Glossary: COVID-19 Testing Technical Terms
Antibody: A protein produced by the immune system that circulates in the blood or mucous. There are several subclasses of antibodies (IgG, IgM, IgA, IgE, and IgD) that are produced by immune B cells. These subclasses of antibodies are typically found in different tissue environments—eg, IgA is typically found in mucous membranes—and emerge at different times during the infection timeline: IgM typically emerges earlier, within 5 to 10 days of infection, and IgG levels rise 8 to 14 days after infection and persist for several months.
Antigen: A substance recognized by the immune system. It can originate outside the body (such as a viral protein) or from within the body (which may lead to autoimmune disorders).
Asymptomatic infection: An infection that never produces significant symptoms throughout the course of infection and recovery. A person with an asymptomatic infection with SARS-CoV-2 could transmit the virus and infect others but not have any symptoms of disease.
Chemiluminescent Immunoassay (ChLIA): An immunoassay which is similar to an ELISA, except that the reporter molecule creates a light-based read-out. A protein of interest is immobilized, and a reporter antibody/reagent is then added. The level of light produced is then measured, and the protein of interest can be quantified. Some tests use multiple luminescent reagents, such as coated beads that can attach to protein-bound antibodies.
CLIA: Referring to the status of a Clinical Laboratory Improvement Amendments- approved laboratory. This is a program run by the CDC that provides certificates to laboratories that certify them to run certain types of assays. A lab with CLIA certification will typically have a CLIA number associated with the lab.
COVID-19 (coronavirus disease 2019): The disease caused by SARS-CoV-2 infection. The disease and causative virus were first identified in Wuhan, China, in December 2019 and quickly spread throughout the world. COVID-19 can cause a variety of symptoms, including fever, loss of smell or taste, diarrhea, extreme fatigue, and coughing. Symptoms appear 2 to 14 days after exposure to the virus, although some individuals may be infected with SARS-CoV-2 and not develop symptoms at all (see asymptomatic infection). COVID-19 may be mild, moderate, or severe.
CRISPR (clustered regularly interspaced short palindromic repeats): Specific sequences found originally in bacteria that serve as an “immune system” for microorganisms. “CRISPR” is often used interchangeably with the technologies manipulating CRISPR sequences for genomic editing or detection of specific sequences, which involve the Cas enzyme (ie, CRISPR-Cas9). These tools allow for precise cutting, and sometimes editing, of DNA.
Diagnostic test: A test intended to diagnose an illness or condition, usually within a symptomatic or suspected presymptomatic population.
DNA (deoxyribonucleic acid): The type of nucleic acid that composes the genome of humans.
End-to-end testing service: A service performed by the same group or organization that includes the distribution, performance, and analysis of tests.
Enzyme-linked Immunosorbent Assay (ELISA): This is typically a plate-based assay run in a laboratory that detects the concentration of a molecule of interest, such as a protein. A sample is added to an ELISA plate, and the protein of interest is bound. Then, reporter-antibodies (linked to an enzyme) specific to that protein are added to provide a color-based read-out. This can quantify the amount of a protein of interest in a sample.
Epitope: A specific segment of an antigen that is recognized by an antibody or immune cell.
False negative: A negative test result from a sample that is truly positive. For example, if a person was truly sick with COVID-19 but received a negative test result, that would be a false negative.
False positive: A positive test result from a sample that is not truly positive. For example, if a person was truly uninfected but got a positive test result, that would be a false positive.
Incidence: The rate of new infections; this is also referred to as the attack rate. The proportion of an initially disease-free population that develops disease, becomes ill, or dies during a specified (usually limited) period of time. This includes only new cases. In other words, the proportion of emerging cases of a disease or attribute in a population.
LAMP (loop-mediated isothermal amplification): A method of DNA amplification that relies on a series of 6 primers and probes that is run at a single temperature. This contrasts with PCR, which relies on cycling of several different temperatures using specialized equipment (thermocycler).
Lateral flow assay (LFA): A paper-based test that detects the presence of an analyte (i.e. an antigen or antibody) in a bodily fluid. The assay has reagents that flow across the paper, along with the sample being tested, that can then be captured by molecules stuck to the paper strip. This capture provides a read-out that can signal the presence of the analyte or provide a negative result.
Medical countermeasure (MCM): Medicines or medical supplies that diagnose, prevent, protect from, or treat conditions associated with chemical, biological, radiological, or nuclear (CBRN) threats, emerging infectious diseases, or natural disasters.
Midturbinate swab: A swab that is inserted beyond the anterior naris (about 1 to 2 inches up the most immediate portion of the nostrils) until resistance is met at the turbinates of the nose. View this diagram.
Molecular: In the context of COVID-19 diagnostics, molecular refers to tests that amplify and detect viral genomic material. For SARS-CoV-2, that genomic material is RNA.
Nasal swab: A swab that is inserted approximately 2 inches into the nostrils/anterior naris.
Nasopharyngeal swab: A swab that inserted past the nostrils and turbinates of the nose, into the nasopharynx area.
Negative predictive value: The probability that a negative test result is truly negative. As an equation,NPV= (TN/(TN+FN)).
Neutralization assay: An assay that tests the inhibitory properties of antibodies (or another substance) on viral growth; the test essentially detects how effectively antibodies “neutralize” a virus from infected and growing in cell culture.
NAAT (Nucleic acid amplification test): an assay that amplifies and detects the nucleic acid from the viral genome; this type of test includes rRT-qPCR, and RT-LAMP and is often used as a synonym for a molecular diagnostic (but does not including antigen tests).
PCR (polymerase chain reaction): A method of DNA amplification that relies on primers specific to a region of DNA and probes that detect any amplified products.
Positive predictive value: The probability that a positive test result is truly positive.
Presymptomatic infection: An infection case in which the individual has not yet developed symptoms but will eventually have symptoms over the course of infection and recovery.
Prevalence: The proportion of people in a population who have a particular disease or attribute at a specified point in time (or over a specified period of time). This includes all cases. In other words, the proportion of a population exposed to a disease or attribute.
PRNT (plaque reduction neutralization test): This is often used to describe an antibody neutralization assay, where antibodies are studies to understand their ability to inhibit the growth of viral plaques.
qPCR (quantitative polymerase chain reaction): Which not only amplifies genomic material but also quantifies it based on signals from probe binding to target regions. This typically requires specialized equipment and software for analysis.
Qualitative test: Data that are descriptive. In the context of COVID-19 testing, a qualitative result gives a positive/negative readout but does not quantify/measure the molecule being detected.
Quantitative test: Data that can be measured using numbers. In the context of COVID-19 testing, a quantitative test result gives an amount of the molecule being detected (for instance, viral copies/mL or a concentration of antibodies).
Reverse transcriptase real-time PCR (rRT-PCR): an assay that couples reverse transcription to real time PCR, so that reverse transcribed DNA can be amplified and quantified by PCR.
Reverse transcription: The reaction using a reverse transcriptase enzyme to produce DNA from a sequence of RNA.
RNA (ribonucleic acid): A molecule composed of repeating units of ribonucleotides (a sugar [ribose], a phosphate group, and a nitrogenous base). This is the type of nucleic acid that composes the genome of SARS-CoV-2. RNA differs from DNA (the type of molecule that makes up human genomes). RNA must be carefully extracted from samples and stored, as it is less stable than DNA.
RPA (recombinase polymerase amplification): A method of isothermal amplification of genomic material that depends on enzymes called recombinases, as well as primers specific to a sequence of interest.
Saliva: A watery mixture that contains molecules such as mucins, proteins, and salts, produced in the mouth by salivary glands. A sample of saliva from an individual is usually procured by the individual spitting into a collection tube or cup
SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2): The name of the causative agent of COVID-19. SARS-CoV-2 is a coronavirus, with a positive-sense, single-stranded RNA genome and is highly contagious in humans.
Screening: A type of test or inquiry intended to routinely survey a population for an illness or condition, regardless of symptoms or epidemiologic context. Usually done in an asymptomatic population. In the context of COVID-19, screening can be performed in populations even when there is no indication of exposure or observation of symptoms.
Serology: The study or diagnostic use of serum; in the context of COVID-19, serology typically refers to the study of human serum for evidence of antibodies specific to SARS-CoV-2, which is indicative of past COVID-19 infection.
Seropositive: An individual who has antibodies specific to SARS-CoV-2.
Seropositivity: Seropositivity does not necessarily indicate that someone is immune to reinfection. The absence of antibodies can mean many things. Antibody levels decline over time naturally, even if the immune system would be able to recognize and fight a reinfection. Or, a person may never have been exposed to the virus. While patients can simultaneously test positive for diagnostic and serologic tests, seropositivity typically occurs later during the disease. Antibodies are one measure of our incredibly complex immune response to infection, and serology tests are one of many tools to understand past exposure to SARS-CoV-2.
Seroprevalence: The proportion of existing and new seropositive individuals in a community over a defined period of time. In the context of COVID-19, it is the proportion of individuals in a population with antibodies specific to SARS-CoV-2.
Serosurvey: Surveillance studies performed using serology/antibody testing (or, equivalently, serological testing), which may be used to identify whether people were previously infected by SARS-CoV-2.
Sputum: Also known as phlegm, sputum is a mucous coating in the lungs and respiratory tract that can be coughed up to provide a sample. It is not the same as saliva, which is secreted in the mouth.
Surveillance: In the context of disease, it is the continuous monitoring of disease in a population. It can also be defined as “ongoing, systematic collection, analysis, and interpretation of health-related data essential to planning, implementation, and evaluation of public health practice.”
TMA: (Transcription mediated amplification) a type of nucleic acid amplification test that uses 2 enzymes to amplify a gene of interest. In TMA, primers that bind to a region of interest include a T7 RNA polymerase promoter, which enables RNA amplification. These RNA strands are then reverse transcribed into cDNA, the old RNA strand is removed by RNAseH, and the cDNA can then be detected and/or quantified. This method is also isothermal, and very rapid.
Test sensitivity: The proportion of positive test results out of all truly positive samples.
Test specificity: The proportion of negative test results out of all truly negative samples.
True negative: A negative test result from an individual who is truly uninfected. For example, a negative COVID-19 test result from an individual who is truly uninfected.
True positive: A positive test result from a sample that is truly positive. For example, a positive COVID-19 test result from an individual who is truly infected with SARS-CoV-2.