Sample preparation prior to molecular amplification: Complexities and opportunities

•Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans.•Sample preparation consisting of virus extraction, concentration and nucleic acid purification is challenging.•Development of a reference detection method as proposed in ISO/TS 15216 is a milestone.•Future risk assessments will benefit from analytical methods which differentiate infectious from non-infectious viruses.

Molecular amplification using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is currently considered as the gold standard to detect enteric human pathogenic viruses such as norovirus and hepatitis A virus in food and water. However, the molecular-based detection requires an adequate sampling strategy and a sample preparation specific for viruses. Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans. The development of a reference detection method including sample preparation as proposed in ISO/TS 15216 represents a milestone to facilitate the evaluation of the performance and eventually validation of future virus detection methods. The potential viral infectivity linked to a positive PCR result is a remaining issue and pretreatments allowing the differentiation of infectious viruses would be useful for future risk assessments.