The number of foodborne disease outbreaks caused by viruses has more than doubled since 2011 and reached the highest level yet reported in 2014 (20.4% of all outbreaks) (EFSA Journal 2015;13(12):4329). Enteric viruses involved in foodborne diseases belong to various viral families and can cause a wide variety of diseases in humans. Human norovirus (NoV) and hepatitis A virus (HAV) are the most frequent causes of viral foodborne outbreaks worldwide.
Detection of HAV and NoV in foodstuffs is complicated by the absence of a reliable cell culture method and the low contamination levels of food. Then, the standardized method (CEN/ISO/TS 15216 published in 2013) for detection and quantification of NoV and HAV in foodstuffs is based on a final detection of viral genome using real-time reverse transcriptase PCR (RT-qPCR). Despite its sensitivity, specificity and rapidity, RT-qPCR is sensitive to substances present in tested samples that can inhibit PCR amplification of viral genomes and may lead to false-negative results. This drawback may be overcome by digital RT-PCR that is more robust for detecting viral genomes in presence of PCR inhibitors.
Another challenge in food virology is the assessment of infectious viral risk. The current RT-qPCR detects viral genomes of both infectious and non-infectious viruses. Two different approaches were evaluated in our lab for measuring the infectivity of enteric viruses: a combined method using intercalating dyes with RT-qPCR and a real-time cell analysis method (xCELLigence, ACEA). This last system measures in real time the electrical impedance of cell monolayers which allows the continuous monitoring of cell behavior following viral infection.
In conclusion, the improvement of the existing methods and the development of new tools for detecting the infectivity of enteric viruses are future challenges needed to be addressed in food virology.