A disease is a disorder of the structure or function of all or part of an organism. (Diseases are distinct from `mental disorders`_ because mental disorders are non-physical conditions. )


Examples of communicable diseases include the `Black Death`_, cholera_, the common cold, COVID-19, ebola_, herpes, HIV, influenza_, malaria_, measles_, polio_, rabies_, tetanus_, tuberculosis_, `yellow fever`_, zika_.

Examples of dental diseases include gingivitis_, `gum disease`_, and periodontitis_.

A deficiency disease is a disease that results from a diet lacking vitamins. For example, scurvy.

Morbidity is the condition of being ill, diseased, or unhealthy. Mortality is the condition of being dead.


1   Classification

The WHO classifies diseases according to the `International Classification of Diseases`_.

An infectious disease is a disease caused by a pathogen_. Infection diseases are ranked as the second leading cause of death worldwide by the `World Health Organization`_.

Communicable disease
A disease that is spread from one person to another through a variety of ways that include: contact with blood and bodily fluids; breathing in an airborne virus; or by being bitten by an insect.

Endemic communicable disease

Non-communicable infectious disease

1.2   Diseases of the skin

Diseases of the skin include acne and eczema.

2   Causes

Diseases can be caused by pathogens, by inheriting abnormal genes, or by inadequate diet.

A pathogen (= "infectious agent") is anything that can produce disease. For example, a virus, bacterium_, protozoan_, prion_, viroid_, or fungus_.

3   Study

3.1   Pathology

The study of disease is called pathology.

3.2   Epidemiology

Epidemiology ("the study of what is upon the people", from Greek epi, meaning 'upon, among', and demos, meaning 'people, district') is the study and analysis of the distribution (who, when, and where), patterns and determinants of health and disease conditions in specified populations.

Epidemiology is concerned with the frequency and pattern of health events in a population.

For example, the number of health events such as number of cases in a population. [2]
The occurrence of health-related events by time, place, and person. [2]

Characterizing health events by time, place, and person are activities of descriptive epidemiology. [2]

Determinants are the causes and risk factors that influence the occurrence of disease and other health-related events. [2]

To search for these determinants, epidemiologists uses analytic epidemiology and epidemiologic studies. [2] They assess whether groups with different rates of disease different in their demographic characteristics, genetic or immunologic make-up behaviors, environmental exposure, or other so-called potential risk factors. [2]

Although epidemiologists and direct health-care providers (clinicians) are both concerned with occurrence and control of disease, they differ greatly in how they view “the patient.” The clinician is concerned about the health of an individual; the epidemiologist is concerned about the collective health of the people in a community or population. [2]

3.3   Serology

Serology is the study of serum_ and other bodily fluids. In practice, the term usually refers to the diagnostic identification of antibodies in the serum.

4   Mutation

How can research identify if a mutation has occurred that makes a disease?

5   Properties

Disease can be acute or chronic.

5.1   Mortality rate

Mortality rate is a measure of the frequency of death in a defined population during a specified interval.

  • The `Black Death`_ killed ~9.7% of the entire world population making it the single deadliest event in human history.
  • Malaria_ is thought to be responsible for the death of about half of all people who ever lived.

5.2   Incubation period

The incubation period is the time elapsed between exposure to a pathogen and when symptoms and signs are first apparent.

5.3   Infectious period

The infectious period is the period of time during which a person could infect others.

The infectious period for diseases varies widely from one week to months to potentially forever.

5.4   Window Period

The time between when a person is exposed to a pathogen and when a test can accurately detect the pathogen.

6   Lifecycle

  1. Exposure
  2. Infection
  3. Incubation

7   Research


8   Examples

8.1   Chlamydia

Chlamydia is ... The incubation period is estimated to be 7 to 21 days. [24]

8.2   HIV

HIV is ...

HIV is no longer the death warrant it once was. Contracting it would be awful and surely life-altering. But you would live. I just hope you have good health insurance. As of 2011, the life expectancy of someone who contracts HIV is 40 years from the day they contract it. When in doubt, just look at Magic Johnson.

There are some demographics which are far more likely to catch HIV than others, primarily gay men and drug users. 80% of all HIV cases come from gay men or drug addicts who use dirty needles. When it comes to vaginal sex, it’s almost impossible for a man to catch it from a woman, while a woman can catch it from a man. But anal sex seems to be the big culprit here.

Also, I hate to say it, but HIV positive cases are predominantly lower income classes. African-Americans account disproportionately for 42% of all HIV cases in the US. The disease practically doesn’t exist in Western Europe at this point.

The symptoms of HIV are flu-like symptoms a couple weeks after contracting it. From there your immune system slowly shuts down over the period of years. There are a lot of therapies and treatments available and most people who contract it are able to live functional, mostly normal lives, assuming they get the proper medical care. So the news on the HIV front over the past few decades has actually been mostly good.

8.4   Prion-disease

Prion disease is ...

Prion disease has a case-fatality rate of 100%. That's not an estimate or approximation and it's not rounded up. They are also untreatable.

There are only five well studied prion diseases (because of their rarity). Two are exclusively heritable: fatal-familial insomnia and Gerstmann–Sträussler–Scheinker syndrome. One, Kuru, is transmitted via cannibalism.

The incubation times are extremely long. Some estimates for Kuru go up to 20-50 years.

The most prevalent form of prion disease in humans is new variant Creutzfeldt–Jakob disease (nvCJD) or Human Mad Cow which has a lag of about 10 years based on CDC data. It is transmitted by eating tainted beef products. Let me stress that this is extremely rare: there have been 3 confirmed cases in the United States.

It is extremely unlikely that Soylent is a vector for prion disease, especially since it's been vegan since version 1.2 and never contained beef as an ingredient. Even if it somehow contained tainted beef, given that it's been available for less than 3 years, it's extremely unlikely that any cases of nvCJD (of which there have only a few in the last decade) or any other cases of prion disease were caused by Soylent.

9   Disease control

The basic reproductive rate (= transmission potential of an infection = \(R_0\)) is the average number of secondary cases produced by one primary case in a wholly susceptible population. [8] An infection cannot be maintained unless \(R_0 >= 1\). To eradicate an infection by mass immunization, it is necessary to reduce the value of \(R_0\) below unity.


Public Health systems are prepared to deal with short-term outbreaks that last for weeks, like an outbreak of meningitis. They do not have the capacity to sustain for outbreaks that last for months. Other solutions will have to be found.


Public Health systems are prepared to deal with short-term outbreaks that last for weeks, like an outbreak of meningitis. They do not have the capacity to sustain for outbreaks that last for months. Other solutions will have to be found.

9.1   Social distancing

Social distancing ...

9.2   Herd immunity

Herd immunity is the resistance of a group to attack by a disease to which a large proportion of the members are immune, thus lessening the likelihood of a patient with a disease coming into contact with a susceptible individual. Under this definition, the concept is applicable only to randomly mixing populations; but truly random mixing is unreasonable except for certain small closed populations. Epidemics in a large population can often be broken down into smaller epidemics occurring in separate regional subdivisions.

9.3   Epidemic

An epidemic (= "outbreak") is the rapid spread of disease to a large number of people within a short period of time.

The term epidemic derives from a word form attributed to Homer's Odyssey, which later took its medical meaning from the Epidemics, a treatise by Hippocrates.

Thucydides' description of the Plague of Athens is considered one of the earliest accounts of a disease epidemic.

10   History

10.1   Diseases

The first major epidemic in the USA was `Yellow Fever`_.

10.1.1   The Black Death

The Black Death took the lives of about a third of Europe's population in the fourteenth century.

10.2   Epidemiology

10.2.1   Hippocrates

The Greek physician Hippocrates, known as the father of medicine, sought a logic to sickness; he is the first person known to have examined the relationships between the occurrence of disease and environmental influences

Hippocrates (circa 400 BC) attempted to explain the occurrence of disease from a rational rather than a supernatural viewpoint. In his essay, "On Airs, Waters, and Places", Hippocrates suggested that environmental and host factors such as behaviors might influence the development of disease. [3]

The distinction between "epidemic" and "endemic" was first drawn by Hippocrates,[3] to distinguish between diseases that are "visited upon" a population (epidemic) from those that "reside within" a population (endemic).

10.2.2   John Gaunt

John Gaunt was a London haberdasher and councilman who published a landmark analysis of mortality data in 1662. This publication was the first to quantify patterns of birth, death, and disease occurrence, noting disparities between males and females, high infant mortality, urban/rural differences, and seasonal variations. [3]

10.2.3   William Farr

William Farr built upon Graunt’s work by systematically collecting and analyzing Britain’s mortality statistics. Farr, considered the father of modern vital statistics and surveillance, developed many of the basic practices used today in vital statistics and disease classification. He concentrated his efforts on collecting vital statistics, assembling and evaluating those data, and reporting to responsible health authorities and the general public. [3]

10.2.4   John Snow


A map of the 1854 cholera outbreak in London's Broad Street region using bars to represent deaths at specified households.

John Snow presented this map on December 4, 1854 at a meeting of the London Epidemiological Society.

In the mid-1800s, an anesthesiologist named John Snow was conducting a series of investigations in London that warrant his being considered the “father of field epidemiology.” Twenty years before the development of the microscope, Snow conducted studies of cholera outbreaks both to discover the cause of disease and to prevent its recurrence. Because his work illustrates the classic sequence from descriptive epidemiology to hypothesis generation to hypothesis testing (analytic epidemiology) to application, two of his investigations will be described in detail. [4]

Snow conducted one of his now famous studies in 1854 when an epidemic of cholera erupted in the Golden Square of London.(5) He began his investigation by determining where in this area persons with cholera lived and worked. He marked each residence on a map of the area, as shown in Figure 1.1. Today, this type of map, showing the geographic distribution of cases, is called a `spot map`_. [4]

Because Snow believed that water was a source of infection for cholera, he marked the location of water pumps on his spot map, then looked for a relationship between the distribution of households with cases of cholera and the location of pumps. He noticed that more case households clustered around Pump A, the Broad Street pump, than around Pump B or C. When he questioned residents who lived in the Golden Square area, he was told that they avoided Pump B because it was grossly contaminated, and that Pump C was located too inconveniently for most of them. From this information, Snow concluded that the Broad Street pump (Pump A) was the primary source of water and the most likely source of infection for most persons with cholera in the Golden Square area. [4]

10.3   Miasma theory

Miasma theory held that diseases such as cholera, chlamydia infection, or the Black Death were caused by a miasma, a noxious form of "bad air" emanating from rotting organic matter

10.4   Germ Theory

The germ theory of disease is the currently accepted scientific theory for many diseases. It states that microorganisms known as pathogens or "germs" can lead to disease.

Basic forms of germ theory were proposed in the late Middle Ages by Girolamo Fracastoro in 1546 and expanded upon by Marcus von Plenciz in 1762. However, such views were held in disdain in Europe, where Galen's miasma theory remained dominant among scientists and doctors.

The Italian scholar and physician Girolamo Fracastoro proposed in 1546 in his book De Contagione et Contagiosis Morbis that epidemic diseases are caused by transferable seed-like entities (seminaria morbi) that transmit infection by direct or indirect contact, or even without contact over long distances.

By the early nineteenth century, smallpox vaccination was commonplace in Europe, though doctors were unaware of how it worked or how to extend the principle to other diseases.

Italian physician Francesco Redi provided early evidence against spontaneous generation. He devised an experiment in 1668 in which he used three jars. He placed a meatloaf and egg in each of the three jars. He had one of the jars open, another one tightly sealed, and the last one covered with gauze. After a few days, he observed that the meatloaf in the open jar was covered with maggots, and the jar covered with gauze had maggots on the surface of the gauze. However, the tightly sealed jar had no maggots inside or outside it. He also noticed that the maggots were found only on surfaces that were accessible by flies. From this he concluded that spontaneous generation is not a plausible theory.

Spontaneous generation refers to an obsolete body of thought on the ordinary formation of living organisms without descent from similar organisms. The theory of spontaneous generation held that living creatures could arise from nonliving matter and that such processes were commonplace and regular. For instance, it was hypothesized that certain forms such as fleas could arise from inanimate matter such as dust, or that maggots could arise from dead flesh.

The doctrine of spontaneous generation was coherently synthesized by Aristotle who compiled and expanded the work of earlier natural philosophers and the various ancient explanations for the appearance of organisms, and was taken as scientific fact for two millennia.

Though challenged in the 17th and 18th centuries by the experiments of Francesco Redi and Lazzaro Spallanzani, spontaneous generation was not disproved until the work of Louis Pasteur and John Tyndall in the mid-19th century.

11   Immune system


White blood cells attacking a parasite.

The human immune system contains two main cellular components: B cells and T cells.

A B cell is a white blood cell programmed to find and bind to foreign invaders. Once it has attached itself to a virus, a B cell copies itself and churns out antibodies, eventually creating an army of neutralizers for that particular invader.

There are different types of T cells. One type called a memory T cell helps the body remember a specific invader in case it comes back.

A recent study found such memory T cells in people infected with SARS-CoV-2, the novel coronavirus that creates the disease called Covid-19. That finding leads to speculation that some people might get milder cases of Covid-19 because their T-cells are reacting to exposure to similar coronaviruses encountered in the past. [23]

A killer T cell tamp down an infection by killing infected cells rather than protecting against infection.

Helper T cells assist the body in remembering the targets for antibodies they deploy.

11.1   Immunity

Immunity to a disease is achieved through the presented of antibodies to that disease in a person's system. An antibody is a protein produced by the body to neutralize or destroy toxins or pathogens. Anti-bodies are disease specific. [5]

There are two types of immunity: active immunity and passive immunity. [5]

Active immunity results when exposure to a disease organism triggers the immune system to produce antibodies to that disease. [5] Exposure to the disease organism can occur through infection with the actual disease resulting in natural immunity, or introduction of a killed or weakened form of the disease organism through vaccination (vaccine-induced immunity). Either way, if an immune person comes into contact with that disease in the future, their immune system will recognize it and immediately produce the antibodies needed to fight it. Active immunity is long-lasting, and sometimes life-long. [5]

Passive immunity is provided when a person is given antibodies to a disease rather than producing them through his or her own immune system. A newborn baby acquires passive immunity from its mother through the placenta. A person can also get passive immunity through antibody-containing blood products such as immune globulin, which may be given when immediate protection from a specific disease is needed. This is the major advantage to passive immunity; protection is immediate, whereas active immunity takes time (usually several weeks) to develop. [5]

Sterilizing immunity is a type of immunity where the host cannot be infected, and therefore can't pass on the virus either. Other forms of immunity may only reduce the severity of infection, but still allow you to get infected and transmit it others.

11.2   Vaccination

Vaccination eradicated smallpox_ worldwide in the late 1970s.

11.2.1   Development

Vaccine development typically centers on creating an antibody response to prevent infection from a virus.

11.2.2   Deployment

The development of a safe, effective, and cheap vaccine is only a first step towards community-wide control. A cost-effective vaccine for measles_ has been available since the late 1960s, yet the infection remains one of the world's major causes of child mortality. [8] There is a need for an improved understanding of how best to use vaccines to protect the community.

The persistence of infectious disease within a population requires the density of susceptible individuals to exceed a critical value such that on average each case of infection generates at least one secondary case. It is therefore not necessary to vaccinate everyone within a community to eliminate infection; the level of herd immunity must simply be sufficient to reduce the susceptible fraction below the critical point. [8] The central questions then are:

  • What proportion of the population should be vaccinated to achieve elimination (in a local program), eradication (in a global program), or a defined level of control?
  • What is the best age at which to immunize?

12   Treatment


13   Further reading

14   Resources

15   References

[1](1, 2, 3) Oscar MacLean. 2020-03-05. Response to “On the origin and continuing evolution of SARS-CoV-2”. https://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418
[2](1, 2, 3, 4, 5, 6, 7) Lesson 1: Introduction to Epidemiology. Section 1: Definition of Epidemiology. https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section1.html
[3](1, 2, 3) Lesson 1: Introduction to Epidemiology. Section 2: Historical Evolution of Epidemiology. https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section2.html
[4](1, 2, 3) Mapping the 1854 Broad Street Pump Outbreak. https://www.ph.ucla.edu/epi/snow/mapsbroadstreet.html
[5](1, 2, 3, 4, 5) CDC. Immunity Types. https://www.cdc.gov/vaccines/vac-gen/immunity-types.htm
[6]Introduction to Epidemic Modeling. http://www.stat.columbia.edu/~regina/research/notes123.pdf
[7]Fox et al. 1971-09. Herd Immunity: Basic Concept and Relevance to Public Health Immunization Practices. Journal of Epidemiology. https://pdfs.semanticscholar.org/5ed7/d293816033a0b486370ad875392d326fca66.pdf
[8](1, 2, 3) Roy M. Anderson & Robert M. May. 1985-11. Vaccination and herd immunity to infectious diseases. Nature. https://www.nature.com/articles/318323a0.pdf
[23]Sandee LaMotte. 2020-08-14. Are you immune to Covid-19 for three months after recovering? It's not clear. https://www.cnn.com/2020/08/14/health/covid-19-3-month-immunity-wellness/index.html
[24]North Dakota Department of Health. 2018-07-01. Time Periods of Interest. HIV, STDs, Viral Hepatitis. https://www.ndhealth.gov/hiv/Docs/CTR/TimePeriodsReference_HIVSTDsHep.pdf