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Imprint
Next Generation Sequencing (NGS) for Foodborne Viruses
Project
Project code: BfR-BIOS-08-1322-713
Contract period: 01.01.2019
- 31.12.2019
Purpose of research: Experimental development
Keywords: Food safety
Foodborne viruses can represent a significant health risk. For example, a norovirus outbreak with a high number of documented cases was caused by the consumption of contaminated strawberries in Germany in 2012. Furthermore, the number of symptomatic cases of Hepatitis E virus (HEV), which is often associated with uncooked or incompletely cooked pork products, is continuously increasing in Germany. In addition, other viruses like hepatitis A virus and rotavirus can be transmitted through contamintaed food. Next Generation Sequencing (NGS) is a powerful technique that facilitates the sequencing of complete pathogen genomes. As such, NGS can be an invaluable tool for food saftety control, e.g. for the identification of viruses in specific food products. In addition, the technique can be used for strain typing of viruses, thus contributing to the identification of transmission pathways, for instance in outbreak situations. However, implementing NGS for viruses is challenging because viral genomes often have a different genome structure than other pathogens such as bacteria. Additionally, some viruses are difficult to grow in cell culture, which necessitates the relative amplification of virus material in samples. In preliminary experiments, our working group could recently demonstrate that metagenomic analysis can be utilized to identify noroviruses in naturally contaminated strawberry samples derived from an outbreak situation. We could also show that NGS generally enables the whole genome sequencing of rotaviruses from cell cultures. The aim of the project is to further develop and optimize the metagenomic and whole genome analysis of viruses for the identification of viruses, viral strain typing, and genome analysis. The developed methods will be used to identify viruses in food products, examine modes of viral transmission, and analyse virus properties such as virulence markers.
Section overview
Subjects
- Biotechnology
- Food microbiology
- Toxicology
