To help everyone better understand the technical terminology associated with the virus, vaccines and treatments, CRB has assembled this “virus vocabulary” – a glossary of key terms associated with the COVID-19 crisis. Our clients, scientists and engineers in the pharmaceutical industry use these terms every day. But there’s an opportunity to expand the public’s understanding, as the more we know about the science and infrastructure behind the world’s response, the better off we’ll be.
To supplement our COVID-19 insights, this resource breaks down the key terms into the four main categories found in the lifecycle of vaccine development: research and development (R&D) for treatments, clinical testing, medical applications and production of a finished medical product.
Virus Vocabulary Catagories Key
Coronaviruses are large, enveloped, positive-strand RNA viruses divided into 4 genera: alpha, beta, delta, and gamma, of which alpha and beta CoVs are known to infect humans. They are not related to the influenza virus.
The surface spike (S) glycoprotein is critical for binding to host cell receptors in the airway. The major coronavirus structural proteins are the E, N, S and M proteins. The N protein is inside the viral particle and protects the RNA. These are the proteins likely to cause an antibody response.
Sequencing the genome of the virus is the first step in developing a specific test for the presence of the virus in infected people. The polymerase chain reaction (PCR) test has primers that identify SARS-CoV-19 the genes for S and N.
This is the scientific designation for the coronavirus identified in Wuhan China in late 2019.
SARS-CoV is the designation for the virus isolated in 2003 that causes the disease now known as SARS.
SARS is an anacronym meaning Severe Acute Respiratory Syndrome
COVID-19 is the disease caused by the SARS-CoV-2 virus, which is analogous to acquired immunodeficiency syndrome (AIDS) being caused by human immunodeficiency viruses (HIV).
An RNA virus is a virus that has RNA as its genetic material, usually single-stranded RNA but may be double-stranded RNA. Notable human diseases caused by RNA viruses include Ebola virus disease, SARS, COVID-19, rabies, common cold, influenza, hepatitis C, hepatitis E, West Nile fever, polio, and measles. An RNA virus does not need to make DNA to replicate but carries genes for replicating using an RNA-dependent RNA polymerase.
A retrovirus, like HIV, is a type of RNA virus that inserts a copy of its genome into the DNA of a host cell that it invades, thus changing the genome of that cell. It will remain as long as that cell lives. The retrovirus uses its own reverse transcriptase (RNA-dependent-DNA polymerase) enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backward).
A virus is a nucleic acid made up of genetic material (RNA or DNA) and coated in a protein. Because viruses are acellular, they need to invade a host cell to reproduce. This normally destroys the host cell and causes disease. A retrovirus is a particular type of virus that uses RNA (ribonucleic acid) as its genetic material. Retroviruses insert their genome into a host genome by reverse transcription. A DNA virus is a virus in which the genetic information is stored in the form of DNA. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). Notable diseases like smallpox, herpes, and chickenpox are caused by DNA viruses. They replicate their genome using a DNA-dependent DNA polymerase.
Basic reproduction number (denoted R0, or R zero) of an infection can be thought of as the expected number of cases generated or infected by each one case in a population. If R is greater than 1, the infection will spread. If R is less than 1, the infection will die out.
Vaccination or immunity due to previous exposure will reduce R0. If half of the population is immune, an R0 of 2 will be reduced to 1. R0 for SARS-CoV-19 is estimated to be 2.2. By comparison, the seasonal flu has an R0 of 1.3, but a large portion of the population is vaccinated each year.
The transmission rate (β) is defined as the number of persons infected per infectious person per day. In a simple model, where γ is the recovery rate (or the inverse of the infectious period), R0 = β/ γ
A fine mist.
Close-range aerosol transmission is an important mode of transmission for infectious respiratory diseases. Talking, breathing, coughing, and sneezing create an aerosol (a suspension of particles in the air) containing particles in a range of sizes, with viable infectious organisms present in both small ≤ 5 µm and large particles ≥ 5 µm or droplets. Airborne transmission can occur through the inhalation of small airborne particles very close to an infectious source—i.e., within 6 feet. Small particles can remain airborne for hours as they are not heavy enough to fall to the ground but move by diffusion.
To prevent, inhibit, make less severe, less serious, less painful. To actively make a change.
In terms of changing the rate or spread of a pandemic, mitigation strategies effectively reduce R0. This could be by reducing the transmission rate or increasing the recovery rate.
Once an infected individual is identified, contact tracking or tracing is the process of identifying, assessing, and managing people who have been exposed to a disease to prevent further transmission. People who may have been exposed are systematically followed for the maximum incubation period for the disease from the date of the most recent exposure. This process allows for the rapid identification of people who become symptomatic. Contact tracing is one of the tools to effectively break chains of transmission and control outbreaks.
The inflammatory response is a part of the innate immune system that responds to infection and injury. It is a protective response involving immune cells, blood vessels, and molecular mediators. The function of inflammation is to eliminate the initial cause of cell injury, clear out necrotic cells and tissues damaged from the original insult, and initiate tissue repair. However, if the tissue area is large, the process itself may cause further tissue injury, edema (swelling), and pain.
Gamma globulins, or antibodies, are a part of the immune system that learns from exposure to foreign or non-self antigens on bacteria or virus or even, in some cases, cancer cells. An antibody is concocted in the immune cells out of pieces of DNA inherent in the genome and pieced together until able to bind to a specific feature, called an epitope, on the non-self antigen. This natural process takes a few weeks or months. The body will form a small collection of antibodies that each attack only one epitope and collectively, with help from the immune system, can neutralize the invader. Each specific binder is from the rearranged DNA in a B-cell clone that remains and can be called up immediately upon reinfection.
In 1975, Georges J.F. Köhler and Céasar Milstein devised a process for isolating and immortalizing mouse B-cells outside the body and some 20 years later the first human therapeutics based on this process entered the clinic. Now monoclonal antibodies represent a huge and effective class of drugs for myriad of conditions, especially cancer.
Antisera is the part of blood, the serum or plasma, that contains circulating gamma globulins. If taken from an individual exposed or immunized to a pathogen, the antisera will contain antibodies that specifically bind epitopes on that pathogen. The concentration of the specific antibodies is also called the titer. High titer antisera can be used therapeutically to treat or prevent the infection caused by that same pathogen. The problem is that the source is limited to a single individual. Using animal antisera may cause a rejection response as parts of the animal antibodies and other proteins in the serum will be seen as foreign.
An individual antibody, derived from a single B-cell, or “clone,” has specificity for a small surface area on a protein, not the whole protein. This surface area is called the epitope and can be a linear sequence of amino acids, usually 4 to 8, or can be where the protein folds over on itself and therefore recognize discontinuous stretches of the protein sequence. To be effective as a therapeutic, a single antibody (monoclonal) has to strategically bind to an epitope in such a way as to prevent something else from binding to that protein, (e.g. a hormone or a virus particle) or interfere with the function of that protein itself.
A class of medication used specifically for treating viral infections rather than bacterial ones. A medication that limits the spread, effect or replication of the virus. Differentiated from anti-bacterial.
Understanding a virus’ mode of infection and replication offers opportunities for attacking the virus or its ability to spread in the body and in the community.
Anti-virals have seen partial success against the flu. Tamiflu® (oseltamivir) is in a class of medications called neuraminidase inhibitors that works by stopping the spread of the flu virus in the body. Broad-spectrum antivirals, such as remdesivir, an RNA polymerase inhibitor, as well as lopinavir/ritonavir and interferon beta have shown promise against MERS-CoV in animal models and are being assessed for activity against Covid-19.
Since 1796, researchers (Edward Jenner and Louis Pasteur were early pioneers) recognized that the immune system when repeatedly exposed to pathogens has the ability to protect itself. Giving a small amount of virus, attenuated (reduced in efficacy) or inactivated, results in the host production of circulating protective antibodies. For over 100 years, vaccines have been produced by growing the pathogen, attenuating or killing it, and injecting the virus or subcomponents of the virus in a controlled fashion to stimulate an immune response in the host to raise antibodies.
Making and purifying proteins can be achieved using several well-worn platforms. Molecular biologists identified specific sequences that the cell uses to mark proteins for export (secretion) out of the cell. These sequences are known as leader or signal sequences. Through genetic engineering, a well-known leader sequence is added to the coding sequence for the subunit protein to be formed by the cell and host cell will dutifully send it on the path to be pushed out into the culture medium in which it is growing. This makes harvesting and purification more facile as new growth mediums do not have added extraneous proteins.
If the protein antigen is a glycoprotein – it has polysaccharide chains appended to the amino acids of the peptide backbone – it may be amenable to ion exchange chromatography.
Purification may include filtration or centrifugation steps and chromatographic techniques that work on general principles: size exclusion, hydrophobic interaction, cation or anion exchange; as specific affinity chromatography is not available.
Platform technology is a term for standardization of technology or process approach that enables the manufacture of multiple products and processes that support present or future development. It establishes the long-term capabilities of research and development institutes. Biopharmaceutical platform technologies include, for example, methods for producing proteins, selecting or producing antibodies, or changing the DNA of a cell.
A passive vaccine is an antisera or monoclonal antibody that recognizes and neutralizes a target pathogen or cancer epitope. It is used therapeutically to treat disease. It will generally not last as long as the body’s own antibody response if one were to develop. Passive immunization is the term used when the antibody formed in one individual is given to another individual who is at risk of infection — the protection is temporary
Rather than introducing a whole inactivated or attenuated micro-organism to the immune system (which would constitute a “whole-agent” vaccine), a specific subunit (protein or fragment) can be used to create an immune response able to kill or remove the microorganism from the body or interfere with the virus’ ability to latch onto and gain entry into human cells. Examples include the subunit vaccine against Hepatitis B virus that is only the surface proteins of the virus and is produced by genetic engineering of those proteins in a yeast culture; the virus-like particle (VLP) vaccine against human papillomavirus (HPV) that is composed of the viral major capsid protein displayed on a lipid vehicle; and the flu vaccine that is composed on only the hemagglutinin (H) and neuraminidase (N) subunits of the influenza virus.
Nucleic acid vaccines are the delivery of DNA or RNA into the body that is engineered with genes that make viral proteins. DNA (or RNA) vaccination involves the direct introduction into appropriate tissues of a plasmid containing the DNA sequence encoding the antigen(s) that trigger the desired immune response. This relies on the in situ (in the body) production of the target antigen. This approach offers a number of potential advantages over traditional approaches, including the stimulation of both B- and T-cell responses, improved vaccine stability, the absence of any infectious agent, and the relative ease of large-scale manufacture. Platforms are based on exploiting the very cleaver machinery developed by viruses for their ability to insert genes into cells in the human body and get the proteins expressed (made) directly in the body. This machinery is called a viral vector. Popular platforms are the AdV (adenoviral vector), AAV (adenovirus-associated vector), lentivirus, and retroviral vectors (derived from HIV). Nucleic acid-based vaccines can only express one or two viral antigens.
A live vector vaccine is a vaccine that uses a chemically weakened non-competent virus to transport pieces of a pathogen in order to stimulate an immune response. The genes used in this vaccine are usually antigen coding surface proteins from the pathogenic organism. Viral vectors are produced by growing the live virus in host cells, which are released by breaking open (lysing) those cells and collecting virus particles. Micro/microfiltration, such as tangential flow filtration or dead-end filtration, combined with chromatography methods are used for large scale purification.
In contrast to harvesting methods using cell lysis, retroviral or lentiviral vectors are harvested from supernatant (the liquid separated from a solid in a solution). Supernatant requires first a clarification and concentration step followed by column purification.
Purification ensures there is an acceptable vector concentration, that the vector product has high transduction (the process by which foreign DNA is introduced into a cell by a virus or viral vector) efficiency, and that it does not compromise target cell functionality due to the presence of contaminants.
PCR stands for polymerase chain reaction as is made possible using a thermostable (not readily destroyed or deactivated by heat) polymerase originally isolated from bacteria. Polymerases require short sections of duplex (where the complementary base pairs associate) DNA as a “priming” structure to begin adding additional nucleotides. Once the new strand is formed, the assay mix is heated to separate the two complete strands, the reaction is cooled and new primed duplexes will form, and so the cycle continues. RT stands for real-time and sometimes for reverse transcriptase. The nucleotides added contain colored markers. The sample will increase in color over time in proportion to the concentration of target DNA or RNA that specific primers bind and form duplexes with. The test is therefore rather complex, requires several sample dilutions to be run concurrently as well as control reactions, and the final determination of positive or negative depends on setting thresholds for reaction rates and signal (color).
PCR tests rely on certain standard reagents (substances used in chemical analysis): sample collection devices, sample preparation reagents, the polymerase (the enzyme that synthesizes the DNA or RNA), and the nucleotides (monomeric units that build each nucleic acid strand) that are available off the shelf. What is unique for each test is determining the sequence of the DNA or RNA of interest that will be unique to that cell or organism and making short ~20 base stretches to both sides of the duplex (a primer set). Positive and sampling control primer sets are also included. The CDC’s initial SARS-CoV-2 test kit was intended to have two primer sets (the test kit reagent) specific for the N protein gene sequence and an additional set of primers to rule out other viruses.
A serology test looks for the presence of antibodies made in response to infections in the blood. An infected person will not develop a detectable titer of antibodies until 3 or 4 weeks after being infected whether the infection resulted in symptomatic disease or not. Antibody test results are important in detecting infections or “exposure” with few or no symptoms.
The active or active pharmaceutical ingredient (API) is the pharmaceutical substance that is responsible for the activity of the drug. A drug or therapeutic encompasses the active and the formulation, and in some cases, the delivery vehicle such as a syringe. Formulations and unit operations like coatings and encapsulation become part of the drug because they can change the release of the active and the distribution in the body.
The amount of active in a drug for each time of administration. The dose may be given once per day or more than once per day, or some other period. It may be an oral solid dosage (OSD) taken once or be a liquid infused over several minutes or hours.
Drugs products are approved for a specific indication, in a specified patient, and at a specific dose or doses at a defined frequency and period of treatment. Drugs are approved by a government authority once found to be safe and effective for the intended use as determined by clinical testing. Actives are not approved by themselves for any treatment protocol. “Off label” use means that a practitioner has prescribed an approved drug but not for the approved indication, patient group, or dosage. A drug may be approved that contains the same active as another drug but in a different dosage form.
Clinical trials are research studies that test new medical approaches for efficacy and safety. Each study answers scientific questions and tries to find better ways to prevent, screen for, diagnose, or treat a disease. Clinical trials may also compare a new treatment to no treatment, to a placebo, or to a treatment that is already available. The Food and Drug Administration’s (FDA) Emergency Use Authorization (EUA) authority allows the FDA to facilitate the availability and use of investigational treatments during public health emergencies such as COVID-19. Hydroxychloroquine is an example for this pandemic.
Every clinical trial has a protocol, or action plan, for conducting the trial. The plan describes what will be done in the study, how it will be conducted, and why each part of the study is necessary. Each study specifies who can take part based on gender, age, disease parameters, and how many participants are needed. Studies may start with healthy volunteers to test safety only and then progress to volunteers with a certain disease. Studies may exclude subjects that have already received some other treatment or have comorbidities (a co-occurring condition) as this may complicate the analysis of the outcome.
An Institutional Review Board (IRB) reviews, monitors, and approves many clinical trials. It is an independent committee of physicians, statisticians, and members of the community. In the United States, a clinical trial must have an IRB if it is studying a drug, biological product, or medical device that the FDA regulates, or it is funded or carried out by the federal government.
Studies must be ethical, protect the rights and welfare of the participants, and have a level of risk that is reasonable when compared to the potential benefits.
This is the first stage of testing a new drug or treatment. Researchers test a drug or treatment in a small group of people (20–80) for the first time. The purpose is to study the drug or treatment to learn about safety, toxicity, and identify side effects in humans. Often this is a dose-ranging study, or a study where different doses are tested against each other, to find the level where no side effects are found after a short exposure. Phase I can only be initiated once efficacy, toxicology, and metabolism studies are completed in animals. A Phase I study may only take a few weeks of testing.
In certain diseases or situations, or if there is already safety information in humans, a trial that combines advanced safety and preliminary efficacy is designed. This mainly means that some parameter is quantified that indicates the drug is working as expected on some disease parameter. For example, a drug is tested in diabetics for safety, and, at the same time, HbA1c is measured to see if it modifies blood glucose. In a respiratory illness, it may be time before progression to needing a ventilator. Phase I/IIa studies inform the protocol for a Phase IIb leading directly to the confirmatory Phase III.
The new drug or treatment is given to a larger group of people (100–300) to determine its effectiveness and to further study its safety. A Phase II study will usually be designed so that it is short and may use “surrogate” endpoints rather than measuring a change in the disease status or patient outcome itself.
A small study designed to rule in or out parameters that will be taken forward to a definitive Clinical Phase III trial.
An experimental drug or treatment is given to groups of people (1,000–3,000 or more) large enough to confirm its effectiveness by statistical analysis of the selected primary endpoint as compared to a control group not receiving the drug. The trial is “randomized” when people enrolled in the study are randomly assigned to the control or treatment group. They are blinded to this fact (single-blind) and the clinicians administering the drug may also not know to which group the test subject is assigned (double-blind). The trial will monitor side effects, quality of life issues, and any other information that will allow the new drug or treatment to be used safely. The trail will also compare the drug with the standard of care or similar treatments. A pivotal Phase III trial is needed for approval to register and use the drug commercially. The duration of the test period will depend on the time it takes to enroll enough patients that meet the study criteria and the time it takes for the benefit to be clearly determined (statistically significant difference in the primary endpoint). In cancer that could be 5-year survival. In kidney disease, it could be the need for a transplant. In infection, measurement criteria could be the number of days in the hospital. The experimental drug used in a Phase III clinical trial will be manufactured under much higher regulatory scrutiny mimicking that of commercial manufacturing, especially parenteral drugs, which are administered non-orally, such as through intramuscular, subcutaneous, intravenous or intradermal injection.
Injecting foreign agents into the body is a delicate proposition that comes with risks. As such, whether whole agent, subunit, DNA, or RNA, all vaccines must be produced by culturing in a biologic milieu, e.g. in an egg or in a laboratory, bacteria, animal, or human cell. It must be harvested from that culture. The active must be isolated and purified from the host culture biomaterial without destroying the structure or activity that will produce the immune response. It will then be formulated, packaged, and qualified.
The advent of molecular biology has enabled the potential to produce parts of the virus (subunits), or to use the genetic machinery of the virus (DNA or RNA), to initiate the production of the virus proteins in situ (in the body). All these actives are most efficiently produced inside other living cells: bacterial, animal, insect, human cells, or within plants. Upstream processing steps for vaccines could include host cell expansion, virus expansion, plasmid manufacturing infection, transfection, harvest, lysis, and clarification depending on the platform used.
Once the vaccine organism, subunit or vector has been produced and harvested, it must be purified to remove impurities that could be dangerous to the host receiving the vaccine. Downstream purification steps could include multiple chromatography and filtration steps including final sterile filtration or thermal sterilization (for parenterals) depending on the platform used.
A nosocomial infection is an infection that is acquired in a hospital or other health care facility. It is sometimes instead called a healthcare-associated infection (HAI or HCAI).