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Glossary of terms

Essential SIV Glossary

This area of flusureXP.com lists over 70 fundamental terms and identifiers related to swine influenza virus in alphabetical order. Look around, learn the terms, and stay in the know.


Adjuvant: An immunological substance added during production of a vaccine to help improve the body's immune response to the antigens that are contained in the vaccine.

Animal culling: Selective slaughter and removal of animals from a population to help reduce the potential spread of disease. Culling of poultry populations has been used to minimize the potential spread of avian influenza.

Animal reservoir: When an animal species is naturally infected by a pathogen and acts as its host, it is said to be an animal reservoir for that pathogen. For example, avian influenza viruses circulate among birds worldwide. Certain birds, particularly water birds, act as hosts for influenza viruses by carrying the virus in their intestines and shedding the virus. These viruses sometimes may "jump" to other species. Changes in the virus's gene structure may occur, increasing the potential for infection of other species and pandemic influenza. (Also see Antigenic Drift and Antigenic Shift).

Animal-to-Human Transmission: An infected pig transmits a pathogen to a human. In influenza, swine influenza viruses may be transmitted from pigs to humans directly from animals or from contact with surfaces contaminated with swine influenza virus.

Antigen: Foreign substance capable of inducing specific immune responses as a result of contact with the appropriate cells; the portions of pathogens that are reacted on by immune cells and antibodies.

Antigenic Drift: Influenza viruses can undergo antigenic changes in two ways: antigenic drift and antigenic shift (see below). Antigenic drift refers to small, gradual changes that occur through point mutations in the two genes that code for the production of the main influenza virus surface proteins, hemagglutinin, and neuraminidase. These point mutations occur unpredictably and may result in minor changes to these surface proteins. Antigenic drift can produce new virus strains that may not be recognized by antibodies to previously recognized influenza strains.

Antigenic Shift: Influenza viruses can undergo antigenic changes in two ways: antigenic drift (see above) and antigenic shift. Antigenic shift refers to major changes to produce a novel influenza A virus subtype that was not previously circulating within that species. Antigenic shift often occurs through direct human-to-pig transmission and is caused by mixing of swine influenza virus genes to create a new subtype virus through a process called genetic reassortment, as well as through mixing of human, swine and/or avian flu genes.

Antiviral: Pharmaceutical capable of destroying or weakening a virus.

Asymptomatic infection: An infection that exists without any apparent disease symptoms. Influenza infection can be asymptomatic.

Attenuate: To weaken, or reduce in strength. (see Live Attenuated Influenza Vaccine).

Attenuated vaccine: A vaccine that consists of live virus that has been weakened through chemical or physical processes to still produce an immune response but without causing effects of the disease. (see Live Attenuated Influenza Vaccine).

Avian influenza: Influenza A viruses can naturally infect wild birds. Infected birds serve as natural hosts from which some influenza viruses can be transmitted into other animal or human populations. Avian influenza viruses do not usually infect humans; however, confirmed cases of human infection from several subtypes of avian influenza infections have been reported since 1997. Currently, outbreaks of avian influenza A (H5N1) among birds have resulted in human cases in Asia and Europe.


Biosafety Level (BSL): Specific combinations of work practices, safety equipment, and facilities designed to minimize the exposure of workers and the environment to infectious agents. BSL-1 applies to agents that do not ordinarily cause human disease. BSL-2 is appropriate for infectious agents that can cause human disease but have limited potential for transmission. BSL-3 applies to agents that can cause serious infection and may be transmitted by the respiratory route. BSL-4 is used when diagnosing or working with infectious agents that pose a high risk of life-threatening disease, may be transmitted by the aerosol route, and for which there is no vaccine or therapy.


Cluster: Sometimes referred to as clades. Genetically and serologically distinct influenza viral groups within the major subtypes. Examples include the four clusters currently identified in the H3N2 subclass: Cluster I, Cluster II, Cluster III and Cluster IV.


Dendrogram (also referred to as Dendograms): a branching 'tree-like' diagram representing a hierarchy of categories based on degree of genetic sequence homology or number of shared characteristics especially in biological taxonomy. In regards to SIV a dendrogram typically shows the level of genetic relatedness between swine influenza virus isolates.

Domain: In the case of SIV, the HA1 domain of the hemagglutinin (HA) gene is the region or area that contains the sites encoding for the portion of the HA protein that is exposed on the surface of the virus.


ELISA Titers: Enzyme-Linked Immuno Sorbant Assay (ELISA) is a common technique used mainly in immunology to detect the presence of an antibody (antibody titer) or an antigen in a sample.

Endemic: A disease or infection that is present in a particular locality, region or people or animals at all times. Avian influenza is considered endemic in wild birds.

Enzootic: A disease that is constantly present in an animal population but occurs only in small numbers of cases.

Epidemic: The occurrence of disease within a specific geographical area or population that is in excess of what is normally expected.

Epidemiology: The study of the factors affecting the health and illness of specified populations, and the applications to the control these health problems.

Epizootic: An outbreak or epidemic of disease in animal populations.

Etiology: The cause or origin of a disease or disorder; the study of the factors that cause disease, and the method of their introduction into the host.



Gene sequencing: Determination or characterization of the sequence of nucleotide bases in a strand of DNA or RNA.

Genotype: The genetic constitution of an organism (in the case of SIV, the HA gene sequence).

Genotyping: The process of determining the genotype of an organism with a biological assay. The RT PCR assay is used for genotyping the HA of SIV. Other molecular methods can be used for other organisms.

Glycoprotein: The SIV hemagglutinin and neuraminidase of SIV are glycoproteins, containing both protein and carbohydrate (sugar) portions.


Hemagglutinin (HA): A type of protein on the surface of influenza viruses. Influenza type A viruses are divided into subtypes on the basis of two proteins on the surface of the virus: hemagglutinin (HA) and neuraminidase (NA) (see below).

Hemagglutination inhibition (HI) Titers: The metric result (antibody titer) of an HI test; a test to identify a virus or to quantitate an antibody by adding virus-specific antibody to a mixture of agglutinating virus and red blood cells.

"High risk" population: Those individuals at greatest risk of developing serious or deadly diseases.

Highly pathogenic avian influenza (HPAI): Avian influenza A H5 and H7 viruses can be distinguished as "low pathogenic" (see below) and "high pathogenic" forms on the basis of genetic features of the virus and the severity of the illness they cause in poultry. A highly pathogenic avian influenza virus can cause severe illness and high mortality in poultry, however some HPAI viruses have been found to cause no illness in some poultry, such as ducks.


Immunization: The process or procedure by which a person, animal, or plant is rendered resistant to a specific disease. This term is often used interchangeably with vaccination or inoculation, although the act of inoculation does not always result in immunity.

Immunosuppression: When the immune system is unable to protect the body from disease due to reduced activation and/or response of the immune system

Immunodominant: A molecule or the region of a antigen that are recognized by the host's immune system and to which antibodies are developed. Immunodominant is not interchangeable with a "protective" immune response, but implies that a host develops antibodies to this site preferentially and possibly to the exclusion, of other antigenic sites on a molecule. However, for inactivated (killed) SIV vaccines, the HA is immunodominant and hemagglutination inhibition (HI) antibodies to the HA are generally considered the primary protective antibodies that develop after vaccination.

Inactivated vaccine: A vaccine made from viruses or bacteria that have been killed through physical or chemical processes. These killed organisms cannot cause disease.

Incubation period: The interval of time between infection by a pathogen and the onset of illness or the first symptoms of the illness. The time from when a human is exposed to the seasonal flu virus to when symptoms begin is about one to four days, with an average of about two days. For pigs, the incubation period is typically about one day.

Influenza (flu): A contagious respiratory illness caused by influenza viruses. It can result in mild to severe illness, and at times can lead to death.

Influenza contagion/spread: Most healthy adults may be able to infect others with human influenza beginning 1 day before symptoms develop and up to 5 days after becoming sick. Influenza virus usually is spread by large respiratory droplets containing influenza viruses that are produced by coughing and sneezing.

Influenza pandemic: A global outbreak of influenza that occurs when a new influenza A virus appears or "emerges" in the human population, causing widespread serious illness, and spreads easily from person to person worldwide. Influenza pandemics have resulted in high rates of illness and death, social disruption, and economic loss. They occur infrequently and at irregular intervals. Three pandemics took place in the 20th century:

  • The 1918-1919 "Spanish Flu" pandemic, which was caused by a Type A (H1N1) virus resulted in more than 500,000 deaths in the U.S. and more than 20 million deaths worldwide.
  • The 1957-58 "Asian Flu" pandemic caused by a Type A (H2N2) virus that killed about 70,000 people in the United States.
  • The 1968-69 "Hong Kong Flu" pandemic was caused by a Type A (H3N2) virus and killed about 34,000 people in the U.S. All of these pandemics spread throughout the world within one year of their identification.

Influenza type A viruses: There are three types of influenza viruses: A, B, and C. Only influenza A viruses are further classified by subtype on the basis of the two main surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Influenza A subtypes and B viruses are further classified by strains. So far, scientists have discovered 16 HA subtypes and 9 NA subtypes. However, in the 20th century, only three subtypes circulated widely in swine: A(H1N1), A(H1N2), and A(H3N2). Influenza A viruses also can infect a number of other animal species including humans, birds, horses, seals and whales.

Influenza vaccine: A vaccine designed to help prevent influenza disease. The vaccine is made from inactivated (killed) influenza virus that prompts an antibody response promoting immunity from the influenza virus used in the vaccine. It takes two weeks for the body to develop protective antibody after vaccination.

Intramuscular Administration: Intramuscular administration or vaccination means the vaccine is injected into the muscle. Inactivated influenza vaccines are currently administered intramuscularly.

In vitro: Refers to the technique of performing a given experiment in a controlled environment outside of a living organism.

In vivo: Refers to experimentation done in or on the living tissue of a whole, living organism.




Low Pathogenic Avian Influenza (LPAI): Avian influenza A virus strains are classified as low pathogenic (LPAI) or highly pathogenic (HPAI) on the basis of specific molecular genetic and pathogenesis criteria. Most avian influenza A viruses are LPAI viruses that are usually associated with mild disease in poultry. LPAI viruses have the potential to evolve into HPAI viruses (see above) and this has been documented in some poultry outbreaks.

Live attenuated vaccine: A vaccine in which live virus is weakened through chemical or physical processes in order to produce an immune response but without causing the effects of the associated disease.


Monovalent inactivated viral vaccine: A vaccine that contains a single killed virus strain.



Neuraminidase (NA): A type of protein on the surface of the influenza virus. Influenza type A viruses are divided into subtypes and named on the basis of two proteins on the surface of the virus: hemagglutinin (HA) (see above) and neuraminidase (NA).

Novel influenza virus: A viral subtype that has not previously circulated in pigs.


Orthomyxoviridae: A family of viruses that includes the viruses which cause influenza.

Outbreak: Sudden appearance of a disease in a specific geographic area (such as a neighborhood or community) or population.


Pandemic: An epidemic occurring over an especially wide geographic area, usually across multiple continents. Many people quickly become ill, and the disease spreads to different countries and continents. Pandemics are unusual events and their timing cannot be predicted. They can occur when a new (novel) influenza A virus emerges and spreads globally. (see influenza pandemic)

PCR (polymerase chain reaction): A process that enables researchers to produce millions of copies of a specific DNA sequence in a matter of hours.

Phylogenetic tree: A form of cladogram (branching diagram), that illustrates how individual SIV isolates are genetically related to each other without reference to time. (see dendrogram)


Quarantine: A strategy used by public health authorities to contain the spread of a contagious disease. It involves the separation of people who have been exposed to a certain illness and may be infected but are not yet sick in order to stop the spread of that disease. Quarantine is medically very effective in protecting the public from some diseases by stopping the spread of that illness.


Reagent: A substance used to produce a chemical reaction to detect, measure, and produce other substances.

Receptor Binding Site: A site on the domain of a virus that attaches to the epithelial cells in the respiratory tract of the host during infection.

Reservoir: An alternate or passive host or carrier that harbors pathogenic organisms, without injury to itself, and serves as a source from which other individuals can be infected.

Reverse Transcriptase PCR (RT PCR): The reverse transcription-polymerase chain reaction is a laboratory technique for amplifying and sequencing an RNA molecule, such as the HA gene of SIV.


Seeding: To inoculate microorganisms into a culture medium.

Serology: The branch of science dealing with the measurement and characterization of antibodies and other immunological substances in serum.

SIV: Swine influenza virus.

Spanish influenza: The common name of the influenza A virus responsible for the 1918-1919 pandemic. (see influenza pandemic).

Strain: A specific genetic variant of an organism. (see Influenza viral strains).

Surveillance: The ongoing, systematic collection and analysis of data and the provision of information which leads to action being taken to help prevent and control an infectious disease.


Trivalent inactivated viral vaccine (TIV): A vaccine that includes three virus strains which have been inactivated. The trivalent vaccine for human influenza contains H1N1, H3N2, and B strains.

Typing and subtyping: The process by which viral or bacterial strains are identified.



Vaccine: A biological preparation that establishes or improves immunity to a specific disease.

Vaccine Production: Influenza virus vaccines usually are produced by growing approved seed viruses in fertilized chicken eggs, purifying and chemically treating the harvest (inactivation).

Vector: An organism that transmits an infective agent from one host to another.

Viral Shedding: The process during which a virus is present in an area of the body and is excreted. Pigs normally shed SIV from the nasal cavity beginning the first day post-infection and for up to 7 days. Shedding of influenza viruses can take place even if an infected animal is showing no symptoms of disease.

Virus: A strand of DNA or RNA in a protein coat that must occupy a living cell to replicate. Viruses cause many types of illness, including influenza. Influenza viruses are composed of RNA. Viruses are not affected by antibiotics.

Virus Isolation (VI): One in a series of tests to isolate and specifically identify H and N subtypes of the swine influenza virus.