Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus...

Area of Science:

• Food safety
• Virology
• Genomics

Background:

• Norovirus causes significant foodborne illness outbreaks.
• Current methods for norovirus detection and characterization in food have limitations.

Purpose of the Study:

• To evaluate metagenomics for whole norovirus genome sequencing and strain-level characterization in contaminated food.
• To assess the feasibility of linking foodborne norovirus to human cases for outbreak resolution.

Main Methods:

• Investigated shotgun metagenomics and hybrid capture preparation methods.
• Sequenced genetic material using Oxford Nanopore technologies.
• Analyzed data with an in-house bioinformatics workflow.

Main Results:

• Achieved whole viral genome sequencing for phylogenetic analysis via shotgun metagenomics (high contamination) or hybrid capture (low contamination).
• Demonstrated superior relatedness to human cases compared to quantitative polymerase chain reaction (qPCR) methods.
• Successfully detected fewer genome copies and multiple viruses (norovirus, hepatitis A virus) in a public dataset using shotgun metagenomics.

Conclusions:

• Metagenomics is a feasible approach for comprehensive norovirus surveillance in food.
• This workflow enhances the ability to resolve foodborne outbreaks by providing detailed genomic information.
• Sharing lessons learned aims to advance the application of metagenomics in foodborne virus detection.