gastroenteritis. 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 wholetranscriptome 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. (C) 2015 Elsevier B.V. All rights reserved. |
| Databáze: | OpenAIRE |
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