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

ABSTRACT: In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load

SUBMITTER: Buytaers FE 

PROVIDER: S-EPMC9654790 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature