Viruses in fermented foods: are they good or bad? Two sides of the same coin

Abstract

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Keywords: Bacteriophage; Fermented milks; Next-generation sequencing; Rotavirus; SARS-CoV-2.

Fig. 1

Main bacteriophages families and contagion routes associated with fermented foods (adapted from Samson and Moineau, 2013). Positive associations are written in green and negative in red on the outer part of the circle. This figure was created using BioRender (https://biorender.com/). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

Schematic workflow for analyzing virus communities in fermented foods by next-generation sequencing. LASLs (linker amplification shotgun libraries) and MDA (multiple displacement amplification). This figure was created using BioRender (https://biorender.com/).

Fig. 3

Main sources of pathogenic viruses and prevention measures associated with fermented foods. VACV (vaccinia virus); TBVE (tick-borne encephalitis virus); NoV (Norovirus); HEV (hepatitis E virus); RVA (rotavirus A). This figure was created using BioRender (https://biorender.com/).