Glossary of terms relevant to the Origins of AIDS debate

Adapted from The River


ACQUIRED Obtained during the life of an organism, not inherited; for example: immunity.

ADENOVIRUS A group of DNA viruses that mainly cause respiratory disease and conjunctivitis.

ADVENTITIOUS AGENT A contaminant (e.g., in tissue culture).

AGM African green monkey.

AIDS (Acquired Immune Deficiency Syndrome) The disease caused by HIV. Common presentations ("opportunistic infections") of AIDS include the following: PCP; toxoplasmosis; candidiasis; cryptococcal meningitis; aggressive KS etc. Other, less specific symptoms may include lymphadenopathy, uncontrolled bacterial infections , and weight loss.

ANTIBODY Protein secreted by the immune system, which interacts with a specific invading antigen in an immune response. The presence of antibodies is used s a test for infection by a virus.

ANTIGEN Any foreign substance which, if present in the body, stimulates the immune system to produce antibodies. Each antigen stimulates specific antibodies.

APATHOGENIC Not causing disease.

ARC (AIDS related complex) A prodromal (early) AIDS condition involving mild symptoms, such as skin and chest infections and sometimes Herpes zoster.

ASSAY Test to determine the content or concentration of a substance.

ASYMPTOMATIC Infected, but without symptoms of infection.

ATTENUATE (virus) To reduce the virulence of a virus, achieved by passaging the virus through tissue culture or live animals. The attenuated virus can be used as a vaccine if it infects and immunizes without causing disease.

AUTO-IMMUNE DISEASE Disease caused when an organism’s immune system responds to molecules normally regarded as "self" but which instead act as antigens.

BATCH In this book, a small quantity of vaccine made in a single process, as part of a production lot.

BSE Bovine Spongiform Encephalopathy ("Mad Cow Disease").

CANCER Disease caused by a benign or malignant growth resulting from abnormal and uncontrolled division of body cells.

CANDIDIASIS ("Thrush"); yeast-like infection, often of the mouth or vagina, caused by Candida fungus.

CARCINOGEN Any substance that causes transformation of a normal cell to a cancer cell.

CELL The smallest living membrane-bound unit capable of independent reproduction.

CD4 CELL A type of T-Cell, or lymphocyte, that is a receptor for HIV.

CDC Centers for Disease Control (Atlanta, US).

CELL CULTURE See tissue culture.

CELL LINE A group of dividing cells derived from abnormal tissue (e.g., a tumor) which are immortal. They have abnormal nuclei and almost always produce tumors when injected into an animal. Example: HeLa cells.

CELL STRAIN A group of dividing cells derived from normal tissue, which are mortal (they die after a certain number of cell divisions). They cannot grow when injected into animals. Example: WI-38 cells.

CETC (Chick Embryo Tissue Culture) An in vitro system used to study and grow viruses.

CHALLENGE To administer virulent virus to a test animal that has previously been vaccinated, to check whether the vaccine was effective, and immunity has been established.

CHAT An oral polio vaccine against Type 1 poliovirus, developed in the 1950’s by Dr Hilary Koprowski.

CHRONIC Persisting for a long time.

CJD Creutzfeldt-Jakob Disease, a fatal degenerative brain disease of humans, believed to be caused by a prion.

CLADE Group of organisms which share a common ancestor and form a phylogenetic lineage. In terms of HIV, the term "clade" is often used to refer to a sub-type.

CMV Cytomegalovirus. A common, normally harmless virus, but which causes disease in immunosuppressed patients.

COHORT A trial group.

CONGENITAL Present at birth.

CONGO Until 1960 called Belgian Congo; then called Republic of the Congo, or Congo-Kinshasa, until 1972, when its name was changed to Zaire. In 1997 the name reverted to the Republic of the Congo. Not to be confused with Congo-Brazzaville CPE (Cytopathic Effect) – The visible abnormality or destruction caused to cells in culture by viruses (e.g., by poliovirus).

CRYPTOCOCCAL MENINGITIS Inflammatory disease of the membranes of the brain and spinal chord (meninges) caused by fungi of the Cryptococcus genus.

DNA (Deoxyribonucleic Acid) Double-stranded molecule that is the genetic material of all organisms (except RNA viruses).

DYSFUNCTION An abnormality or impairment of function.

ELISA Enzyme-Linked ImmunoSorbent Assay. A technique used for testing sera for viral antibodies.

ENDEMIC An endemic infection is one which is present in a community without causing epidemics.

ENDOGENOUS VIRUS Virus incorporated into the host cell DNA; generally non- infectious, but capable of replication; only transmitted vertically (from parent to child).

ENTEROPATHIC Pertaining to disease of the alimentary tract.

ENZYME Protein that catalyses biological reactions, eg reverse transcriptase.

EPICENTER Geographical area of highest incidence, eg of a disease.

EPIDEMIC Outbreak of a disease in a region, affecting many people at the same time.

EPIDEMIOLOGY The study of epidemics: their origin, distribution, control etc.

EPIDEMIOLOGY INTELLIGENCE SERVICE (EIS) The department of the CDC which investigates outbreaks of new diseases; formerly, in the fifties, concerned with biowarfare research.

ETIOLOGY The cause of a disease.

EXOGENOUS VIRUS Infectious particle, capable of horizontal transmission (contagious spread from one individual to another).

EXPLANT Fragment of animal or plant tissue from which tissue culture is made.

FACTOR VIII One of the proteins involved in blood clotting, whose deficiency causes hemophilia.

FIBROBLAST Characteristic cell type of the connective tissue.

FORMALIN Chemical used to inactivate poliovirus to produce IPV.

FOUNDER EFFECT Evolution of a closely-related population in a geographical region following the initial introduction of a "founder" pathogen (such as a virus which has been carried there by a human host).

GENE Unit of hereditary information. One gene usually contains the information required to make one protein.

GENETIC ENGINEERING Manipulation of genetic material.

GENETICS The study of heredity and its variations in biological systems.

GENOME Total genetic material of a cell or virus.

GENOTYPE Genetic constitution of a cell or individual.

GERM LINE The cells in an organism that have the potential to form gametes (sperm and eggs).

GROUP M HIV-1 main group.

GROUP N HIV-1 new group.

GROUP O HIV-1 outlier group.

HDCS (Human Diploid Cell Strain) A tissue culture system based on a cell strain of semi-stable, mortal human cells which, because they are diploid (containing pairs of identical chromosomes), can reproduce by division. Such cells will die after about fifty doublings, by which time they can theoretically have produced several tonnes of cells for tissue culture. Example: WI-38 cells.

HEARTH The place where a disease seems to have originated.

HeLa A vigorous human cell line originating from the cervical tumour of American Henrietta Lacks, who died in 1951.

HEMOPHILIA Hereditary disease in which blood fails to clot at normal speed, due to absence of Factor VIII.

HIV (Human Immunodeficiency Virus) A type of lentivirus which is the cause of AIDS. The virus attacks the body’s T-cells, so impairing the immune system. Three HIVs have been identified: HIV-1 Group M, the most common cause of AIDS, with an apparent epicenter in central Africa; HIV-1 Group O, with an apparent epicenter in Cameroon; and HIV-2, with an apparent epicenter in western Africa.

HOMOLOGOUS genetically related and therefore similar.

HOST Organism or cell that supports a parasite or other organism.

HTLV (Human T-lymphotropic Virus) An oncogenic retrovirus. One type, HTLV-I, causes adult T-cell leukemia. HTLV-III was one of the original names for HIV-1, as proposed by Robert Gallo.

HYPOTHESIS A set of proposed ideas to be used as the basis for further reasoning, without assumption of its truth; a postulated solution used as the basis for investigation or experiment.

IATROGENIC DISEASE Disease caused by medical intervention.

ICL (Idiopathic CD4+ Lymphocytopenia) Immunosuppression similar to AIDS but caused by unknown factors other than HIV. IFA Immunofluorescence Assay. Use of fluorescently-labelled antibodies to detect presence of antigens in a sample.

IMMUNE SYSTEM Animal system that resists infection by pathogens. It involves the production of antibodies by lymphocytes, which bind to antigens, marking them for destruction by other cells.

IMMUNIZATION Administration of antigens to create immunity.

IMMUNOCOMPROMISED Having a defective immune system.

IMMUNODEFICIENCY Condition resulting from a defective immune system.

IMMUNOSUPPRESSION Reduction in the immune system’s response to antigens.

INCIDENCE Rate of occurrence e.g. annually.

INDEX CASE First case in a group to come to medical/scientific attention; case being studied.

INDIGENOUS DISEASE Disease native to a certain place.

INFECTION Invasion and growth of a microorganism in a host.

INFECTIOUS PARTICLE (of virus) An individual virion capable of both infecting a cell and reproducing.

INOCULATE Introduce a pathogen (living or dead) into a human or animal, usually by injection (eg of vaccine).

INTRACEREBRAL (Injection) into the brain.

INTRASPINAL (Injection) into the spinal cord.

IN VITRO In the test tube – literally, "in glass".

IN VIVO In the living creature.

IPV (Inactivated Polio Vaccine) Vaccine containing killed poliovirus.

ISOLATE Microorganism found in an infectee and cultivated on tissue culture.

IVDU Intravenous Drug User; generally applies to non-medicinal use.

KARYOLOGY The study of cell nuclei.

KS (Kaposi’s sarcoma) Type of cancer that can be a symptom of AIDS, particularly in homosexual patients. Discovered in 1995 to be caused by a human herpes virus.

LABILE Unstable.

LENTIVIRUS (also LENTIRETROVIRUS) Type of "slow virus" in the retrovirus family; includes the immunodeficiency viruses (HIV, SIV).

LEO Leopoldville; present-day Kinshasa, Congo.

LEUKEMIA Malignant disease in which bone marrow and other blood-forming organs produce white blood cells in excess.

LOT (or production lot) A quantity of virus (or vaccine virus) that has been grown from a viral seed pool, usually by one or two further passages in tissue culture. In the literature of the fifties and sixties the word "pool" is sometimes used loosely, instead of "lot", to describe a quantity of vaccine – thus "pool 1A of vaccine" would actually mean a vaccine lot produced from the 1A viral seed pool.

LYMPHADENOPATHY Disease causing enlargement of the lymph nodes, often characteristic of AIDS.

LYMPHOCYTE Type of white blood cell, including T-cells.

LYMPHOMA Cancer of the lymph tissue.

MACROPHAGE Large white blood cells produced by the immune system to engulf and destroy foreign bodies.

MALIGNANT (Of a disease) virulent; exceptionally contagious or infectious. (Of a tumor) tending to spread and recur after removal.

MITOCHONDRION The part of the cell that contains enzymes for respiration and energy production. Present only in cells with nuclei.

MKTC (Monkey Kidney Tissue Culture) An in vitro system used to study and grow viruses. Still today the substrate of choice for most polio vaccines.

MOLECULAR CLOCK A theoretical tool used by geneticists in an attempt to determine the rate at which mutations occur.

MONOCYTE Type of white blood cell; differentiates into macrophages.

MONOLAYER Tissue culture consisting of a single layer of cells.

MUTABLE Liable to mutate.

MUTATION An inheritable alteration in the DNA of an organism (or RNA if that is the genetic material); the presentation thereof.

MYCOPLASMA Any of a group of single-celled organisms which possess the smallest known cells. Usually parasitic; probably bacterial in origin.

NATURAL TRANSFER HYPOTHESIS Theory that the four HIVs were introduced to Homo sapiens during the "natural" process of hunting and butchering African primates for food. By itself, this theory fails to explain the apparently recent emergence of the AIDS epidemics.

NFIP National Foundation for Infantile Paralysis, a private charity which bank-rolled polio research in the US in the forties and fifties, largely through fund-raising campaigns like "The March of Dimes".

NEOPLASM New growth; a tumor.

NEUROTROPIC (Virus) affecting the brain.

NEUROVIRULENT Causing damage to the central nervous system (often leading to paralysis or brain dysfunction).

NIH (National Institutes of Health) Bethesda, Maryland.

NOSOCOMIAL (Infection) acquired in a hospital.

NUCLEOTIDE The "building blocks" that make up DNA; the four types are called Adenine, Thymine, Cytosine and Guanine, and are abbreviated to A, T, C and G. The order in which they appear is the DNA sequence. In RNA, the Thymine is replaced by Uracil.

NUCLEOTIDE SUBSTITUTION (also base substitution) Mutation that becomes fixed in the genome and passed on to the next generation.

ONCOGENE Genes which render cells malignant.

ONCOGENIC Any substance capable of inducing such transformation.

ONCOVIRUS Type of retrovirus responsible for causing cancer.

OPPORTUNISTIC INFECTION (OI) Infection with agent that is normally apathogenic, but which causes disease in cases of immunodeficiency.

OPV (Oral Polio Vaccine) Vaccine containing live, attenuated poliovirus.

OPV/AIDS HYPOTHESIS Theory that a contaminated oral polio vaccine was responsible for introducing HIV to Homo sapiens; Louis Pascal’s version is also sometimes known as "the CHAT hypothesis".

OUTLIER In phylogeny, an isolate which is only distantly related, or which lies outside the main cluster of isolates.

PANDEMIC Epidemic of a disease which spreads to more than one continent. Most commonly, however, used to describe a global epidemic.

PARENTERAL Pertaining to the blood stream.

PARENTERAL ADMINISTRATION By injection, not via the alimentary canal.

PASSAGE A passage of virus through a living creature, or through tissue culture, involves inoculating the virus into the chosen medium, allowing it to multiply, and then harvesting it again. The process often causes genetic changes to the virus.

PATHOGEN Disease-causing agent.

PCP (pneumocystis carinii pneumonia) – Infection of the lungs caused by a microorganism, Pneumocystis carinii; the major presentation of AIDS in the Western world.

PCR (Polymerase Chain Reaction) Process involving isolation and amplification of a specific DNA sequence which can then be studied.

PERINATAL Pertaining to the moment of birth, or the few weeks before or after birth.

PHYLOGENETIC TREE A family tree constructed by comparing the genetic differences between species, to determine the possible evolutionary history.

PHYLOGENY Evolutionary history.

PICORNAVIRUS A member of a family of small RNA viruses, e.g., poliovirus.

PIV (Primate Immunodeficiency Virus) – SIV or HIV.

PLAQUE PURIFICATION Technique for purification of viruses. A single virion is selected from a culture, then grown up on a fresh tissue culture. This process is usually repeated three times.

PLASMA Liquid component of blood; what remains when cells (but not clotting factors) are removed.

POLIOMYELITIS (POLIO) Viral disease that can cause paralysis if the spinal cord becomes infected; (formerly also called infantile paralysis).

POLIOVIRUS Virus that normally lives in the gastrointestinal tract, but can cause disease if it migrates to the central nervous system.

POOL (or seed pool) A term used to identify the passage level of a virus (e.g., poliovirus) that has been manipulated (or attenuated) in the laboratory. Sometimes also used, loosely, to describe the production lots (of vaccine), made from a numbered viral pool (e.g., pool 2A of vaccine would mean vaccine produced from the 2A viral seed pool).

PREVALENCE Frequency of disease or infection found in a group, expressed as a proportion or in percent.

PRIMER Short fragment of DNA which is introduced into a PCR reaction in order to define the sequence which one wishes to multiply.

PRION A tiny infectious protein particle, smaller than a virus, that entirely lacks genetic material such as DNA. Prions are thought to be the cause of BSE in cows, scrapie in sheep, and the human diseases CJD and kuru.

PRODROME Early symptom indicating onset of disease.


PROVENANCE Chain of ownership from origin (or birth) to present (or death).

QUASISPECIES The cloud of slightly different viral mutations found in a living host, as distinct from a laboratory clone of a single variant.

RECOMBINATION Process by which genetic material of a cell is exchanged and thus reorganized, for example between two viruses which both infect the same cell. Has important implications for "dating" the AIDS pandemic: because HIV-1 is highly prone to recombination, many researchers doubt that phylogenetic dating is a meaningful technique to apply to this virus.

RETROVIRUS Virus with RNA as its genetic material, which uses an enzyme, reverse transcriptase, to convert the RNA to DNA so that it can become incorporated into the host genome.

REVERSE TRANSCRIPTASE Retroviral enzyme that converts viral RNA into DNA. RIPA RadioImmunoPrecipitation Assay. A technique used to confirm antibody presence.

RNA (Ribonucleic Acid) Type of genetic material present in all living cells, where its role is in the synthesis of proteins from the DNA template. RNA is also the genetic material of RNA viruses (including retroviruses).

RUANDA-URUNDI UN trusteeship in central Africa administered by Belgium until July 1962 when it split into independent Rwanda and Burundi.

SAMPLE A portion; a group being tested.

SAPROPHYTE An organism which lives off dead or decaying matter.

SARCOMA Cancer of the connective tissue.

SEQUENCE The order of the nucleotides in a strand of DNA or RNA.

SEQUENCING Technique used to determine the sequence of nucleotides in fragments of DNA.

SEROCONVERSION Point at which the first antibodies against a pathogen are produced (and detected).

SEROCONVERSION ILLNESS Mild, often ‘flu-like illness sometimes occurring at the time of seroconversion.

SEROEPIDEMIOLOGY Epidemiology based on serological data.

SEROLOGY The study of sera to determine presence of antibodies [or antigens].

SERONEGATIVE Lacking antibodies against (and therefore, usually, immunity to) a specific pathogen.

SEROPOSITIVE Possessing antibodies against (and, therefore, usually immunity to) a specific pathogen.

SEROPREVALENCE Frequency of occurrence of antibodies in a sample, expressed as a proportion or in percent.

SERUM (plural SERA) Liquid component of blood that remains when blood cells and clotting factors are removed.

SIV (Simian Immunodeficiency Virus) Group of lentiviruses found naturally in many monkeys and apes in Africa in which they appear not to cause disease. When acquired by other primates (eg Asian monkeys), SIVs often causes disease. The SIVs are the closest known relatives of the HIVs.

SLIM Common name give to AIDS in parts of eastern Africa where the main symptoms are wasting and diarrhoea.

SPECIATION The generation of two different species from a common ancestor.

SPIROCHETE Large, spirally twisted, unicellular bacterium eg Treponema pallidum which causes Syphilis. STAN Stanleyville, present-day Kisangani, Congo.

STAR-BURST The divergence of a species into different subgroups at around the same time, as represented on a phylogenetic tree. This formation may indicate a time of rapid passage (and mutation), for instance, as a virus spreads in a new host, or an unusual occurrence at the time of divergence.

STD Sexually Transmitted Disease.

STRAIN (viral) Group of closely related viruses.

SUBSTRATE The medium in which a reaction takes place; in the context of this book, the tissue culture used in vaccine production.

SUB-TYPE (viral) Group of viral isolates which are closely related.

SUPERNATANT The liquid above a tissue culture preparation.

SV40 (Simian Virus-40) Tumorigenic monkey virus. It contaminated batches of IPV and OPV in the fifties and early sixties.

SYMBIOSIS Relationship between two organisms that benefits each one.

SYNDROME Disease characterised by a range of symptoms rather than a single presentation.

T-CELL Type of lymphocyte; target cell of HIV.

TISSUE CULTURE Material made by culturing certain animal or plant cells under appropriate conditions to maintain them. Used for cultivating other organisms, such as viruses, in vitro. Also called cell culture.

TITER Measure of the amount of virus, or antibody, present in a given amount of fluid (such as blood).

TITRATE To assess the concentration of a substance in solution.

TOXOPLASMOSIS Fungal infection, typically of the brain, caused by Toxoplasma gondii.

TRANSMISSIBLE Capable of being transmitted; infectious.

TUBERCULOSIS Infectious disease caused by Mycobacterium tuberculosis: the classic opportunistic infection of AIDS in Africa.

TUMORIGENIC Tumor-causing.

VACCINE Preparation that produces immune reaction and acquired immunity to a pathogen, often a virus such as polio. Inactivated vaccine consists of killed pathogen and live vaccine consists of an attenuated pathogen.

VIRAL LOAD Amount of virus in the blood.

VIREMIA Presence of virus in the bloodstream.

VIRION Single, complete virus particle, consisting of a core of nucleic acid, within a protein envelope.

VIRULENCE The destructive or malignant properties of a disease.

VIRUS Minute infectious agent, only able to multiply inside a living host cell.

WESTERN BLOT Technique used to confirm presence of a disease; it identifies the presence in the blood of antibodies to proteins of specific size. WI-38 A human diploid cell strain developed in 1961 by Leonard Hayflick.

ZOONOSIS A human disease acquired from animals (e.g., AIDS, new variant CJD).