This glossary explains technical terms used throughout Foodborne Viruses: What Every Food Professional Needs to Know. The definitions are written in plain English and are intended to help learners who do not have a microbiology or virology background.
Viruses, infection and illness
Virus
A very small infectious agent that can only reproduce inside a suitable living cell.
Virus particle / virion
A complete virus particle outside a host cell.
Genome
The genetic material of a virus. For norovirus, hepatitis A virus and hepatitis E virus, the genome is RNA.
RNA
Ribonucleic acid. A type of genetic material used by many viruses, including the main foodborne viruses covered in this course.
Host cell
A living cell that a virus infects and uses to make more copies of itself.
Replication
The process by which a virus makes new copies of itself inside a host cell. Foodborne viruses do not replicate in food.
Foodborne virus
A virus that can be transmitted to people through contaminated food.
Enteric virus
A virus associated with the intestinal tract and commonly spread by the faecal-oral route.
Norovirus (NoV)
A highly infectious virus that commonly causes acute gastroenteritis, including vomiting and diarrhoea.
Hepatitis A virus (HAV)
A virus that infects the liver and can be transmitted through contaminated food or water, or from person to person.
Hepatitis E virus (HEV)
A virus that infects the liver. In Europe, foodborne infection is particularly associated with infected pigs, wild boar and inadequately cooked pork or offal.
Genogroup
A broad genetic grouping of related viruses. Norovirus is commonly described using genogroups such as GI and GII.
Genotype
A more specific genetic grouping within a virus species or genogroup.
Zoonotic
Describes an infection that can pass naturally between animals and humans.
Reservoir
A host or environment in which an infectious agent is normally maintained and from which infection may spread.
Infection
The entry and multiplication of a virus in the body.
Asymptomatic infection
An infection in which the person has no noticeable symptoms but may still shed the virus.
Symptoms
Effects of illness experienced by the infected person, such as vomiting, diarrhoea, abdominal pain, fever or jaundice.
Incubation period
The time between becoming infected and the appearance of symptoms.
Shedding
The release of virus from an infected person or animal, for example in faeces or vomit. A person can sometimes shed virus before symptoms begin and after symptoms have stopped.
Infectious period
The period during which an infected person can transmit infection to others.
Gastroenteritis
Inflammation of the stomach and intestines, commonly causing vomiting, diarrhoea and abdominal discomfort.
Hepatitis
Inflammation of the liver.
Jaundice
Yellowing of the skin or whites of the eyes caused by increased bilirubin in the blood. It can occur with hepatitis A or hepatitis E.
Acute infection
An infection that develops over a relatively short period and usually resolves.
Chronic infection
An infection that persists for a prolonged period. Chronic HEV infection can occur in some immunocompromised people.
Immunity
Protection against infection produced by the immune system, for example after previous infection or vaccination.
Infectious dose
The amount of virus needed to establish infection. For some foodborne viruses this may be very low.
Infectivity
The ability of a virus particle to infect a susceptible host cell and potentially cause infection.
Transmission and food safety
Faecal-oral route
Transmission in which virus shed in faeces reaches another person’s mouth, directly or indirectly through hands, food, water, surfaces or other routes.
Contamination
The unwanted presence of a hazard, such as a virus, on or in food, water, equipment or the environment.
Cross-contamination
The transfer of contamination from one person, food, surface, utensil or area to another.
Fomite
An object or surface that can become contaminated and contribute to transmission.
Aerosolisation
The formation of very small droplets or particles that can become airborne. Vomiting can generate droplets that contaminate nearby surfaces and food.
Ready-to-eat food (RTE)
Food intended to be eaten without a further cooking step that would reduce or remove contamination.
Primary production
The early stages of food production, such as growing crops, raising animals, harvesting and fishing.
Irrigation water
Water used to supply crops. If contaminated with human sewage, it can introduce enteric viruses onto fresh produce.
Sewage contamination
Contamination arising from human waste or wastewater. This is an important route by which norovirus and HAV can enter food and water.
Bivalve molluscs / bivalve shellfish
Shellfish such as oysters, mussels and clams that filter water for food and can concentrate viruses from contaminated growing waters.
Bioaccumulation
The build-up of a substance or microorganism within an organism. Filter-feeding shellfish can bioaccumulate enteric viruses from surrounding water.
Depuration
Holding live shellfish in clean seawater so they can purge contaminants. Depuration can reduce some contamination but may be less effective for some viruses than for bacteria.
Traceability
The ability to follow food, ingredients or animals through the supply chain and identify where they came from and where they went.
Recall
The removal of food from the market or consumers when it may be unsafe.
Hazard
Something with the potential to cause harm. In this course, a foodborne virus may be the hazard.
Risk
The combination of the likelihood that harm will occur and the seriousness of that harm.
Control measure
An action or procedure used to prevent, eliminate or reduce a food-safety hazard.
HACCP
Hazard Analysis and Critical Control Point. A systematic approach used by food businesses to identify significant hazards and establish appropriate controls.
Indicator organism
A microorganism measured as an indication of hygiene or faecal contamination. Bacterial indicators such as E. coli do not reliably predict whether enteric viruses are present.
Microbiological criterion
A formal requirement that defines the acceptability of a food, process or batch based on specified microorganisms, sampling and limits.
Process hygiene criterion
A microbiological criterion used to indicate whether a production process is operating acceptably. It is not the same as a direct food-safety limit for the finished product.
Exclusion period
The period during which an ill food handler should remain away from food-handling duties to reduce the risk of transmitting infection.
Disinfection
The use of physical or chemical methods to reduce microorganisms on surfaces or equipment.
Virucidal
Capable of inactivating viruses.
Contact time
The length of time a disinfectant must remain in contact with a surface to achieve its intended effect.
Thermal inactivation
The loss of virus infectivity caused by heat.
Log reduction
A way of expressing how much a treatment reduces a microorganism or virus. A 1-log reduction is a 90% reduction, a 2-log reduction is 99%, and a 3-log reduction is 99.9%.
Outbreaks, surveillance and epidemiology
Outbreak
Two or more linked cases of illness associated with a common source or exposure, although definitions can vary by disease and surveillance system.
Case
A person who meets the defined criteria for being counted as part of an infection or outbreak investigation.
Cluster
A group of cases occurring close together in time, place or circumstance that may share a common cause.
Epidemiology
The study of how disease occurs and spreads in populations, including who is affected, where, when and through which exposures.
Surveillance
The systematic collection and analysis of disease information to identify trends, outbreaks and changes over time.
Food attribution
Estimating what proportion of illness is associated with particular foods, food groups or transmission routes.
Traceback
An investigation that follows an implicated food or ingredient backwards through the supply chain towards its source.
Prevalence
The proportion of a population, food group or set of samples that has a particular characteristic at a specified time, such as the proportion of samples in which viral RNA is detected.
Incidence
The number of new cases of disease occurring in a population over a defined period.
Burden of disease
The overall impact of a disease on a population, which may include the number of illnesses, hospitalisations, deaths, healthcare use and economic cost.
Under-reporting
The difference between the number of illnesses that actually occur and the smaller number recorded by official surveillance systems.
Molecular epidemiology
The use of genetic information from pathogens to help investigate relationships between cases, outbreaks and possible sources.
Sequencing
Determining the order of genetic material in a virus. Sequence information can help compare viruses from different cases or samples.
Laboratory testing and detection
Molecular detection
Detection based on the genetic material of a microorganism or virus rather than growing the organism itself.
RT-PCR
Reverse transcription polymerase chain reaction. A laboratory method in which viral RNA is first converted to DNA and then amplified so it can be detected.
RT-qPCR
Real-time quantitative reverse transcription PCR. The amplification reaction is monitored as it occurs, allowing detection and, when appropriately calibrated, estimation of the amount of target RNA.
Reverse transcription
The conversion of RNA into complementary DNA before PCR amplification.
Amplification
The process in PCR by which copies of a selected genetic target are produced through repeated reaction cycles.
Target
The specific viral genetic sequence that a PCR assay is designed to detect.
Ct value / Cq value
The PCR cycle at which the fluorescence signal crosses a defined threshold. In general, a lower Ct value indicates that more target RNA was present in the reaction, but Ct values should not be interpreted in isolation.
Genome copy
One copy of the viral genome or target sequence. Genome copies measured by PCR are not the same as infectious virus particles.
Sample matrix
The type of material being tested, such as berries, lettuce, shellfish, pork or environmental material.
Extraction
The process of releasing and isolating viral RNA from the sample so it can be analysed.
Concentration
A laboratory step used to collect virus from a relatively large sample into a smaller volume before detection.
PCR inhibition
Interference from substances in the sample that reduce or prevent the PCR reaction from working properly.
Process control virus
A known virus added to a sample before processing so the laboratory can estimate how well the extraction and recovery procedure worked.
Recovery efficiency / extraction efficiency
The percentage of the process control recovered after the laboratory extraction procedure compared with the amount originally added.
Internal amplification control
A control included in PCR to help show whether substances in the sample are inhibiting the amplification reaction.
Limit of detection (LOD)
The lowest amount of target that a method can detect with a defined level of confidence under specified conditions.
Limit of quantification (LOQ)
The lowest amount of target that can be measured quantitatively with acceptable performance.
Qualitative test
A test designed primarily to determine whether the target is detected or not detected.
Quantitative test
A test designed to estimate how much target is present.
Validation
Demonstrating through planned studies that a method is suitable for its intended purpose and performs to defined criteria.
Verification
Confirming that a laboratory can achieve the expected performance of an established or validated method under its own conditions.
Analytical sensitivity
The ability of a method to detect low amounts of the target.
Analytical specificity
The ability of a method to detect the intended target without incorrectly detecting unrelated material.
ISO 15216
The international standard method used for detecting norovirus and hepatitis A virus in specified food matrices using real-time RT-PCR.
Cell culture
A laboratory system in which living cells are grown and used to study viruses. Routine culture methods are not available for all foodborne viruses.
Infectivity assay
A test designed to determine whether detected virus is capable of infecting cells or a host, rather than only detecting viral genetic material.
Surrogate virus
A virus used in experiments as a substitute for another virus that is difficult to grow or study directly.
Terms used when interpreting results
Detected
The test found the target viral RNA in the portion of sample analysed.
Not detected
The target viral RNA was not detected in the portion of sample analysed under the conditions of the test. This is not the same as proving that the entire food or batch contains no virus.
Positive result
A result in which the assay detects the target viral RNA according to the laboratory’s interpretation criteria.
Negative result
A result in which the target is not detected according to the laboratory’s interpretation criteria. The meaning depends on sampling, recovery efficiency, assay sensitivity and other factors.
Inconclusive result
A result that cannot be confidently classified as positive or negative, for example because controls fail or the signal is inconsistent.
Sampling
Selecting a portion of food, water or another material for testing. The test result directly describes the material sampled, not automatically the whole batch.
Heterogeneous contamination
Contamination that is unevenly distributed. Some units or portions may contain virus while others from the same batch do not.
Sampling uncertainty
Uncertainty caused by testing only a small portion of a larger batch or consignment, particularly when contamination is unevenly distributed.
Viral RNA
The genetic material detected by RT-PCR. Detection of viral RNA shows that the target sequence is present, but PCR alone does not determine whether the virus is infectious.