Evaluation of three virus RNA extraction platforms for the detection of human norovirus, hepatitis A virus, hepatitis E virus and tick-borne encephalitis virus in different foodstuffs.

In the investigation of foodborne outbreaks, molecular detection of foodborne viruses involves virus extraction, RNA purification and quantitative detection using RT-qPCR. The NucliSENS® easyMAG® platform, previously used for virus RNA extraction from various foods, has been discontinued and alternative methods are needed. Here, we compared eMAG® (fully automated) and eGENE-UP® (semi-manual) RNA extraction systems with the easyMAG® platform for detecting viruses from virus stocks and food matrices. Various foods (couscous vegetable mix, green beans, goat milk, bottled water and ham pâté) were artificially contaminated with virus inocula (human norovirus, hepatitis A virus, hepatitis E virus and tick-borne encephalitis virus) at levels close to detection limits. Virus detection was carried out using adapted methods. All analyses included a process control virus and external amplification controls. The quantification of RNA from the eMAG® platform was compared using either RT-qPCR or digital PCR (dPCR). The eMAG®, easyMAG® and eGENE-UP® systems demonstrate comparable performance in detecting viruses in suspensions and in artificially contaminated food samples. Process control virus and external amplification controls were validated in all RNA extracts. Additionally, virus quantification by RT-qPCR tended to result in higher genomic copy numbers compared with RT-dPCR. In conclusion, the EMAG® and eGENE-UP® platforms can serve as suitable alternatives to the easyMAG® system for the detection and quantification of enteric viruses in simple matrices and various foodstuffs.