AFI is the medical term for a rapid onset of fever and symptoms such as headache, diarrhea, chills or muscle and joint pain, cough or other respiratory symptoms. AFIs are one of the most common reasons people seek health care and can be caused by viruses, bacteria, parasites or fungi that people inhale, eat or drink from contaminated food or water, or are exposed to by contact with animals, including insects.
An adenovirus is a common virus that causes a range of diseases. The can cause a cold, sore throat, bronchitis, pneumonia, diarrhea and pink eye. People with weak immune systems or existing lung or heart disease can get very sick from an adenovirus infection. The virus can attack the lining of lung, eye, intestines, urinary tract and nervous system. They account for about 10 percent of fever-like symptoms, severe respiratory infections and diarrhea. The virus can be spread through the breath via coughing and sneezing. Usually people heal from an adenovirus within three to seven days.
Alpha-gal syndrome is a red meat allergy – is caused by the bite of certain ticks. The allergy is known as Alpha-gal syndrome, because it is linked to the sugar molecule galactose-α-1,3-galactose, or ‘alpha-gal.’ Alpha-gal is found in mammalian meat but not primate – human – meat, and some ticks carry it in their saliva. When they bite a human, for reason still not understood, the alpha-gal triggers a life-long allergy to red meat.
When an antibiotic has lost its ability to effectively control or kill bacteria, the bacteria are considered "resistant.” These bacteria continue to multiply even in the presence of therapeutic levels of an antibiotic. Bacteria become resistant through a genetic mutation or by acquiring the resistance from another bacterium. Every time a person takes antibiotics, sensitive bacteria (bacteria that antibiotics can still attack) are killed, but resistant bacteria survive. The number of drug-resistant bacteria can increase in the environment if an antibiotic is overused.
“Antigenic” drift and shift
Often used when discussing flu virus because it is among the fastest mutating viruses on the planet. As part of its evolutionary process, viruses mutate to try to escape the immune system. As the virus copies itself, its mix of genes can change slightly. This is called “antigenic” drift. Because the new virus is still mostly like the previous version, people usually have some immunity to a virus that has “drifted.” When the numbers of gene “drifts” start to pile up, the virus can become significantly different from its predecessor. This is called antigenic “shift.” When a virus “shifts,” humans have more vulnerability to becoming sick because their immune system doesn’t recognize it.
A healthy person who is infected by a pathogen and showing no symptoms of disease. People can become infected with a pathogen and experience no symptoms. That person then can transmit, or “carry” the pathogen to another person, infecting them. That person may then become sick, even if the original carrier does not.
Single-celled microorganisms that don’t require living hosts. They come in many different shapes and thrive in diverse environments including extreme heat and cold. They live in soil, oceans and the human gut. Bacteria are classified by the makeup of their cell walls and are identified by a Gram stain. Hence the term, a “Gram-positive,” or “Gram-negative” bacteria. Some bacteria share space and resources in our body and are beneficial to human health. Other bacteria cause infections and disease.
Phages are viruses that are the natural enemies of bacteria. The word ‘bacteriophage’ means “bacteria eater.” Phages exist anywhere bacteria are found. There is a phage for each kind of bacteria, whether it is Escherichia coli (E. coli) or Clostridium difficile (C. diff). These viruses attack the specific bacteria, hijack their metabolic processes and destroy them. They exist to keep bacteria in check. Modern medicine has just begun to research ways to use phages as an alternative to antimicrobial medicine as resistance to these drugs is rising globally.
A form of terrorism involving the deliberate release of biological agents, such as a virus or bacteria, or toxins to injure or kill people, with the aim of furthering personal or political agendas. This is also called germ warfare. Bioterrorism differs from other methods of terrorism in that all that is needed to turn biological material into a weapon is determination and access to medical supplies or a laboratory. Further, unlike other forms of terrorism, if a bioweapon was unleashed, it could be days or weeks before the attack is known. This means that initial victims could be incubating a disease and then carrying and spreading it to all parts of the U.S. and world before it could be stopped.
Blood borne pathogens
Blood borne pathogens are bacteria, viruses and other microorganisms that live in the bloodstream and can cause disease. They are found in blood, semen, vaginal secretions, cerebrospinal fluid, fluid in the chest and joints and oral secretions during dental procedures. Any human tissue, alive or dead can carry these pathogens. Hepatitis B, hepatitis C and the human immunodeficiency virus (HIV) are the most common blood borne pathogens.
A breakthrough infection is defined as someone developing an infection with a pathogen that is resistant to a vaccine or another preventative measure meant to head off disease. In the case of COVID-19 disease, a breakthrough infection is meant as someone who develops an infection with SARS-CoV-2, the virus that causes COVID-19, two weeks after they have become fully vaccinated.
Chronic wasting disease
This is a potentially emerging disease for humans, though it has not yet jumped from animals to people.
The disease is caused by prions, proteins that can cause brain degeneration, and affects deer, elk, reindeer, sika deer and moose. The disease is now established in wildlife found in North America and public health officials have been warning people not to eat meat from animals found to be positive with the disease. The concern is the consumption could cause brain disease in humans.
The most commonly known prion disease is mad cow disease, which is caused when a person eats meat from an infected cow.
The term referring to a disease that is spread by direct physical contact between people or animals. Direct physical contact includes items that the ill individual may have touched, coughed or sneezed on. All diseases are infectious, meaning they are contracted in the environment. But not all of those diseases can be spread to other humans or animals. A person can be infected but non-contagious. Only a disease that can spread via direct contact is considered contagious. Some examples of contagious diseases are smallpox and influenza.
Coronaviruses are a family of viruses, which cause respiratory illness in humans. It gets its name from the crown-like halo (or corona) surrounding the virus and can be seen under an electron microscope. Scientists have long identified coronaviruses circulating among animals, such as camels, cats and bats. Still, only a few have jumped to people – a spread that is defined by epidemiologists as “zoonotic.”
Before 2020, six coronaviruses were known to be circulating among people, four of which cause about 25 percent of colds. Two others were known to cause extreme illness – Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). SARS and MERS spread between humans via respiratory droplets with close contacts, the way influenza and other respiratory pathogens have spread, but they don’t spread easily and could be controlled. Around 8,000 people worldwide were infected with SARS and approximately 800 died and MERS infected 2,500 and killed about 860. There has been no known community spread of SARS since 2003 and very little community spread of MERS. In January 2020, China announced the emergence SARS-CoV-2019, the virus that causes COVID-19. The genetic sequence of the coronavirus causing COVID-19 shares some of the same genes as SARS. That is how SARS-CoV-2019 got its name. The “2019” designation was given because the virus is known to have begun circulating at some point late in 2019.
Disease X stands for an “unexpected” disease. The World Health Organization declared in 2018 that Disease “X” was among the diseases it most worries about because it has no medical countermeasures to treat. It stands for an unknown bacteria, or virus that might be lurking in animals or humans, with the potential to suddenly become virulent and contagious, spreading around the world.
A scientist who studies how animals and plants interact with the environment. Disease ecologists study the interactions between pathogens (i.e., bacteria, viruses, and fungi) or parasites (i.e protozoa) and their human and non-human hosts. This work is important because the majority of human infections originate in animals and the environment. Outbreaks are often caused by changes in the interactions between pathogens, humans, animals and the environment.
In biology, an endemic species is one that is native to specific regions, such as the kangaroo being endemic to Australia. The cane toad, on the other hand, was a species introduced to Australia and hence was not endemic (though it is now). In epidemiology, endemic refers to the circulation of a disease within a certain population or geographic area that continues without outside interference or introduction. Once a disease has been eliminated from a geographic region, such as a continent, it is no longer endemic to that region.
The term for a disease of the intestine. It is commonly used in reference to pathogens that have been ingested and produce chemical or allergic reactions. Among bacteria that can cause an enteric infection are Escherichia coli (E. Coli), Vibriocholerae (cholera), Salmonella and Shigella. The pathogen generally causes diarrhea, abdominal discomfort, nausea, vomiting and significant loss of fluid.
A group of viruses that typically occur in the gastrointestinal tract, but on rare occasions, can spread to the central nervous system causing serious illness. Enteroviruses are the most prevalent viruses globally. In the U.S., around 10 million to 15 million infections are caused by the enterovirus, but most people don’t get sick, or just experience mild illness, like the common cold. Some people, especially infants and those with weakened immune systems can have more serious complications. If the virus spreads to the nervous system, brain or heart, it can cause life-threatening symptoms, such as paralysis. Polio, hepatitis A and hand, foot and mouth disease are among the diseases caused by an enterovirus, which spreads between humans through contact with an infected person’s saliva, sputum, mucus or feces. The virus seems to spread the fastest during the summer and fall seasons.
A group of cases of a specific disease or illness clearly more than what one would normally expect in a particular geographic area. There is no absolute criterion for using the term epidemic; as standards and expectations change, so might the definition of an epidemic, such as an epidemic of violence.
Scientists who study the causes, patterns, frequency and locations of diseases, and use the information to prevent future outbreaks. Epidemiologists are considered “disease detectives” in the public health world and provide the scientific basis for evidence-based medicine.
The cause of a disease or condition; most often etiology refers specifically to the biological mechanisms underpinning a particular condition.
Filoviruses are part of a virus family called Filoviridae and are the cause of severe hemorrhagic [internal bleeding] disease in humans and nonhuman primates. Three branches have been identified – Cuevavirus, Marburgvirus and Ebolavirus. Six species of Ebolavirus have been identified: Ebola, Sunda, Bundibugyo, Tai Forest, Reston and Bombali. Four of these are known to cause illness in people: Ebola, Sudan, Tai Forest and Bundibugyo. In January 2019, scientists from Singapore and China said they found a new branch of the Filoviridae family - called Mengla virus. The virus is zoonotic, meaning it is transmitted to humans from animals - most likely bats. The new Mengla virus was discovered in Asian bats. Once the virus is transmitted to people from an animal, the disease spreads between people through bodily fluids. The disease was first recognized in 1967, when German lab workers in Marburg were handling monkeys with the virus, and got sick. Ebolavirus was identified in 1976 near the Ebola River in the northern Congo basin of Central Africa. Ebola has emerged sporadically in Africa since then, with the largest outbreak occurring from the end of 2013 through 2015 in West Africa. While there is no known cure for filoviruses, a new experimental vaccine for Ebola has demonstrated effectiveness during the 2018-19 Ebola outbreak in the Democratic Republic of Congo.
Fungi are spore producing organisms like yeast, molds and mushrooms. They are common in the environment and are seen as more of nuisance, like mold on cheese. However, there are hundreds of kinds of fungi that are known to cause infections, particularly in people with weakened immune systems, such as those who are hospitalized or living with an immune disease. Usually, these infections can be treated with antimicrobial drugs, but an increasing number of fungal diseases are becoming resistant to drugs, worrying public health officials that they may cause a rise in infections that cannot be treated.
Gain of function
The term refers to laboratory techniques used to augment aspects of a pathogen and make it more dangerous. This is usually done via a combination of gene editing and serial passage of the pathogen between animal hosts. In the context of the development of therapeutics and vaccines, the goal is to learn how the pathogen may mutate.
Gram-positive and gram-negative bacteria
Bacteria are classified based on a chemical stain that can be seen through the microscope. The Gram stain test was developed by Hans Christian Gram in the late 1800’s. He found that when he stained some bacteria turned purple under the microscope. These were called “gram-positive.” Other bacteria didn’t turn purple and appeared pinkish or red under the microscope. These were called “gram-negative.”
Whether the stain attaches to the bacteria or not, is related to its structure. Gram positive bacteria, like those that cause strep throat or many skin infections, have a thick wall made out of a protein that retains the chemical in the purple dye. Gram negative bacteria, like those that cause cholera or urinary tract infections, has two protective walls, making it harder to penetrate, and doesn’t retain the purple dye.
Hand, foot and mouth disease
This is a common and mild contagious viral infection that usually affects children younger than five. It is most often caused by the coxsackievirus, which is part of a family of enteroviruses. The virus, which is usually passed orally between children, can cause fever, skin rash and mouth sores. There is no treatment for it, but it generally resolves on its own. This disease is often confused with foot-and-mouth disease (also called hoof-and mouth disease), which only affects cattle, sheep and swine. The virus that affects these animals is different than the virus that affects humans.
Helminths are parasitic worms. Worms can be transmitted to humans in fecal material, from insects or from walking barefoot on contaminated soil. Once they enter the body, they tend to live in the intestines. Parasitic worms make up the majority of neglected tropical diseases. Most helminths are either roundworms or flatworms.
Roundworms live in the soil and are the biggest contributor of human illnesses in the developing world. Around 3 billion people are chronically infected with these worms across the globe and can contribute to the development of asthma. Other symptoms caused by the worms include itching, diarrhea, constipation and nausea.
The worms grow best in warm climates. Poor hygiene and poverty can contribute to developing disease from these parasites.
A means of protecting a whole community from the spread of an infectious disease. The more people (a herd) that are immune from a disease, the better protected the entire community is from an outbreak of that disease. The most common modern way to achieve herd immunity is through vaccination. Each disease, depending upon how they spread, has a threshold, or the minimum number of individuals that need to be immunized to prevent an outbreak. Measles, for example, requires 95 percent of the population to be immunized to prevent an outbreak.
The branch of biology that covers the study of the immune system in all organisms. Immunologists study the physiological function of the immune system, the complex system of the body that fights viruses, bacteria, fungi, and parasites, that may cause disease.
The ability of the body to response and resist bacteria, viruses, fungi, and parasites based on its ability to produce defensive proteins called antibodies or sensitized white blood cells, called T-cells and B-cells.
Incidence and prevalence
Incidence is the rate of newly diagnosed cases of a disease. Prevalence is the total number of cases of a disease existing in a population.
The relationship between incidence and prevalence depends on the contagiousness of the disease and the ability to treat it and prevent further spread. There can be a high number of diagnosed cases of a disease, but low prevalence because the disease is treated quickly. With a disease with a low cure rate, but maintenance treatment permits sustained survival, then incidence contributes to a continuous growth of prevalence.
Incidence may be a measure of how well surveillance and prevention measures for a disease are working while prevalence may be an indication of the effectiveness of treatment methods.
Infection-to-fatality rate (IFR)
An epidemiology term that quantifies the chances that a person who contracts an infection from a pathogen, will die from it. Not everyone who is infected by a pathogen will show symptoms of a disease. Not everyone who is infected by a pathogen will die. Knowing the IFR helps scientists determine the danger of a particular pathogen and develop countermeasures to prevent its transmission. With novel pathogens, like with the virus that causes COVID-19, this rate is initially difficult to determine because people who aren’t sick aren’t being tested for infection. As time goes on, and more people are tested for the virus, epidemiologists can determine a more accurate figure for the mortality rate of a pathogen.
A disease that can be transmitted to other individuals. An infectious disease is a disease that is caused by the invasion of a host by agents whose activities harm the host's tissues and cause disease. Diseases are spread by direct person-to-person contact, such as through coughing, sneezing, sweating or sexual interaction. Fleas, mosquitos and other carriers (known as vectors) can spread disease when they bite animals with a disease and then bite humans.
Infectious diseases spread when a healthy person comes in contact with a pathogen expelled by someone sick, such as through a cough, sneeze, sexual activity, or contact with fecal material. The amount of that pathogen necessary to make that healthy person sick is the infectious dose. With SARS-CoV-2, the virus that causes COVID-19, the infectious dose is unknown, but because no one has immunity to it, researchers suspect the dose is low.
This policy involves separating people known or suspected to be infected with a contagious disease from those who are not sick to prevent them from transmitting disease to others. The definition of “suspected” is based on whether the person is showing symptoms of a contagious disease or whether they met certain laboratory criteria demonstrating they have likely been infected.
The microbiome refers to the army of microbes - bacteria, viruses, yeasts and fungi - that live on and in the body. There are more than 10,000 of these microbial species in the body and they are vital to human health. Scientists are still trying to figure out why it is so important to health, and why sometimes these microbes can turn deadly to their human hosts. Read more.
Non-communicable diseases are illnesses that aren’t physically transmissible from person to person. No bacteria, virus or parasite has caused the illness. Non-communicable diseases are usually chronic health conditions, meaning they last three months or longer and can’t be prevented by vaccines or cured with medicine. Heart disease and diabetes are examples. Non-communicable diseases now cause more than 75 percent of the world’s deaths, according to the World Health Organization.
This term is usually used in reference to an infection acquired while under medical care, usually at a hospital. Many times the infection is caused by microbes that are resistant to antibiotics. A nosocomial infection is specifically one that wasn’t present or incubating prior to the patient’s being admitted to the hospital. Two common nosocomial infections are clostridium difficile (c. Diff) and methicillin-resistant staphylococcus aureus (MRSA). C. Diff is a bacteria that can cause diarrhea and dangerous inflammation of the colon. MRSA is a microbe that can cause dangerous skin and blood infections.
An infection caused by pathogens — a bacteria, fungi, parasite or virus — that has taken advantage of a person’s weakened immune system. A person’s immune system can be compromised by another illness, such as virus, or because they are taking immune suppression drugs to fight cancer, or have an altered microbiome caused by malnutrition, leaving their immune system less able to fight off a disease-causing pathogen.
For example, the human immunodeficiency virus (HIV) causes progressive failure of the immune system, causing acquired immune deficiency syndrome (AIDS). The virus also enables bacterial infections such as meningitis and tuberculosis to gain a foothold in the body. A list of opportunistic infections associated with HIV can be found here. An otherwise healthy immune system likely would have fought off these pathogens.
Hospitalized patients are vulnerable to fungal infections [spore-producing organisms like yeasts and molds] like Candida auris and increasingly, these infections are resistant to antibiotics and antimicrobial drugs.
The CDC now considers fungus to be among the newest emerging microbe threats in the world, because hospitals are reporting many new cases of resistant fungi causing illness.
A disease outbreak is the occurrence of cases of a disease in excess of what would normally be expected in a defined community, geographical area or season. An outbreak may occur in a restricted geographical area or may extend over several countries.
The definition is subject to debate among public health officials and scientists, but generally it is an epidemic extending over a large geographic area involving a disease with a potentially high mortality rate that is spreading quickly from person-to-person.
Any organism that causes disease. Pathogens include bacteria, virus, and fungi. The body comes in contact constantly with pathogens, but the immune system usually destroys them before they cause harm. A person is considered exposed when they have been in contact with a pathogen and infected when the pathogen has entered the body and caused disease.
Pertussis is also known as whooping cough. It is a contagious respiratory disease, spread by air droplets in breath, and caused by the bacteria Bordetella pertussis. The bacteria causes mucus to build in the respiratory tract resulting in severe coughing, and gasping, or whooping, for breath. Before a vaccine was developed in the early 20th century, around 200,000 Americans got whooping cough and 9,000 died annually from the disease, which mostly strikes children.
This is a term used by the Centers for Disease Control and Prevention related to the diagnostic testing process for a disease. A presumptive positive result is when a patient has tested positive by a state or local public health laboratory to infection by a pathogen, but has yet to have been confirmed by the CDC. Public health laboratories are a network of specialized governmental health laboratories that operate at the state and local level across the country. Every state and the District of Columbia, has a public health lab and many states have local public labs in metropolitan areas and smaller communities. They are among the keys to public health surveillance and work closely with the CDC and other federal agencies, as well as international health agencies.
Prion diseases, also called transmissible spongiform encephalopathies (TSEs) are a family of rare brain disorders. The disease agent is believed to be a prion, which is a type of protein that can cause other normal brain proteins to fold abnormally and clump, thus creating holes in brain tissue. The disease usually evolves rapidly and is always fatal. There is no known cure to prion disease. Prions can be spread to humans through infected meat products or exposure to infected tissue. They can also be inherited. The most common form of prion disease that affects humans is Creutzfeldt-Jakob disease. In animals, it is Bovine Spongiform Encephalopathy, or mad cow disease. Prion diseases are rare. About 300 cases are reported a year in the U.S., according to Johns Hopkins Medicine Health Library.
Involves health authority separating and restricting the movement of people who have potentially been exposed to a contagious disease, until it can be determined whether they have become sick or no longer pose a risk to others. For example, those suspected of exposure to Ebola were quarantined up to 21 days. Quarantines may take place in the home, or other locations determined by health authorities. If a person shows no symptoms of the disease within the time when a person is considered contagious, they are considered disease-free and released from quarantine.
R0, which is pronounced “R-naught” is the mathematical term for explaining how contagious an infectious disease may be to a population. The number defines how many people a sick person may infect on average, if no one else in the population has immunity to the disease. If the R number is less than 1, it means the outbreak is either on the decline or isn’t likely to cause an epidemic. If the number is higher than 1, it means the disease may be highly contagious or an outbreak may be spreading. For example, measles is one of the most contagious diseases on the planet. It’s R ranges between 12 and 18. It means one person with measles can infect 12 to 18 people, if none of them are vaccinated against the disease. If everyone is vaccinated, then the R drops essentially to zero. Ebola has an average R1.5 to R2.5.
Sepsis is an extreme bodily response to an infection. The body sends a flood of chemicals to the blood stream to fight the infection, which in turn causes widespread inflammation and slows blood flow. If blood flow becomes too slow, it can cause damage to organs and the circulatory system, eventually leading to septic shock and death.
It is most common among the elderly, those with a chronic illness that has severely weakened the immune system and babies under 3 months. More than 1.7 million people get sepsis each year and 270,000 die from it, according to the Centers for Disease Control and Prevention. One in three patients that die in the hospital, die from sepsis.
A blood test to detect the presence of antibodies against a microorganism. Antibodies are proteins that the body creates when it detects a foreign presence, such as bacteria or virus.
A serologic test can determine whether a person has been exposed to a particular microorganism, and the potential that they are immune to a disease.
Social epidemiology is a subset of epidemiology. It is the study of causes, patterns, frequency and locations of diseases to prevent future disease outbreaks. In social epidemiology, researchers study the distribution and determinants of health, with a focus on societal patterns, structures and exposures that shape a population's health. They look, for example, at what economic, environmental and governmental policies may be affecting the health of certain groups in a population. They also look at the conditions in which people are born, grow, live, work and age. The field emerged in the mid-1800's during cholera outbreaks, as researchers worked to understand differential rates of infectious-disease outbreaks and higher mortality rates in certain groups within society.
Symptomatic case-fatality rate (sCFR)
An epidemiology term that quantifies the risk that a person who is infected with a pathogen, and showing signs of illness, will die. Knowing this figure helps scientists determine the danger of a particular pathogen. With a fast moving and novel pathogen, like the virus that causes COVID-19, this figure may be a moving target, because only those with illness are tested. As time goes on, and more people are tested for the virus, epidemiologists can determine a more accurate figure for the mortality rate of a pathogen. That is why journalists may want to caveat the mortality rate figures early in an outbreak with something to the effect of: "a mortality rate, based on the information that scientists have."
It is a biological preparation that improves immunity to a particular disease. A vaccine typically contains an agent that resembles a disease-causing microorganism and is often made from weakened or killed forms of the microbe, its toxins or one of its surface proteins. The agent stimulates the body's immune system to recognize the agent as foreign, destroys it, and "remembers" it, so that the immune system can more easily recognize and destroy any of these microorganisms that it later encounters.
Vaccine hesitancy is a term that has emerged over the past decade as a more neutral way to discuss attitudes toward vaccines, without identifying people strictly as “anti” or “pro” vaccine. The terms describes people that may be open to vaccination if their concerns are addressed, but for varying and complex reasons, aren’t ready to vaccinate their children, or themselves.
This is the measure of virus particles. Generally, it refers to the amount of virus present in the body, once a person has become infected and the virus has replicated in the person’s cells. For most people, the higher the viral load, the worse the symptoms and outcomes.
The degree of damage a pathogen can cause to the body.
Virology is the study of viruses and virus-like agents, including their types, disease-producing properties, how they multiply and their genetics.
A biological entity with a protein covering that is neither alive nor dead. Viruses circulate in the environment until they find living cells to latch onto and enter. Once inside a cell, a virus hijacks the cell’s genetic material and tells it to make more viruses instead. The hijacked cell then creates so many viruses that it explodes and moves on to enter other healthy cells. Viruses, which are smaller than bacteria, need hosts, like people, animals or plants to multiple.
A zoonotic disease refers to a pathogen that has been living within an animal, and then, for an environmental or genetic reason, jumps into the human population where it can cause disease. Two of the best known zoonotic diseases are influenza and the plague. The flu virus lives in the guts of water fowl. The flu can spread to humans through a genetic shift that causes people to become ill. The plague is caused by the bacteria, Yersinia pestis. It can live inside fleas, which then bite humans and cause illness. In 1346, rats carrying fleas with Yersinia pestis, traveled through trade routes in western Europe, causing a pandemic known as the Black Death. Around 60 percent to 75 percent of all new diseases that affect humans are zoonotic in origin.