Next generation sequencing (NGS) has recently emerged as a new tool allowing the characterization of food-borne pathogens including viruses with an unheard precision, thus providing new insights in Norovirus diversity and genetic evolution. NGS techniques are rapidly contributing to the understanding of multiple aspects such as the epidemic spread of Norovirus, the discovery of emerging genotype variants and pathogenic determinants, and the source identification in food-borne outbreak investigation.

There is an urgent need for EFSA to acquire expertise on the tools available and on their application on food-borne virus molecular epidemiology. Despite the fact that this technology is very promising and is evolving quickly, in the EU there is limited experience with its application in public health. It is still not clear when and how this technology will be ready for routine surveillance activities. Thus, “proof of concept” projects are necessary and of high priority.

The recent EFSA Scientific Opinion of the BIOHAZ Panel on the public health risks associated with the hepatitis E virus (HEV) as a food-borne pathogen recommended that there is a need for harmonisation of typing, subtyping and strain comparison methodologies. Thresholds for definition of types, subtypes and ‘identical’ strains based on sequence comparisons should be defined. These recommendations are also applicable to the surveillance of other very important food-borne viruses like Caliciviruses, including Noroviruses.

VirCapSeq-VERT approach which combines agnostic sequencing with a specific capture assay for vertebrate viruses, using the Illumina technology. TSS1's samples are norovirus in pure water. TSS2's samples are norovrirus bio-accumulated in oysters.