A Handy Glossary of COVID-19 Terms and Definitions

What do all these new terms mean? The COVID-19 outbreak has forced us all to take a crash course in infectious disease epidemiology. To help you understand what these terms mean, here is my glossary. I’ll be updating this every day or two.

Feel free to leave me a comment requesting a new term to be added to this list, or letting me know if something needs to be clarified.

Basic rate of reproduction (aka reproduction rate, R0, R-naught)
R0 has gone viral! This is for good reason because, in an epidemic, the most important number used to understand and predict what will happen is the basic rate of reproduction. The term has a technical meaning (I won’t bore you with that) and a more general one; it is the average number of secondary cases each person with the disease will infect. Or, how many other people will a sick person pass the disease to. It can be thought of as a measure of how contagious a disease is. It is important to understand that this is not just about the pathogen, but has as much to do with the pattern of mixing behaviors that bring those infected in contact with those who are susceptible. As a general rule, if R0 is greater than 1, an outbreak cycle will continue until there are insufficient numbers of susceptible persons left to infect, and the epidemic cycle is broken. When R0 is less than 1, the outbreak can be contained and suppressed. Therefore, epidemic control measures (such as social distancing) are aimed at lowering R0 to below 1. The seasonal flu generally has an R0 of about 1.3 (each person with the flu gives it to 1.3 others). While we still don’t know the R0 of this novel coronavirus with certainty, we now believe it is between 2 and 2.5. That means the SARS-CoV-2 virus is about twice as contagious as the common flu. If we are to flatten-the-curve, we must put epidemic control measures in place to lower this number in time to a value below 1.
Case fatality rate (CFR)
Epidemiologists consider the case fatality rate to be one of the most important parameters for understanding an outbreak. The CFR can be thought of as the risk of dying from the disease among those who are infected. It is determined by the lethality of the pathogen, but also the effectiveness of treatment. As is true for all epidemics of a brand new pathogen, the estimation of CFR in COVID-19 has been very challenging. Current estimates range from 0.5% (5 out of 1000) to 5.8% in Wuhan China during the initial outbreak (58 out of a 1,000). The WHO has been estimating 3.4% since March 3, but very few people are happy with this number. The main problem is that because the CFR is calculated by dividing the deaths from COVID-19 by the total number of infections, any big problems in estimating either of these quantities can make the result useless. Right now we do well enough at counting COVID-19 deaths, but it’s not yet possible to accurately estimate the true number of infections because such a high proportion of those have mild or no symptoms and because we haven’t done enough testing. My opinion is that the CFR will be between 5-times and 30-times worse than seasonal flu, which translates to between 5 out of 1,000 (0.5%) to 30 out of 1,000 (3.0%).
Community mitigation strategies
In an infectious disease outbreak, community mitigation strategies are control measures put in place to reduce the negative impact of the outbreak once community transmission has started. For more information, see the CDC’s page on community mitigation strategies (PDF).
Community transmission
This refers to a key part of the epidemic cycle where an infectious disease enters a new area or population and begins to spread (or be transmitted) from person to person within that area after an initial period during which cases came from somewhere else. The start of community transmission is a very important tipping point in an outbreak that separates the containment phase (before) and the mitigation phase (after). You can think of community transmission as the point at which a disease becomes established and is ‘homegrown’, regardless of where it might have come from. The United States is now experiencing sustained community transmission of COVID-19.
Contact tracing
An outbreak control measure used during the containment phase. It is a labor- and time-consuming process of identifying, locating and contacting any and all persons who might have had contact with infected persons who have brought the disease to a new area. The goal of contact tracing is to stop community transmission in its tracks by isolating those who might act as bridges between an outside outbreak and a new area. Contact tracing is generally not a good use of resources once community transmission is firmly established and the strategy shifts from containment to mitigation.
An outbreak control strategy designed to stop an epidemic cycle from taking hold in a particular place. Containment is used early in an outbreak when the people who were infected elsewhere come into a new population and community spread has not yet begun in earnest. This usually involves isolating infected persons and doing careful contact tracing to find and isolate anyone who has had contact with those who are infected.
There is nothing new about coronavirus. The term refers to a family of common viruses that have been known about for a very long time. The name refers to the ‘crown’-like shape seen on the outside of the virus under a very powerful microscope. There are seven different versions of coronavirus that can infect and cause illness in humans. In nature, these viruses live in bats and other animals, often without causing disease. Most coronaviruses cause only mild symptoms; a large percentage of ‘common colds’ every year are caused by a version of coronavirus.
Covert cases
People who are infected with a pathogen, but who have mild symptoms or no symptoms at all are referred to as covert cases. In the COVID-19 pandemic, identifying and counting covert cases remains a top priority. It is likely that covert cases are driving the epidemic because even though these people have mild or no symptoms, we now believe they are capable of spreading the disease to others. Covert cases are not the same as pre-clinical cases. It is now estimated that up to 60% of all infections are covert cases. This is a major reason the R0 value for COVID-19 is higher than 1 and why the disease is spreading so fast. For details, see the commentary in Nature Microbiology.
Refers to the disease in humans caused by a version of coronavirus that recently jumped from animals to humans in the fall of 2019. More specifically, the disease is caused by SARS-CoV-2. It is closely related to an earlier version of coronavirus that caused an epidemic (but not pandemic) of illness in 2003 called SARS. COVID-19 is more easily transmitted (contagious) and more severe than regular flu or the common cold. The main symptoms are fever, cough and shortness of breath. Not everyone who has the disease has all these symptoms. Only 88% of people with COVID-19 had a fever. Muscle pain, runny nose, congestion, nausea and sore throat are less common symptoms. The majority of cases involve only mild symptoms, but some develop a severe lung infection (pneumonia).
The occurrence of disease in a particular time and place in excess of what is expected. A disease that is consistent at expected levels is referred to as endemic (meaning it is ‘normal’ part of a given place). An epidemic is an outbreak of disease that is greater than expected and indicates that something about a disease, a place or the people has changed.
Epidemic cycle
In infectious disease outbreaks, the epidemic cycle refers to the time between the start and end of an outbreak, during which the disease tries to survive and spread itself, and the population tries to prevent the spread and defeat the illness. This tug-of-war leads to a dynamic process that is well-understood to the science of epidemiology. We track the progress of an epidemic cycle by counting new cases over time (by hour, weeks or days), creating an epidemic curve that shows how the disease is moving through the population. That curve takes on a predictable shape determined by the number of infected persons, the number of people who are susceptible to become infected, and the contact between them. How fast the outbreak occurs, and when it stops is determined by the pathogen, the place, and by people’s behavior. Outbreaks tend to end on their own even if we do nothing to stop them because, at some point, there are not enough susceptible persons left to keep the cycle going and the outbreak fizzles. Social distancing and other control measures are designed to alter the shape of the epidemic curve and to slow the cycle of the epidemic.
The science of how diseases occur in populations and how to prevent and treat them. It is a main arm of public health and a branch of medical science. Epidemiologists are ‘disease detectives’ who use data, models and science to understand where diseases come from and how to prevent or stop them. Within the field, infectious disease epidemiology is the particular subfield that specializes in diseases like COVID-19.
This has become one of the hottest memes to emerge from the COVID-19 pandemic. That’s a good thing because it is very important. However, the term is often not well-understood. Once an infectious disease outbreak takes hold in a population, the emphasis shifts from containment (keeping it from starting) to mitigation (reducing negative impacts). As we have seen in Italy and elsewhere, the rate of spread largely determines our ability to handle the workload of caring for the sick and protecting those who are most vulnerable. We have only a finite number of doctors, hospital beds and breathing machines available, and if the outbreak moves too fast, we will exceed capacity and deaths and suffering will rise. To keep this from happening, we enact community mitigation strategies (called control measures in the graph below) to slow the pace of the outbreak. This means two crucial things: 1) While we hope we can reduce the total number of infections, this may not be possible and is not the point of flattening the curve; 2) the objective is to slow the epidemic so that we can stay below the breaking point where we run out of capacity to treat the sick. This implies that the outbreak will actually go on longer than it might without these control measures. The epidemic will end when there are too few people left who are susceptible to keep the transmission cycle going. That’s how epidemics have worked throughout history. When containment is not possible (as is the case for COVID-19 in many countries), and a vaccine is not yet available, slowing the pace of transmission is the number one goal. That requires everyone to pitch in and understand that what we all do together (or don’t do) is not just to protect ourselves, but to reduce the risk of death and suffering for our grandparents, and those who are otherwise vulnerable.


Incubation period
Epidemiologists use the term incubation period to describe the length of time between infection and the onset of symptoms. When a person is infected with a disease, it takes time for the body to recognize the presence of the pathogen and to launch an immune response to fight it. It also takes time for the virus itself to multiply (or propagate) inside a new host. The symptoms that arise from viral infections (like fever, runny nose and fatigue) are actually signs of the body’s defensive reaction to the illness, not the pathogen itself. The reason the incubation period is so important is because it can help diagnose the disease, but more importantly, it helps us understand and predict how fast the disease will spread in a population. Currently, we believe the incubation period for COVID-19 is between two and 14 days. That’s a very wide range. The best studies show average incubation periods of between three and six days. The main thing to keep in mind is that we believe this coronavirus can be transmitted during the incubation period, before symptoms appear. For this reason, taking the temperature of travelers is not a foolproof control measure. Knowing the incubation period is also vitally important for determining how long people who have been exposed to the disease through contact or by travelling should remain isolated from others (see Quarantine).
Isolation (aka self-isolation)
An infection control measure used in times of infectious disease outbreak to contain or slow the epidemic cycle. Isolation refers to identifying and separating persons who have been diagnosed with the disease in question, or who are a presumptive case. Isolation is one of several social distancing measures. The concept applies at the community level (staying home and away from people) and the household level (staying separate and away from people who reside together).
Public discourse and social media are filled with conjectures about how the SARS-CoV-2 virus might have, or might in the future mutate into something more dangerous. I am not a virologist, but I listen to what they say. Mutation is one of those scary words that has gone, well, viral! The reality is that all viruses mutate randomly all the time. That is because the replication process for an RNA virus is very prone to error. As a result, the SARS-CoV-2 virus, like all viruses is constantly mutating. There is no surprise in that. In fact, within one infected person, there will be countless different “versions” of the virus in circulation, like documents spewing from an old broken Xerox machine. All viruses mutate; those mutations rarely make any meaningful difference in how the virus works or how it spreads. The vast majority of mutations are just genetic noise; they don’t take hold and change the behavior of the pathogen because they don’t produce a meaningful survival advantage. Big changes do occur in viruses, but not generally on the time-scale of a specific outbreak. We do know that one such big change occurred when this coronavirus ‘spilled over’ from it’s natural host to people (possibly though an as yet unknown intermediate host). In science fiction, viruses (like superheroes) mutate suddenly and acquire extraordinary capabilities. In real life, meaningful mutations that matter are rare, unlikely and impossible to predict. That doesn’t mean that a qualitative change in the disease due to a mutation is impossible. But, we now have more tools than ever in human history to monitor this pathogen in real time, to watch for mutations that change the infectivity, transmissibility or lethality of the disease. That usually doesn’t happen. Nature is more complex. Yes, the virus is always mutating. That’s all part of what experts described in a comment in Nature Microbiology as the “…humdrum aspect of life for an RNA virus”. Most mutations don’t matter.
Basically, a pandemic is a global epidemic.  Like all epidemics, a pandemic implies an outbreak of infectious disease in excess of what is normal and expected for a particular time and place.  Key things to remember are that a) an epidemic must cross multiple national boundaries and must occur on multiple continents; b) a pandemic refers to the spread of the disease, not it’s severity; c) the declaration of a pandemic implies that an epidemic can no longer be contained to 1 or more countries or a single regions but has become a challenge for the planet.  Once you try to define it more specifically, things get fuzzy and controversial fast.  The World Health Organization had, until recently, a very specific definition.  But the term has lost favor in many circles; in the case of COVID-19, there was fear that even using the word would cause panic. The WHO declared COVID-19 a pandemic on March 11, 2020.
Preclinical case
A person who has been infected with a virus but has not yet shown any signs or symptoms of illness is considered a preclinical case. These are cases in the period of incubation. It is widely believed that preclinical cases are infectious (meaning they are capable of passing the disease to others, but the details remain uncertain. Persons who have been exposed to someone who is infected should be considered presumptive preclinical cases during a period of quarantine. Because preclinical cases are a infectious, the COVID-19 epidemic spreads faster (and has a higher R0).
Presumptive case
A major challenge in any outbreak investigation is how to define, identify and count cases. In situations where a gold-standard test is available, this can be easy. In COVID-19, a major problem is that while we have a test, we can’t test enough people fast enough to know what we are dealing with. So, we are forced to assume that any and all persons with a cold or flu-like symptom profile is a presumptive case, meaning that until they can be tested, we act as though they might have COVID-19. In this disease it is especially challenging because we currently have a very vague case definition based solely on clinical symptoms (e.g., fever, dry cough and shortness of breath). As an epidemiologist, I am very unhappy with this situation because it is neither sensitive or specific. Since COVID-19 is known to be spread by people with mild symptoms or no symptoms at all, any occurrence of anything that could be COVID-19, should be assumed to be COVID-19.
This is the official name (for now) of the virus that causes COVID-19. It is one of seven coronaviruses that are known to infect humans and to be capable of spreading from person to person. It is spread mainly through contact with respiratory droplets from coughs and sneezes. The virus does not spread primarily through the air, but rather through contamination of surfaces. Wearing surgical masks therefore does little to protect those who are not infected; it can actually make infection more likely because mask wearers touch their faces more often. We know that the virus can live on surfaces for up to three hours (shorter if the surface is dry and smooth). Fortunately, this virus is fairly fragile in the sense that it is easily killed by contact with disinfectants such as rubbing alcohol, hand sanitizer, soap, Lysol and even vodka (although each of these works differently depending on its alcohol content).
Secondary transmission
Secondary transmission is the transfer of an infectious disease from primary cases to persons in close proximity to them. It means different things in different diseases but in COVID-19, primary cases are generally those who are identified, tested and hospitalized because they are very sick. In primary cases, the source of the disease is often unknown; primary patients tend to be older and more vulnerable than the general population. We study secondary transmission because it gives us invaluable clues about transmission dynamics that are more typical. It is also easier and more practical to do contact tracing of those who live with, work with or take care of a primary case than to do it on everyone. Those who acquire the illness through secondary transmission are referred to as secondary cases. The secondary infection rate (SIR) is a measure of the frequency of new cases among the household contacts of a primary case in a defined period.
Serial interval
The serial interval is the time interval (in days) between when person A (the infector) develops symptoms, and when Person B (the infectee) develops symptoms as a result of secondary transmission. This number is very important because it is a vital clue to whether people can transmit an infection before they are sick. A study by Du and colleagues finds this interval is around 4 days in COVID-19. That is a short interval and supports the view that this coronavirus can be spread before symptoms are apparent.
Shelter in place (SIP)
Shelter in place refers to a strategy of epidemic control that involves remaining in your home as much as possible to avoid being exposed to a disease or to transmit the disease to others. It can be used either informally to mean hunkering down, or it can refer to an official order issued by local or federal officials in response to an emergency such as a mass shooting, chemical spill or natural disaster. The term implies the need for provisioning your household for a period of non-contact with the outside world, which requires having adequate supplies of food, medicine, cleaning supplies and other essentials in order to ride out the storm.
Social distancing (SD)
Epidemiologists use the term social distancing to refer to actions intended to slow the rate of disease transmission by keeping infected persons and susceptible persons from coming into contact with each other. Since we don’t know who is infected, social distancing measures can be aimed at everyone. SD is the most important community mitigation strategy we have to slow the spread of the disease (see Flattening the curve). Common measures include closing schools, shopping malls, theatres and other places where crowds gather, spacing people out in stores, restaurants and health care centers, telecommuting for work and school, restricting public social gatherings, self-quarantine, restricting access to public transportation etc. For more information, see The Atlantic’s article on The Dos and Don’ts of ‘Social Distancing’.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s