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Food-Borne Virus Burden and Implication for the Food Industry

July 16, 2020



Human enteric viruses are the number one cause of food-borne outbreaks worldwide. Whether you are a producer, an importer, an exporter, a processor, a retailer, a wholesaler, taking into account the viral risk is crucial to protect consumers. Unlike most bacteria, food-borne viruses do not change the flavor nor the aspect of the food products; moreover, they are hard to get rid of with the usual agro-industrial processes.

The main viruses present in foodstuffs are enteric viruses. They can be classified into 3 categories according to symptomatology:

  • Viruses causing gastroenteritis: norovirus, rotaviruses, enteric adenoviruses, astrovirus, aichivirus, sapovirus ;
  • Hepatitis A virus and Hepatitis E virus ;
  • Viruses multiplying in gut but with a different tropism such as the central nervous system for enterovirus.

Viruses transmitted via foods are reproduced in the human body and shed in feces or in vomitus. A large diversity of viruses can be detected in human stool, however only few families have been implicated in food-borne outbreaks (Table 1).

AdenoviridaeAdenovirus* (type 40-41)Gastroenteritis (moderate)Rare
AstroviridaeAstrovirusGastroenteritis (moderate)Rare
CaliciviridaeNorovirus  SapovirusGastroenteritis,      1-3 daysFrequent: shellfish, berries, food handler
CoronaviridaeCoronavirus (SARS)Common cold, pneumonia, enteric diseaseSuspected zoonotic, food handler
FlaviviridaeFlavivirus, tick borne encephalitis virus (TBEV)Fever, vomiting, fatigue, pain in the neck, back, encephalitis, 7-14 daysRare: cow sheep goat milk
HepeviridaeHepevirus (Hepatitis E virus)Hepatitis, 3-8 weeksRare, pig meat, oyster
OrthomyxiviridaeInfluenza A      (H5N1 virus)Flu (fever, muscle pain)Rare: bird meat (chicken, duck, geese...)
ParamyxoviridaeHenipavirus    (Nipah virus)Influenza-like illness, febrile encephalitisRare, food suspected in two outbreaks
PicornaviridaeKobuvirus          (Aichi virus)Gastroenteritis, 1-2 daysUncommon: shellfish
PicornaviridaeEnterovirusDiverse clinical syndromes, 3 to 10 daysRare
PicornaviridaeHepatovirus (Hepatitis A virus)Hepatitis, 2 to 6 weeksFrequent: shellfish, vegetbles, food handler
ReoviridaeRotavirusGastroenteritis, 1-3 daysRare

Table 1: viruses transmitted by food. * virus with a DNA genome. (adapted from Le Guyader et al. 2012)


The main two viruses involved in food-borne outbreaks are norovirus and Hepatitis A virus whose classification is as follows:

Genomic organizationGenogroups GI, GII, GIV (affects humans)Genotypes Ia, Ib, IIa, IIb, III
Size27-40 nm27-32 nm

* Discovered by the use of immune electron microscopy in Norwalk city (Ohio, United-States), the virus was classified in the genus Norwalk-like Virus (NLV), before taking the definitive name of Norovirus in 2002.


Transmission from person to person by direct contact with an infected patient or indirect (with fecal matter or vomit) is the most important, but the role of food is not negligible. It is estimated at about 14% ( 6Verhoef, 2015).

Food-borne viruses and contamination routes

In the external environment, because of their adsorption on particles and their resistance to pH variations and disinfection agents (chlorine, ozone, UV radiation), these viruses will be able to resist to treatments applied in wastewater plants and rejected into the environment with sometimes concentrations around 104 to 106 particles/L (Le Guyader and al., 2010).

Food can thus be contaminated during different phases of production:

  • contamination during preparation by a person excreting the virus;
  • contamination of food (filtering shellfishes, fruits or vegetables, etc.), drinking or distribution waters by rejections (sewage, irrigation water, etc.) in which viruses are present



From farm to fork

At world level, the Codex Alimentarius has published new directives for global consumer protection. These include fruits, vegetables, fishes and fishery products and animal feed. Fresh berries can contribute to healthy diet, but are also the subject of microbiological contaminations. Furthermore they are associated to many outbreaks caused by food viruses (Hepatitis A viruses, norovirus). The new text of the Codex gives advices to producers and consumers to prevent contaminations.

GAP, GHP, GMP, HACCP and food-borne virus

In Europe, according to EFSA, the European Food Safety Agency, who published numerous  scientific opinions about risks posed by pathogens (including noroviruses) in food of non-animal origin, the most efficient measure to minimize the risks should be to implement food safety systems including GAP (Good Agricultural Practices), GHP (Good Hygiene Practices), GMP (Good Manufacturing Practices) and HACCP (Hazard Analysis and Critical Control Points). These systems should be carried out from Farm to Fork and applicable to a set of microbiological risks. To date exists a network of trained laboratories, some of them being  ISO 17025 accredited, working on five continents and offering to industrials, testing solutions for the most common food viruses.



ISO 15216-1 specifies a method for the quantification of levels of HAV and norovirus genogroup I (GI) and II (GII) RNA, from test samples of foodstuffs (soft fruit, leaf, stem and bulb, vegetables, bottled water, bivalve molluscan shellfish) or food surfaces. Following elution of viruses from the test sample, viral RNA is then extracted by lysis with guanidine thiocyanate and adsorption on silica. Target sequences within the viral RNA are amplified and detected by real-time RT-PCR.

  • ISO 15216-1:2017 Part 1: Method for quantification - Horizontal method for determination of hepatitis A virus and norovirus using realtime RT-PCR.ISO 15216-1:2019 Part 2: Method for detection - Microbiology of the food chain - Horizontal method for determination of hepatitis A virus and norovirus in food using real-time RT-PCR. This method is not validated for detection of the target viruses in other foodstuffs (including multi-component foodstuffs), or any other matrices, nor for the detection of other viruses in foodstuffs, food surfaces or other matrices of the food chain.



Food-borne viruses and food processes:

A contamination of persons or surfaces via aerosols (droplets sprayed during vomiting) can also occur. It is noticed that these viruses present an important resistance to different processes used in the food industry. Only a thermal treatment such as sterilization (at least 100°C for several minutes) allows to ensure a viral elimination. Other treatments (thermal, chlorination, UV, high pressure, etc.) will have a variable impact to be validated according to the food types and their composition (a high sugar or fat content will have a protective effect against the virus) (EFSA Annual report).

Microbiological safety criteria in Europe:

European regulation EC 178/2002, also called « Food Law », constitutes the basis for food safety and for the "Hygiene package". Its scope includes foodstuffs and animal feeding. 

Article 14 of the regulation indicates that no foodstuff is to be placed on the market if it is unsafe and a foodstuff is considered as dangerous if it is injurious to health and/or unfit to human consumption.

Regulation EC 2073/2005 concerns microbiological criteria applicable to foodstuffs. In its recital (2), it specifies that foodstuffs should not contain micro-organisms or their toxins or metabolites in quantities that present an unacceptable risk for human health. 

Moreover, Regulation EC 2073/2005 specifies in its recital (27) that in particular criteria for pathogenic viruses should be established in live bivalve mollusks if analytical methods are developed sufficiently.

Enteric viruses, such as norovirus, and Hepatitis A viruses thus take place within the regulatory framework of these texts that are the basis of the "Hygiene package " in force since 2006.

In France

FCD (French Trade and Retail Federation) has defined new microbiological criteria applicable as of 01/01/2015 for norovirus and Hepatitis A virus.




Noroviruses are the main causative agent of gastroenteritis in all age groups, mainly in winter. These viruses are the major cause of acute gastroenteritis (AGE) in adults and the second among children. Symptoms are characterized with sudden vomiting (sometimes violent) with diarrhea, and sometimes with abdominal pain, nausea and fever.

Incubation period is about 12 to 72 hours with persistence of clinical signs from 2 to a maximum of 4 days ; it should be noticed that the viral shedding prolongs during two to three weeks after symptoms have stopped. During the acute phase of the disease, the viral shedding is of 1011 viral particles /g of stools and stabilizes at about 108 after symptoms have stopped. Due to the low infective dose estimated at 10 to 100 viral particles, the potential for transmission from person to person is important. 

Noroviruses of genogroups I and II (main implicated genogroups) have an important gene diversity and they are divided in several genotypes. To date, 9 genotypes have been described for NoV GI and 22 genotypes for NoV GII. 

Hepatitis A virus 

Hepatitis A virus induces hepatitis with associated clinical signs (anorexia, nausea, influenza-like syndrome, hives, jaundice). Asymptomatic forms are frequent, notably in children younger than 6 years of age (70% of cases). For older children and adults, the proportion of asymptomatic forms increases with the age. A jaundice is present in more than 70% of cases in adults. Severity of symptoms increases with the age. The average incubation time is 28-30 days. The viral shedding in stools is high, 15 days before onset of symptoms, and then decreases quickly. The disease evolution is generally rapidly favorable. Prolonged forms are rarely observed (15% of cases) without passage to chronic forms. There are fulminating forms, fatal or needing a liver transplant (< 1% of cases). Lethality for hepatitis A is of 0.6%.

Hepatitis A virus can cause long-lasting liver disease and spreads typically through raw or undercooked seafood or contaminated raw produce. Infected food handlers are often the source of food contamination.



According to the WHO, norovirus is the most common pathogen implicated in outbreaks.
1.7 billion cases of diarrhea occur each year in the world. Diarrhea is the second cause of mortality for children under five years-old, and more than 525000 die every year.

In 2018, EFSA and ECDC reported that in the European Union: Hepatitis A and norovirus ranked second and third, after Salmonella, for the number of hospitalizations with 6.8% and 4.8% of all outbreak-related hospitalizations reported in 2018.

A causative agent was identified in 3,923 food-borne and waterborne outbreaks (76.2% of total outbreaks) causing 36,294 illnesses (75.0% of total illnesses).

Viruses were reported as known causative agents of 13.5% of food-borne and waterborne outbreaks after bacteria (57.0%) and bacterial toxins (24.2%).

Norovirus was the virus most frequently identified in food-borne and waterborne outbreaks and was the fourth most commonly reported agent detected in outbreaks. Norovirus caused the second highest number of illnesses (17.6%) of all outbreak-related illnesses, after Salmonella.

Hepatitis A and norovirus ranked second and third, after Salmonella, for the number of hospitalizations with 6.8% and 4.8% of all outbreak-related hospitalizations reported in 2018.



A series of documented food outbreaks related to food-borne virus contaminations highlights how broad food matrices are; raw bivalve shellfish (oysters, clams, mussels) in particular are the matrices most at risk as those filter feeders become contaminated when their waters are polluted with raw sewage. Stoneless red fruits (raspberries, strawberries, blackberries,…) are also often implicated in large outbreaks, whether fresh or frozen, even further processed in smoothies. Vegetable, and more specifically leafy greens can also become easily contaminated. 

Norovirus contamination in Food

Some products contaminated with norovirus are frozen oysters, live oysters, mussels, scallops, blueberries, cockles, frozen seaweed, clams, red currants, frozen boiled whole clams, sour cherries, blackcurrants, raspberries, strawberries, cherry tomatoes, lingonberries, baby spinach, physalis, lettuce, bottled water…

Hepatitis A virus contamination in Food

Some products contaminated with Hepatitis A virus are frozen tuna, raw scallops, frozen strawberries, pomegranate seeds, blackberries, date fruits, frozen berries, iceberg lettuce, pitted dates, clams, mussels, wedge shells, oysters …

Hepatitis E virus contamination in Food

Some products contaminated with Hepatitis E virus are figatelli, fried or fresh liver sausages, quenelle and quenelle paste, dried salted liver, products mostly made of raw pork liver or game offal. 

Discover our white paper FOOD-BORNE VIRUS RISK



Virology R&D Manager, Food business bioMérieux

Working group member of CEN/ISO, molecular detection of viruses (CEN/G6/TC275/TAG4)

Foodborne pathogens (CEN/WG6/TC275/TAG3) and parasites (ISO/TC34/SC9/WG6)