Epidemiology and Infectious Diseases
How to understand articles about the Coronavirus
What is Epidemiology?
Epidemiology comes from the Greek words epi meaning on or about, demos the common people, and ology meaning to study a certain subject. Literally then, epidemiology is the study of people. However, these days we use other terms like sociology and demography to cover the study of people. Instead, we use epidemiology to mean the study of diseases in people.
In particular, epidemiology is the study of what causes diseases, where, when and in whom diseases take place, and how we prevent or control them. When epidemiology was being developed, it was because of major outbreaks of infectious diseases usually among poor people.
Over time, there were fewer infectious disease outbreaks, and more people were dying from acute non-infectious diseases like heart disease and cancer. So, epidemiologists started studying these as well.
Eventually, epidemiology expanded to cover chronic conditions such as diabetes and asthma. It also moved into the areas of mental health, quality of life, and how social factors and poverty influence health.
And like most things in life, things have come around in a full circle, and now the priority is on infectious diseases again!
Who are Epidemiologists?
Epidemiologists are health professionals who have studied epidemiology and public health. Epidemiology is usually taught at the postgraduate level, with most epidemiologists having an initial undergraduate degree in medicine or biostatistics (the study of statistics applied to medicine). However, epidemiologists can come from a wide variety of disciplines such as nursing or psychology.
Epidemiologists either become a specialist in a given area such as cancer epidemiology, or infectious disease epidemiology, or become a generalist focusing more on epidemiological methods. Biostatistics is a slightly separate discipline in its own right, with much overlap with epidemiology, and many biostatisticians like myself are also epidemiologists.
Perhaps a good analogy is that medical doctors look after the health of individuals, whereas epidemiologists look after the health of a population.
Epidemiology and infectious diseases
Deaths due to infectious diseases are still very common despite the huge progress in antibiotic and vaccine development. In fact, five infectious diseases account for 1 in 8 deaths globally. They are: lower respiratory tract infections (including pneumonia), diarrhoeal diseases, HIV, Malaria and Tuberculosis. For both Malaria and Tuberculosis there are currently major concerns about multiple drug resistance (in other words most treatments not being effective), and there are concerns especially in Africa and Asia about counterfeit drugs containing little or no active ingredients.
So, although chronic diseases have overtaken infectious diseases as leading causes of death in developed countries, tackling infectious diseases is still vitally important in both developed and less-developed economies.
Outbreak, endemic, epidemic and pandemic
These are the terms we use to describe the status of a disease within a population. The continuous presence of an infectious disease in a geographical location is called endemic. For example, there are many parts of the world where Malaria is endemic — it is always present and kills over 400,000 people each year.
An epidemic is the occurrence of a disease that is greater than that expected in the location region. For example, there is currently an epidemic of Ebola virus in Congo and Uganda which started in 2018.
An outbreak is like an epidemic but is often used for a more limited geographic area. For example, there has recently been an outbreak of measles in Samoa.
Finally, when the epidemic involves different countries and a large population it is called a pandemic.
Infectious diseases
Formally, an infectious disease is an illness caused by the transmission of an infectious agent, or its toxic products, from an infected animal, person or other reservoir, to a susceptible host. That sounds very formal, so we will break down the statement into some of its component parts.
In epidemiology, we often describe disease transmission in terms of the infectious agent, the host, the environment and the vector. This is often put into a diagram called the epidemiological triangle.
The infectious agent or pathogen
An infectious agent is a pathogen (an organism that causes disease). There are many types of pathogen including bacteria, viruses, rickettsia, fungi, protozoa, helminths, prions, and parasites. In the case of the current pandemic, it is the SARS-associated coronavirus (SARS-CoV-2) that is the infectious agent or pathogen that causes the disease, while the disease itself is called COVID-19.
Reservoir of the infectious agent
The infectious agent must live somewhere, and the place where it is usually found is called the reservoir of infection. In the case of SARS-CoV-2, the reservoir is humans. For many infectious agents, the reservoir is animals — for example, bats are thought to be the reservoir for the Ebola virus, and camels for the MERS-CoV virus.
The host
The host is the animal or human that gets infected by the infectious agent. For COVID-19, it is again humans. Factors such as age, sex and personal hygiene can greatly influence disease transmission. For COVID-19, we know that age, sex (men are at greater risk), having one or more chronic conditions, and attention to hand washing are important factors.
The environment
This refers to external factors that affect the infectious agent and the opportunity for exposure. It may include things such as geography, climate, and socioeconomic factors such as crowding, sanitation, and the availability of health services. For COVID-19, the key environmental factors are social distancing and the availability of ICU beds and ventilators.
Vectors
Vectors are non-human agents (like animals or insects) that transmit an infectious agent to humans. For example, in the case of yellow fever, the infectious agent is the Yellow fever virus, the vector is the tiger mosquito, and the host is humans. There is no vector in COVID-19, as humans directly pass on the infection to each other.
Ways a disease can be transmitted
An infectious agent is transmitted from its natural reservoir to a susceptible host in different ways. In the case of COVID-19, transmission is either from direct contact with virus-containing droplets when an infected person coughs, sneezes, or even talks, or by touching a surface contaminated with virus particles, and then touching your nose, mouth or eyes.
Other terms used in infectious disease epidemiology
Like all sciences, there are a several commonly used terms in epidemiology that would be helpful to understand.
Infectivity
Infectivity is the ability of an infectious agent to cause a new infection in a susceptible host. By susceptible, I mean that the host (think person) is not immune and can therefore catch the disease. It is measured by the secondary attack rate, which is the proportion of susceptible contacts that develop the infection after exposure to a primary case. So, if an individual with COVID-19 is in contact with 10 susceptible individuals, and 5 get infected, then the secondary attack rate is 50%.
Virulence
This is the ability of the infectious agent to cause damage to the host. A measure often used is the case fatality rate, which is the proportion of deaths in relation to the number of diagnosed cases of a disease within a specified time. In other words, the case fatality rate is the number of deaths from the disease divided by the number of diagnosed cases. It is usually expressed as a percentage.
For COVID-19 this differs widely by country. For example, in Italy, the current case fatality rate is 10%, whereas in Australia it is more like 0.5%. The denominator (bottom part) of the case fatality rate equation is the number of diagnosed cases of the disease. For COVID-19, this number is likely greatly under-estimated as in most countries only a fraction of the population has been tested. This means that the real number of people with the disease is much larger. Therefore, the current estimates of the case fatality rate are likely exaggerated, and globally, it is probably closer to 1%.
Rates and other measures
In epidemiology, a rate is a measure of how often an event occurs in a defined population over a specified period of time. We have already come across the case fatality rate and secondary attack rate, and there are several other rates commonly used in infectious disease epidemiology. Let us look at some of these rates and some other terminology now.
Overall attack rate
The overall attack rate is the proportion of the population that develops illness during an epidemic or pandemic. Figures proposed for COVID-19 range from 35% to 70% of the population, depending upon how well social distancing measures are undertaken.
Serial interval
The serial interval is the time between one person developing the symptoms of a condition and a second person becoming infected from the initial case and developing symptoms. For COVID-19, the latest estimate is 4 days.
Incubation period
The incubation period is the time from first becoming infected until first symptoms show. For COVID-19, the latest estimate is 5 days. Because the average serial interval is less than the average incubation period, it means that some people will transmit the disease when they have no symptoms (called asymptomatic). Latest estimates are that 10% of people who are infected get it from asymptomatic cases.
Infectious period
The infectious period is the length of time someone is infectious for. This is estimated to be about 5 days on average but may be much longer for people with severe illness.
Latent period
This is the time between someone becoming infected and then becoming infectious. We do not appear to have a good estimate of what the latent period is for COVID-19, but it is likely to be equal to or less than the incubation period, and some mathematical models are using 3 days as their best estimate.
Reproduction number and Herd immunity
Basic reproduction number (R0)
R0 is the basic reproduction number — it is the average number of people each infected person infects. R0 is a function of three factors: (1) the number of contacts an infectious person has; (2) the risk of transmission per contact; and (3) the duration of infectiousness. Social distancing mostly acts on the first factor, by reducing the number of contacts. Hygiene measures such as sneezing into your elbow, hand washing or wearing a face mask if infected, mostly act on the second factor. R0 assumes that there is a constant mixing of the population and that no measures such as social distancing have been put into place. In other words, it is the worst-case scenario.
Based on data from China and a cruise ship, we are pretty sure that R0 is about 2.5, that is each infected person on average infects 2.5 other people. While R0 is greater than 1, the epidemic will keep increasing. If we can get R0 down to 1, it will become endemic, that is it will be permanently in the population grumbling along at a low level. However, if we can get R0 below 1, the epidemic will die out.
Herd immunity
If enough of the population become immune, either from vaccination or recovery, then the risk of transmission becomes smaller, driving R0 down. This is called herd immunity. It is usually expressed as the percentage of the population required to be immune for the disease to be slowed down and then stopped.
The proportion of the population necessary to achieve herd immunity is calculated as 100 — (100 / R0). At the start of the epidemic in China, R0 was found to be 2.5. So, to achieve herd immunity, we needed:
100 — (100 /2.5) = 60% of the population immune, either from recovery or vaccination to achieve herd immunity.
Effective reproduction number (R)
Clearly, as the pandemic continues, people will become immune, and social distancing measures reduce the mixing of the population. A second measure has therefore been developed called simply R, the effective reproduction number. R is the average number of susceptible people plus non-susceptible each infected person infects. If p is the proportion of susceptible people in the population, then:
R0 = R x p
When someone recovers from an infection, their body’s immune system remembers what the pathogen looks like and is prepared in case it ever hits again. However, this is not always the case, and sometimes a person only gets partial immunity or no immunity, depending on the disease. It is likely that after recovering from COVID-19, we do get immunity, although this is not certain yet. If enough people have recovered and become immune, or been vaccinated, then each infected person on average meets fewer susceptible people, and this drives R down.
Suppose that R decreases to 1.5. Putting this in the formula for herd immunity instead of R0, then only 33% of the population need to be immune for herd immunity to kick in. This is one of the reasons that epidemics like COVID-19 start off with an exponential increase in cases, peak, and eventually slowly die down. Of course, social distancing measures also help in this regard.
The epidemic curve
The epidemic curve is a visual representation of an epidemic showing the number of cases over time. The number of cases is represented by the vertical axis and the date by the horizontal axis. Here is the epidemic curve for COVID-19 for South Korea.
The epidemic appeared to peak about the 29th February, then started tailing off, almost certainly because of widespread testing for COVID-19, and enhanced social distancing. It is unlikely to be due to herd immunity, since up until that date there had only been about 4,000 cases, an overall attack rate of only 7%. With only 7% of the population infected, R would have to be close to 1 for there to be any herd immunity.
The epidemic curve also tells us what type of epidemic it is. A point source epidemic is where the epidemic starts at a single place or source, at a single point in time. A typical example is when we have an outbreak of food poisoning. The epidemic curve usually rises very fast to a peak, then slowly dies off, giving the epidemic curve a long right-hand tail.
A continuous common source outbreak is typically where you have an environmental hazard that continues for a long time. For example, you might have a polluted water supply that causes cholera. The epidemic curve rises to a peak and then tends to plateau off at that level.
A propagated epidemic curve is where you have person-to-person transmission like in the current COVID-19 pandemic. It usually follows a bell-shaped curve.
I will leave it there, but hopefully these explanations have helped you interpret other articles that you read.
I do hope you enjoyed this article. I have written several other about COVID-19. Here are the links:
COVID-19 — facts and fiction
Infectious diseases and their impact on civilisation
Epidemiology and infectious diseases
Are the statistics we see in articles about the Coronavirus accurate?
A fascinating history of clinical trials from their beginnings in Babylon
Should the USA have cancelled funding to the WHO?
