Acute Febrile Illness (AFI)

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, including 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

Alpha-gal syndrome is a red meat allergy 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 reasons still not understood, the alpha-gal triggers a life-long allergy to red meat.

Antibiotic resistance/anti-microbial resistance

When an antibiotic or antimicrobial has lost its ability to effectively control or kill a bacteria, fungi, or parasite, it is considered "resistant.” These microbes continue to multiply even in the presence of therapeutic levels of an antibiotic or antimicrobial medication. Microbes become resistant through a genetic mutation or by acquiring the resistance from another pathogen. Every time a person takes an antibiotic or antimicrobial, sensitive microbes (that antibiotics can still attack) are killed, but resistant microbes survive. The number of drug-resistant microbes can increase in the environment if an antibiotic is overused.

First introduced to the public in 1944, antibiotics and antimicrobials are drugs that kill harmful bacteria, fungi and parasites. They have all but eliminated the threat of diseases that once killed millions including sepsis, tuberculosis, plague and cholera. But overuse of these drugs in people and livestock animal farming has resulted in the breeding of “superbugs,” microbes that are resistant to most or all existing antibiotics.

Microbes become resistant to antibiotics naturally. When an antimicrobial is used, a few resistant strains survive, and continue to multiply and spread. They are resistant due to a genetic mutation, or through acquired resistance from other microbes. Mutations, rare spontaneous changes in bacteria’s genetic material, enable bacteria to inactivate or close off from an antibiotic. Bacteria can also acquire resistance by “mating” with one another, transferring genetic material with antibiotic resistance. Bacteria can collect multiple resistance traits, making it resistant to many if not all antibiotics.

Until the early 1980’s, pharmaceutical companies invested in developing new antimicrobials to keep ahead of evolving resistance, but the scientific and economic challenges of developing new antibiotics have led to a steep drop in the availability of new types of drugs, even as superbugs have spread.

Food farming has contributed to antimicrobial resistance. In the 1950’s, American agriculture researchers Thomas Jukes and Robert Stokstad discovered that giving small doses of antibiotics to chickens could speed up their growth and prevent infection. Their observation profoundly changed animal food production. It enabled the rise of concentrated animal feeding operations, where farmers could inexpensively raise hundreds of animals — chickens, pigs, and cows — and keep them healthy, even in close confinement. With the rise of industrial farming, millions of people have been able to get access to cheap animal meat. Approximately 65 percent of the medically important antibiotics sold in the United States in 2019 went to food animals — animals humans will eat, according to the Center for Infectious Diseases Research and Policy.

The routine use of antibiotics has also exposed quintillions of bacterial pathogens to antibiotics, increasing the evolutionary pressure on bacteria to develop resistance. Antibiotic resistant bacteria can then pass from animals to people through direct contact, contaminated meat, or environmental pathways such as water runoff or airborne dust.

Since the 1970s, a growing number of public health advocates have warned that the practice of feeding antibiotics to otherwise healthy animals, will result in more humans contracting antibiotic resistant pathogens. To read more about the risks of using antibiotics in food farming, see this 2021 Pew report.

For more details and resources on writing about antimicrobial resistance, see these two AHCJ tip sheets – Antibiotic resistance: how to cover this ongoing health story beyond the COVID-19 pandemic and What reporters need to know about antibiotic resistance.

Antibiotic stewardship

Antibiotic stewardship is a public health effort to work with health providers to ensure the judicious use of antibiotics prescribing. The effort includes fine-tuning and targeting the prescribing of antibiotics to treat the correct infections (for example, not viral-caused diseases) with the lowest dosages for the lowest amount of time to reduce patient harms caused by unnecessary antibiotic use and slow the development of antibiotic resistance.

About 30% of all antibiotics prescribed in U.S. acute care hospitals are unnecessary or inappropriate, the CDC estimates.

Overuse of antibiotics in hospital settings is one of the factors in the rise of “superbugs,” the term for bacteria that has become resistant to many if not all antibiotics. Inappropriate use of antibiotics has also caused some patients to develop serious side effects, like a hard-to-treat illness from clostridium difficile. C. diff is a bacterium that can live harmlessly in the gut, kept in check by healthy bacteria. But when a person gets too many antibiotics, healthy bacteria are killed off, enabling C. diff to flourish.

Antibiotic stewardship programs in hospitals aim to curb the inappropriate use of antibiotics to ensure that existing drugs remain effective, and patients don’t experience adverse events.

Over the past decade, the CDC has been publishing infection control and antibiotic stewardship guidelines for hospitals to follow. See the CDC’s core elements of hospital antibiotic resistance stewardship programs as of 2021 here.

Generally, stewardship programs include support for physicians to help them determine whether a patient really needs an antibiotic and what type of antibiotic would be most appropriate. Support includes providing physicians with rapid diagnostic testing to determine if a patient is sick with a bacteria or virus [viruses cannot be treated with antibiotics] and determine the type of bacteria making a patient ill. Once the bacteria is diagnosed, the hospital then can help the physician determine the best antibiotic to treat the patient. To do so, a hospital program might assign one hospital pharmacist with a specialty in antibiotics, to work with the physician. See the CDC’s guidelines here.

Culturally, hospital doctors tend to prescribe an antibiotic to a patient, even if they don’t know what is wrong with the person, out of an abundance of caution. Often physicians will also give patients a broad-spectrum antibiotic. Broad-spectrum means a type of antibiotic that kills all kinds of bacteria. The problem is that these medications will also kill healthy bacteria that a patient needs to stay well, and a narrow antibiotic might have been better suited for the patient.

"Antigenic" drift and shift

Before COVID-19, this term was often used when discussing the influenza virus because flu 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. Like the flu virus, the SARS-CoV-2 virus which causes COVID-19 has demonstrated an ability to mutate and escape vaccines.

Drifts and shifts have resulted in new variants of the SARS-CoV-2 virus.

SARS-CoV-2 is a virus with a strand of 30,000 letters [which represent chemical properties] that make up its genome. To reproduce, the coronavirus, via a spike on its membrane, binds itself to the outside of a human cell and then enters it, hijacking the cell’s original genome, directing it to make copies of the virus instead.

Each time the SARS-CoV-2 virus reproduces, there is a natural possibility for a copying error in the letters, resulting in new variants of the virus. Much of the time, the copying errors are inconsequential or even weaken the ability of the virus to replicate. However, as most of the world has become infected with the virus, there has been the opportunity for an increased number of copying errors, resulting in mutated variants that make the pathogen more transmissible, more able to evade vaccines and potentially more lethal. In the summer of 2021, people became infected with the delta variant, then in the winter of 2021 and 2022, the omicron variant and in the spring and summer of 2022, people have been infected with variants of omicron. Each of these variants has caused a wave of illness, hospitalizations, and death.

The CDC has been monitoring these variants and classifies them in 4 ways, each representing and escalation in risk of causing waves of illness: variants being monitored, variants of interest, variants of concern and variants of consequence.

Asymptomatic carrier

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.

Phage therapy involves the use of bacterial viruses (bacteriophages) to treat bacterial infections. This therapy was discovered more than a century ago, but never caught on as worldwide topic of medical research because anti-microbial medications became the preferred and easier method for treating bacterial infections. With the rise of antimicrobial resistance, there is a growing interest in harnessing this natural enemy of bacteria as an alternative to antibiotics.

Phages exist anywhere there is bacteria and are one of nature’s ways of keeping bacteria from growing out of control. They hijack bacteria’s genetic code and then destroy it.

Scientists at the Pasteur Institute in Paris first discovered phages in the early 20th century. A Georgian scientist, George Eliava, took the discovery back to his country, where the Eliava Institute was created. Phages were used through the Soviet Union during and after World Work Two to treat infections, but the scientific community outside the USSR mostly ignored their work. The challenge is that phages are particular to the bacteria. There is a phage for each strain of Escherichia coli (E. coli) or Clostridium difficile (C. diff), but they aren’t interchangeable. Antibiotics, however, can kill many strains of bacteria, and they became the preferred method for treating infections globally.

With the rise of antimicrobial resistance, phage therapy is getting more attention. In 2010, Texas A & M opened a Center for Phage Technology, the University of California at San Diego founded the Center for Innovative Phage Applications and Therapeutics, the University of Pittsburgh has built a research team around phage therapy and so has the US Naval Medical Research Center.

Researchers are now making use of advances in genetic technology to build phages that can attack bacteria. The process is time-consuming and expensive. It requires scientists to find the exact phage that will kill the bacterial strain. Among the places scientists look for phages that attack pathogens dangerous to humans include sampling sewage. The research has advanced far enough to have saved several people who were dying from antibiotic resistance.

See this June 2022 story for more on how bacteriophage therapy has been used to save 20 people.


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.

Bioterrorism, the act of turning biological agents like microbes or toxins into weapons, has been used by military leaders for more than 2,000 years. One of the first known uses of bioterrorism occurred in 184 B.C., when Hannibal, the leader of Carthage (modern-day Tunisia), directed his sailors to fill earthen pots with serpents and launch them at enemy ships led by King Eumenes of Pergamum (Turkey).

During the 1960s, the U.S. military had a biological arsenal that included numerous weaponized pathogens, as did Canada, France, Britain, and the Soviet Union. But concerns about risks of such programs to society led to a 1972 U.N. Convention prohibiting the development, production and stockpiling of infectious diseases. The agreement was signed by 103 countries, and the U.S. confiscated its arsenal of bioweapons. But the convention had no enforcement mechanism. The Soviet Union, for example, kept working on bioweapons, through a program it called Biopreparat. Not until the late 1990s, when the Soviet Union dissolved, did the U.S. learn of the program.

The U.S. helped to dismantle the Biopreparat program, but security experts believe some countries, like North Korea, are still working on bioterrorism. Further, terrorists no longer need the backing or the resources of a nation-state to build a bioterrorist weapon. With developments in technology, only determination and access to medical supplies and a laboratory are needed, as the U.S. learned in the 2001 anthrax attack.

Anthrax isn’t communicable between people, but the bacterium can be altered to easily spread through the air. When inhaled, anthrax can cause lung damage and death. Not long after the Sept. 11 terror attacks, someone altered anthrax spores and sent them to the media and members of Congress through the mail. After a years-long investigation, the Federal Bureau of Investigation declared that Bruce Ivans, an Army microbiologist, was responsible for sending the spores, which infected twenty-two people and killed five. Ivans killed himself before he was charged and doubts remain about whether he was the culprit.

The anthrax attack remains the worst bioterrorism attack in U.S. history, and national security experts worry another one could occur.

Since 2001, the government has spent billions on programs to develop a strategy for responding to a potential biological attack.

The current federal government strategy for responding to biodefense can be found at the U.S. Department of Health and Human Services’ Office of the Assistant Secretary for Preparedness and Response here.

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.

Breakthrough infection

In vaccinology, a breakthrough infection means a person develops an infection from a pathogen after vaccination and may indicate the pathogen has become resistant to the vaccine. Almost no vaccine is 100 percent effective in preventing infections, but breakthrough infections are tracked in clinical trials to determine how well inoculation is working in a population.

With COVID-19, the Centers for Disease Control and Prevention defines a vaccine breakthrough case as someone who tests positive for COVID-19 (with or without symptoms) 14 days or more after being up-to-date with their vaccines. Up to date means depending upon age, and health status, the individual has received at least 1 dose of Johnson & Johnson vaccine or 2 doses of the Pfizer/BioNTech, Moderna or Novavax vaccine, called the primary series, and a booster shot in addition to the primary series, if recommended.

The CDC initially tracked all breakthrough infections of COVID-19 to determine if the vaccines were working, but on May 1, 2021 transitioned to tracking only breakthrough infections among people with COVID-19 that were hospitalized or died.

Data from the end of May 2022 indicate that breakthrough infections are common the longer the time after receiving a COVID-19 vaccine, however severe illness is less common.

Adults with 3 doses of Pfizer/BioNTech, Moderna vaccines had a 62.8 percent lower chance of developing a breakthrough infection two to four months after the third dose. Data as of the end of March 2022, indicated that 3 doses of the Pfizer/BioNTech, Moderna vaccines reduced the risk of hospitalization by 86 percent. As these numbers will continue to evolve, see up-to-date data on the latest on vaccine effectiveness, on this CDC site.

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 known prion disease is mad cow disease, which is caused when a person eats meat from an infected cow.

Contact tracing

Contact tracing is a monitoring process used to stop the spread of an infectious disease outbreak. The process is a bit like detective work. Individuals are trained to interview those diagnosed with a contagious disease and learn who they may have recently been in contact with and potentially infected. Those individuals, in turn, may be asked to quarantine themselves to prevent further spread.

Contact tracers find the index patient, and then learn about the circle of individuals who may have been exposed and infected, as well as those who were not infected by the person. By building a “ring,” around the individual, public health officials can then seal off the contagion and prevent transmission of the pathogen to others in the community.

Contact tracing takes a lot of time and manpower, however. Interviewing and reaching out to patients takes lot of effort and relies on people answering their phones and being willing to accept they may have been exposed and willingness to self-quarantine. Technology can be used to help with the labor. Some countries use cell phone data to augment tracing.

Contract tracing was deployed at the beginning of the COVID-19 outbreak. Federal, state, and local public health officials tried to build a ring around those individuals who were sick and tested positive for the SARS-Cov-2, the COVID-19 virus. However, because the pathogen spread via individuals without symptoms, and there was no testing of those without symptoms, contact tracers were unable to manage the virus's quick spread through communities.

Masking, vaccination and vaccine mandates have since largely replaced contract tracing as the primary means of containing and controlling the spread of COVID-19, as well as asking the public to voluntarily follow CDC guidelines by testing and then following quarantine and isolation guidelines after a positive diagnosis to reduce spread of the virus.


The term referring to a disease that is spread by contact between people or animals.

Direct contact includes disease spread through eating an infected animal, or through items that the ill individual may have touched, coughed, or sneezed on, or through skin or sexual contact. Indirect contact can occur through pathogens carried via air droplets that linger in a poorly ventilated room. Measles and COVID-19 are two diseases that can be spread through air droplets.

All diseases are infectious, meaning they are contracted in the environment. But not all those diseases can be spread to other humans or animals. A person can be infected but non-contagious.

During a fast-moving infectious disease outbreak, public health officials respond with tools to stop its spread. First, they try measures aimed at containing the disease, and if that doesn’t succeed, they move to reduce the severity of illness with mitigation efforts.

Containment versus mitigation in infectious diseases

Containment and mitigation tools differ depending upon the kind of infection that is spreading, and the availability of medical treatments and vaccines. With a known disease, it is easier to stop an outbreak. Containment tools include vaccinations, contact tracing and quarantines.

With a disease with no medical treatment option, public health officials must find non-pharmaceutical methods for reducing the severity of the outbreak. These measures can include mitigation efforts such as quarantines, social distancing and banning gatherings of large numbers of people.

When there is a rapidly evolving outbreak, with no known treatment option, as there was with COVID-19 until late 2020, U.S. officials first tried to contain its spread by restricting travel into the U.S. from China, where the virus first emerged. As the virus spread to other countries, like South Korea and Iran, the U.S. restricted travel from these countries as well.

Federal, state, and local public health officials tried to contain COVID-19 spread through contract tracing, and currently with masking, vaccines, and testing.

These containment and mitigation measures save lives. According to the Centers for Infectious Diseases Research and Policy, COVID-19 vaccines have saved an estimated 20 million lives globally between December 2020 and December 2021.

Cordyceps fungus

A spore-producing organism (scientifically its full name is Ophiocordyceps unilateralis) that can invade the brains of ants and other insects, causing strange behaviors like a “zombie” walk. The fungus was made famous in the popular 2023 HBO Max television show called, “The Last of Us.” In the show this fungus invades human brains and turns them into zombies. In real life, the cordyceps fungus is no threat to humans. However, other kinds of fungi 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.


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 [or SARs-CoV-2 for short] got its name. The “2019” designation was given because the virus is known to have begun circulating at some point late in 2019.

Disease elimination vs. eradication

Eradication refers to a disease being completely, literally eradicated from the earth: no cases occur at all, from any source. The best-known example is the eradication of smallpox in 1980. Elimination refers to a permanent interruption in indigenous transmission of a disease, making it no longer endemic, but the disease can still be introduced by a case from another geographical region.

Vaccines led to the elimination of polio in the United States in 1979 and measles in 2000. Yet measles cases still occur in the U.S. and in July 2022, New York state health officials reported the nation’s first polio case in a decade in an unvaccinated individual. The key here is that “elimination” and “eradication” are different things, though they are often confused by readers and sometimes even by journalists.

For example, there have been numerous outbreaks in the U.S. introduced by a person visiting from outside the U.S. None of them began with a person already living in the U.S. because the virus no longer circulates on its own in the U.S., due to the measles vaccine.

The distinction is important because an eliminated disease can always return if conditions allow for it, such as a sufficiently deep, sustained decline in vaccination rates, which is what allowed measles to circulate again in certain communities.

Disease X

Disease X is a placeholder name for an “unexpected” disease. The World Health Organization declared in 2018 that Disease “X” was a hypothetical unknown pathogen that could cause an epidemic. COVID-19, caused by the virus SARS-CoV-2 is the first to meet the requirements of a ‘Disease X.’

When infectious disease experts are asked about what the next pandemic might be, they often answer “Disease X.”

Disease X 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, just as occurred with SARS-CoV-2 and COVID-19 at the end of 2019.

“Disease X” was named in 2018 by the World Health Organization as one of nine diseases that public health officials believe is of high risk to blow up into an epidemic. The WHO list, called the “Blueprint Priority Diseases” and was developed to spur research investment in finding vaccines, treatments and medical counter measures for these pathogens, where few or none currently exist.

On the list includes COVID-19, Crimean-Congo hemorrhagic fever, Ebola and Marburg virus disease, Lassa fever, Middle East Respiratory syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS), Nipah and henipaviral diseases, mosquito-borne diseases Zika and Rift Valley Fever, and Disease X.


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 most 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. 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 just experience a mild illness, like the common cold, or don’t get sick. 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.

Epidemiological triangle

The components that contribute to the spread of a disease.

To understand how an infectious disease spreads, public health officials ask questions reminiscent of journalists. They want to know: What was the agent that caused the disease? Who was the host? Where did the transmission occur? These three questions create the “Epidemiologic Triangle” model, which is used to determine the nature of an outbreak.

Question one: “What is the agent?” refers to the microbe — a bacteria, virus, fungi, or parasite — that is causing the disease. How did it invade, leave, or transmit to the host? Was the transmission direct (from a person coughing on another person)? Or indirect? (from eating contaminated food, or drinking dirty water?) Or through an animal or insect? (from the bite of a mosquito?)

Question two: “Who is the host?” refers to the human or animal that is exposed and harboring a disease. What was the risk, or the susceptibility of the person of getting the disease? The answers to the questions may be biological (do they have a genetic predisposition for the disease? Or a weak immune system?), behavioral (what are the person’s eating habits?), demographic or cultural (do they have access to clean water? Do they live on a farm?)

Question three: “Where did the transmission occur?” refers to the environment. The environment impacts the risk of an animal or person’s exposure to a pathogen. For example, what is the climate, geology, and habitat of the person or animal? Is the person living in a nursing home? What is the biological environment? Does the person live near a jungle or river, where there are mosquitos? And what is the person’s economic status? What is their occupation? Was there a natural disaster, like a hurricane, which caused mold to grow? Other environmental factors include the weather. In the winter, flu viruses spread more quickly, than in the warm summer months.

In the middle of the triangle is time. It is the period between exposure and signs of symptoms, which is called the incubation period. The time can provide information to epidemiologists about the nature of the pathogen, its source and identify those who were likely infected.

These are all questions journalists may ask public health officials as well when they are covering a disease outbreak and want to know more about what it means for their community.


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.

False balance

A lapse in responsible reporting referring to using outliers’ voices to state opinions that contradict the facts simply to provide “balance” to a story.

Click for a deeper dive into false balance.


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 filoviruses 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 vaccine for Ebola has demonstrated effectiveness during the sporadic Ebola outbreaks in the Democratic Republic of Congo that have flared in the region since 2018.

Flattening the Curve

It is a term used to refer to the curve in the projected number of people who will contract a pathogen over a period of time. If models are showing that the pathogen is expected to infect people quickly, the curve upward is sharp. So public health officials look for ways to slow the spread the pathogen, or flatten that curve, to prevent hospital systems from becoming overwhelmed with patients.

The term became part of the American lexicon during the early months of the COVID-19 pandemic as government leaders and public health officials sought to explain why strict social distancing measures were being enacted to stop the spread of SARS-CoV-19.

Before vaccines became widely available in early 2021, the only option to slow the transmission rate, and flatten the infection curve, was through collective social distancing, which meant avoiding other people whenever possible.

When someone is infected with COVID-19, that individual can spread it to multiple people and if nothing is done to slow its transmission it could overwhelm hospitals. As of mid-2022, rather than emphasizing social distancing, public health officials are emphasizing testing, masking in indoor public places, vaccination, and quarantine for five days if infected, to prevent spread of COVID-19.


A kind of virus found primarily in ticks and mosquitos that can occasionally infect humans. Members of this virus family belong to a single category called “Flavivirus.” The word “flavus” means “yellow” in Latin. Some of the mosquito-transmitted flaviviruses include yellow fever, dengue fever, Japanese encephalitis, West Nile virus and Zika virus. Other flaviviruses transmitted by ticks include tick-borne encephalitis, Kyasanur Forest Disease, Alkhurma disease, and Omsk hemorrhagic fever.

Fungal infection

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.


The term refers to laboratory techniques used to enhance aspects of a pathogen to make it more deadly and transmissible. This is usually done via a combination of gene editing and infecting several animal hosts. The aim is to learn how a pathogen may mutate and develop vaccines and therapeutics to stop its spread.

In 2017, the National Institutes of Health announced that it would renew funding for gain-of-function projects after a three-year ban to give the federal government time to develop a framework for safely permitting gain-of-function research. The decision was controversial as some in the research community feared that there was no way to guarantee the safety of such research.

Gain-of-function research was occurring at a research facility in Wuhan, China where the SARS-CoV-2 emerged at the end of 2019, spawning ongoing questions about whether the virus originated from a research project gone wrong, or from an animal that spread it to people. (The majority of new diseases are caused by a jump from animals to people, a term called zoonotic disease.) The latest research published in summer 2022 suggests that SARS-CoV-2 emerged from an animal and not from a lab.

Gram-positive and gram-negative bacteria

Bacteria are classified based on a chemical stain that can be seen through the microscope. Bacteria that turn purple under the microscope are called “gram-positive” and those that turn pinkish or red under the microscope are called “gram-negative.”

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 and how the stain attaches to the bacteria or not, is related its structure. Gram positive bacteria, like those that cause strep throat or many skin infections, have a thick wall made 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 will look red or pink under a microscope.

Hand, foot and mouth disease

This is a mild contagious viral infection that usually affects children younger than five.

Hand foot and mouth disease is most often caused by the coxsackievirus, which is part of a family of enteroviruses (viruses that like to replicate in the gastrointestinal tract). 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.

Hand hygiene

Washing one’s hands is among the most effective ways of reducing the spread of infections.

In health care settings, those providing services wash their hands less than they should, which contributes to the spread of disease in hospitals where patients are already sick. Prior to the COVID-19 pandemic, studies showed that only about half of people working in a hospital washed their hands, resulting in patients getting an infection. But post the pandemic, hyper awareness of washing hands resulted in health care staff using hand sanitizers four times more often than they did before the pandemic, according to the December 2020 Journal of Primary Care Community Health.

The CDC recommends health care providers use an alcohol-based sanitizer on their hands immediately prior to touching a patient and to wash their hands with soap and water if their hands are visibly soiled. The agency also recommends using sanitizer before handling medical equipment, before moving from work on a soiled body site to a clean site on the body, after touching a patient’s immediate environment and after removing gloves. They also say providers should wash their hands with soap and water after touching a patient with diarrhea or suspected exposure to a spore, like c. difficile.

In non-clinical settings, the CDC recommends everyone wash their hands at certain times to prevent disease. They recommend doing so before, during and after preparing food, before eating, before and after caring for someone who is sick, before and after treating a wound, after using the toilet, after changing a diaper, after blowing your nose, or coughing, after touching a pet and after handling garbage. Proper hand washing includes wetting the hands, putting on soap, and scrubbing hands for at least 20 seconds, rinsing hands, and then drying them with a clean towel or letting them air.

For preventing COVID-19, if soap and water aren’t available, the Food and Drug Administration recommends using hand sanitizer with at least 60 percent alcohol.

Helminth-caused infections

Helminths are parasitic worms. Worms can be transmitted to humans in fecal material, from insects or from walking barefoot on contaminated soil.

Most helminths are either roundworms or flatworms. Once they enter the body, they tend to live in the intestines. Parasitic worms make up the majority of neglected tropical diseases.

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.

Herd immunity

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 immune system is among the complex functions in the body. There are two layers to the system – the innate immune system and the adaptive immune system. The system also works in three phases - first the body detects that an enemy is trying to launch an assault, a messenger then sends for help to fight the threat, and then the body builds an army to counterattack to eliminate the enemy.

The innate immune system works quickly and is the part of the body that detects the enemy pathogen has entered the body. This part of the immune system tries to immediately neutralize the pathogen by creating proteins called cytokines and interferons, which both try to kill the invader as well as interfere with the pathogen’s replication. They also set off alarms in the body’s adaptive immune system that it may need help fighting the threat.

If the cytokines and interferons aren’t enough to stop the invasion, the second layer, or the adaptive immune system, joins the fight. The second layer is triggered by messenger cells, which grab pieces of the invader and carry it to the lymph nodes where specialized white blood cells are waiting to be called into service. In this Atlantic article, journalist Ed Yong likens the moment to being in a bar, where a bunch of mercenary killers, called T-cells, are waiting to be hired. Each T-cell can only kill one type of enemy, however, so when the ‘messenger’ shows up at the bar, the piece of the invader is shopped around to all the mercenaries sitting in the bar, until the messenger finds a match. Then the T-cell arms up by cloning itself into a huge army, and marches into the pathogen battle.

T-cells battles the pathogen in two ways. T-cells blow up cells invaded by the pathogen, and they activate another set of immune cells called B-cells, which produce proteins called antibodies. Antibodies are proteins that attach to pathogens and halt their ability to replicate in the body.

The adaptive immune system has a memory. Once the army has eliminated the pathogen in the body, most of the T-cells and B-cells die off, but the body keeps a few of the T-cells around in the lymph nodes just in case the pathogen tries to attack the body again. This is how vaccines work. They train the adaptive immune system to be ready for an attack. For a more detailed description of how the immune system works, look at this video produced by a Yale University School of Medicine immunologist Akiko Iwasaki.


The ability of the body to respond to 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 pathogens, like the SARS-CoV-2 virus that causes COVID-19, the exact IFR rate has been difficult to determine because most people who aren’t sick aren’t being tested for infection. Therefore, scientists have been more closely tracking observed case fatality rates (the chances of someone with a confirmed COVID-19 case dying from it). The observed case fatality rate from COVID-19 varies by region because some countries have less robust medical resources than others.

For example, as of August 2022, Peru’s observed case fatality rate from COVID-19 was 5.3 percent, compared with the United States, which has a case fatality rate of 1.1 percent, according to Johns Hopkins University & Medicine Coronavirus Resource Center.


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.

Infections diseases as cancer cause

Cancer is a set of diseases characterized by abnormal cell growth triggered by a genetic defect. Sometimes an infectious agent can trigger a genetic defect leading to cancer.

Researchers know that genetic defects that cause cancer can be inherited, or the defects can be caused by environmental factors, such as smoking, and exposure to radiation. Infectious agents, such as viruses, bacteria and parasites also can increase a person’s risk of developing cancer.

Though the full reasons why some pathogens may increase cancer risks aren’t fully understood, researchers believe they either contribute to genetic changes in cells or inhibit the body’s ability to fight cancer. Generally, infectious diseases are linked to about 10% of cancer types, according to a 2017 Caspian Journal of Internal Medicine report.

Infectious agents known to be linked to cancer include hepatitis B and C viruses (liver cancer), Epstein-Barr virus (Burkitt’s lymphoma, nasopharyngeal carcinoma, Hodgkin lymphoma), human papillomavirus (cervical cancer), human immunodeficiency virus type 1 (Kaposi sarcoma, non-Hodgkin lymphoma, cervical cancer), Helicobacter pylori (Adenocarcinoma and lymphoma) and Streptococcus bovis (colorectal cancer).

With human papillomavirus, HPV, there is a vaccine, Gardasil, that can reduce the risk of developing cervical cancer if a person becomes infected with the virus. And treating people with antibiotics who have been infected with the bacteria H. Pylori, can reduce their risks of developing stomach cancer.

Given there are many approaches to fighting infections, from vaccines, to antibiotics, to safe sex practices, researchers are continuing to work on understanding how pathogens play a role in causing cancer.

Infectious disease modeling

Despite great strides in medication, sanitation, hygiene and in animal and pest control, infectious diseases remain an enormous threat to human and animal health, as COVID-19 demonstrated to the world.

How these infectious diseases spread and become epidemics depends on a range of interconnected dynamics of pathogens, people, and animals. Some microbes are transmitted between people, or between people and animals; some circulate among multiple hosts before they are transmitted, and others must be carried in an insect vector before spreading. Many factors including, increasing antibiotic resistance, human connectivity and behavior, population growth, climate change, land-use change, farming, urbanization, and global travel, also impact the emergence and spread of infectious disease, as well as pose challenges for prevention and control.

Given these huge complexities, scientists have increasingly turned to mathematical models to understand epidemiological patterns to target public health decisions. These models hark back to Isaac Newton, who had the fundamental insight that there are unchanging universal laws that govern the actions of natural phenomena. The hope is that with more data and more computing power, the most complex outcomes can be predicted.

In the past 20 years, growing computing power and infectious surveillance has enabled scientists to gather more data for developing these models. Researchers are collecting volumes of data from epidemiology, evolutionary biology, immunology, sociology, climate, and public health resources to develop models that mimic how infections might evolve and spread.

The challenge with modeling infectious disease, however, is that pathogens, the environment, the rate of contagiousness, the rate of transmission, the availability of vaccines, and the climate are ever changing. But most models rely on data from past events to predict the future.

In 2021, the Centers for Disease Control and Prevention launched the Center for Forecasting and Outbreak Analysis to make use of data modeling to forecast and respond to future public health outbreaks.

Infectious dose

Infectious diseases spread when a healthy person encounters 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.


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.

Influenza (flu)

Influenza is a respiratory disease caused by the influenza virus, and is endemic to humanity. The virus is always around, most often striking populations in the late fall or winter seasons. The flu virus attacks not only the respiratory system but also can cause headaches, muscle and joint pain and other complications. The overwhelming majority of the time, people who are infected with the flu recover within about ten days, though it still kills tens of thousands of people around the world annually.

Until the COVID-19 pandemic in 2020, most public health officials thought the most likely source for a pandemic would be an influenza virus because among the fastest mutating viruses is influenza. Global surveillance of influenza viruses has enabled vaccine makers to adjust vaccine formulas to target the changing virus each year, which is why there is an annual flu vaccine. However, scientists believed it is only a matter of time before influenza could mutate to evade humans’ immune systems.

Between 1918 and 1919, the world was struck by the largest flu outbreak in modern history. Though it was called the “Spanish” flu, it may have actually started in the U.S. in an agricultural district in Kansas. It was called the Spanish flu because Spain was the first country to report on a widespread flu. Epidemiologists say the 1918 strain spread from an army base in Kansas, where recruits brought it to Europe and then the rest of the world. What made the flu particularly dangerous is that it sickened young people and pregnant women more often than the old and immune-compromised. The virus caused otherwise healthy people’s immune systems to overreact, damaging organs and killing them. The process is called a cytokine storm. Estimates range on how many people died worldwide, with the largest suggesting that about 100 million died. About 500,000-650,000 people are estimated to have died in the U.S.

Since 1500, there have been more than a dozen flu pandemics recorded, with at least five occurring in the past 140 years: in 1889, 1918, 1957, 1968, and 2009.


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.

Lyme disease

Lyme disease, in the U.S., is caused by the bacteria B. burgdoreri, and is transmitted through the bite of a tick. About 300,000 to 500,000 Americans develop Lyme disease annually, making it the worst vector-borne disease in the U.S.

B. burgdoreri bacteria can cause tissue and immune system damage. In most people, a course of antibiotics can kill the bacteria. For 10 percent to 20 percent of people, antibiotics don’t work. The symptoms of Lyme, such as nerve tingling, fever, fatigue, and headaches, persist for months or years.

There is division within the medical community whether these non-responding patients ever had Lyme. There is also debate over the best options for continuing treatment of these patients too.

Arguments over the treatment of Lyme disease is “one of the biggest controversies that medicine has seen,” Dr. John Aucott, a physician and director of the Johns Hopkins Lyme Disease Clinical Research Center said in a September 2019 article in The Atlantic.

Since the 1990’s, mainstream medical consensus, has been that Lyme disease is easy to diagnose. If a person develops a bulls-eye rash and flulike symptoms after being bitten by a tick, they have Lyme. The prescribed treatment protocol is ten days, to a few weeks of oral antibiotics, usually doxycycline, and the disease clears up. If the disease is found in a later stage, a month of intravenous antibiotics could be necessary. This remains the treatment recommended by the Infectious Diseases Society of America (IDSA), the organization that represents the consensus of infectious disease specialists in the country.

For patients who failed to respond to antibiotics, some physicians began to refer to the symptoms as chronic Lyme disease or post-treatment Lyme disease (PTLD). The International Lyme and Associated Disease Society and the U.S. Centers for Disease Control and Prevention now recognizes PTLD as a diagnosis for people with symptoms of Lyme that persist after treatment. In many cases, physicians, using this diagnosis, recommend long-term use of antibiotics.

The IDSA, however, concerned about overuse of antibiotics, doesn’t recognize this diagnosis. Often diagnostic tests that look for Lyme disease don’t find it or contradict one another. Many physicians believe patients that complain of PTLD may have an undiagnosed auto immune disease, or that the Lyme triggered an autoimmune disease and therefore antibiotics are useless. Still other physicians think patients may have been infected with other tick-borne illnesses, or maybe a virus that no one has been looking for.

Until research is more definitive in being able to answer the question of why some people don’t respond to Lyme disease treatment, controversy over how to best respond will continue.


The microbiome refers to the community 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.

There are millions of microorganisms in humans. It used to be said that they outnumber human cells 10 to one, but that is now known as a myth and that it is more likely that there are as many microbes in and on the body as there are human cells.

Most of the time microbes live in harmony with the body and play a key role in the proper functioning of the immune system and human health. Scientists are still trying to figure out why.

Research into the microbiome has flourished since 2007, when the National Institutes of Health launched the NIH Human Microbiome Project to map the human body’s microbiome. Through that work, researchers learned there are more than 10,000 microbial species in the body. Scientists also discovered the microbiome varies drastically throughout the body.

“Each body site can be inhabited by organisms as different as those in the Amazon Rainforest and the Sahara Desert,” says the NIH.

Most scientists now believe microbes live in and on the body to help extract energy from food and store it in the body and may help to “train” the immune system to determine what pathogens may be deadly for a human host and which are harmless. Among the most promising areas of microbiome research is connected to fecal transplants to treat recurring illness from clostridium difficile, a bacterium that can cause life threatening inflammation of the colon.

Most microbiome research, however, is preliminary and has been conducted on mice. Hence, scientists urge journalists to use caution when writing about the microbiome and its promise for healing human diseases.


On Nov. 28, the World Health Organization renamed monkeypox disease as ‘mpox’ to remove the ‘racist and stigmatizing’ language that surrounded the use of the original name. Still, the WHO will take its time with the renaming. Both names will be used for a year until ‘monkeypox’ is phased out, allowing publications and journals to update the name usage. Mpox is caused by a variola virus that results in the ‘pox-like’ scars on the skin. The disease was first reported in 1958 when pox-like diseases occurred in monkey colonies used for research – hence the original name “monkeypox.” The first human mpox case was reported in 1970.

The mpox name change reflects an effort the WHO began about a decade ago to reduce the insult and stigma inflicted by diseases named for people, places and animals. Badly chosen names can stigmatize people. For example, an early name for AIDS was gay-related immunity deficiency, before it was renamed acquired immune deficiency syndrome. In another example, the flu that became a pandemic in 2009 is still called the swine flu. Though is not transmitted by pigs, some countries initially slaughtered pigs and banned exports of pork because they thought the disease could spread from pigs. Most recently, with COVID-19, the WHO took pains to make sure the disease was not named the ‘China’ flu. COVID-19 is short for ‘coronavirus disease 2019.’

The WHO urges researchers, health officials, and journalists to use more neutral, generic terms, such as severe respiratory disease or novel neurologic syndrome.

Neglected tropical diseases

Diseases that could be controlled or even eliminated through mass administration of medication or vaccination but haven’t been because of extreme poverty of the environment or country.

About 1.4 billion people around the world live below the poverty line. These individuals, mostly the world’s subsistence farmers and their families as well as the urban poor, often do not have access to clean water and adequate sanitation. They also may live in close contact with livestock and vectors that carry disease, such as flies and mosquitoes. As a result, they are at risk of becoming infected with at almost two dozen parasitic and related infectious diseases such as amebiasis, Chagas disease, cysticercosis, echinococcosis, hookworm, leishmaniasis, and schistosomiasis. They produce a level of global disability and human suffering. See the World Health Organization complete list here.

The world’s poor receive little attention from governments and health organizations and don’t have access to much of modern medicine. Further, because of the absence of financial incentives, multinational pharmaceutical companies have not embarked on substantive research and development programs to develop vaccines for many of these neglected tropical diseases.

Non-communicable diseases

Non-communicable diseases are usually chronic illnesses that aren’t physically transmissible from person to person and last three months or longer. They can’t be prevented by vaccines or cured with medicine. They are caused by a combination of factors including genetic, physiological, lifestyle and environmental factors. Heart disease and diabetes are examples.


This term is usually used in reference to an infection acquired while under medical care, usually at a hospital. 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), bacteria that can cause colon inflammation and bloodstream infections respectively.

One Health

One Health is a growing field within public health that embraces the connection between animals, humans and the environment and solves complex health problems such as emerging infectious diseases, food safety and antibiotic resistance.

The medical community observed that human and animal health were closely linked back in the late 1800s, but the concept of One Health has risen in prominence as the world’s population has exploded. By 2025, there are expected to be more than 8 billion people living on the planet, up from about 7.4 billion at the end of 2017.

Scientists estimate most emerging infections are a zoonotic, meaning they come from animals. Commonly known zoonotic diseases include avian influenza, Ebola, rabies, Middle East Respiratory Syndrome and Lyme Disease and likely COVID-19. Worldwide, the number of infectious disease outbreaks has tripled. More than a dozen new infectious diseases have emerged over the past 25 years in the U.S. alone.

As One Health is relatively new in the public health field, the definition of the term is imprecise. One Health has been defined as an initiative, a movement, a strategy, a framework, an agenda, an approach, and a collaborative effort. In general, One Health involves the intersection of biology, comparative medicine, earth sciences, ecology, engineering, human medicine, social sciences, humanities, and veterinary medicine. One Health programs link physicians, nurses, public health professionals, veterinarians, agricultural scientists, ecologists, social scientists, engineers, biologists, and other professionals, to develop holistic solutions for keeping humans, animals, and the environment healthy.

The CDC created the first One Health office in 2009, to foster collaboration between international, federal, state and local governments, as well as the academic, health and private sectors.

Opportunistic infection

An infection caused by pathogens — a bacteria, fungi, parasite, or virus — that has taken advantage of a person’s weakened immune system from illness, drugs, or malnutrition.

An example of an opportunistic infection is acquired immune deficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV). If unchecked, the HIV virus causes progressive failure of the immune system and 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 considers the Candida auris fungus to be among the newest emerging microbial threats in the world as hospitals are reporting many new cases of resistant fungi causing illness.


A disease outbreak is the occurrence of cases of a disease more than 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.

A community’s culture can impact how an infectious disease outbreak evolves. Outbreak culture is a term to describe the collective mindset that develops within communities and by public health and humanitarian responders as a disease outbreak unfolds and the ways that the mindset can inhibit initial action and even worsen an epidemic.

The mindset can develop from challenges in communication and coordination between individuals, agencies, organizations and governments, resistance by local people, uncertainty about the cause and source of a disease, health provider and infrastructure gaps, media coverage and politics.

For example, pandemic fatigue and distrust in the federal government led many Americans to reject public health officials’ requests for people to wear masks in public and to refuse to receive COVID-19 vaccines, which has likely lengthened the time of the pandemic.

To prevent future pandemics, public health leaders say that there needs to be a focus on ways to enhance collaboration between individuals, providers, responders, communities, and governments.


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.

Since 1500, there have been many recorded pandemics, with six occurring in the past 140 years: in 1889, 1918, 1957, 1968, and 2009 and then 2020.

Until the 2020 COVID-19 pandemic, none were as deadly as the influenza outbreak in 1918. Public health officials thought that the next pandemic would be caused by an influenza virus, because it is among the fastest mutating viruses, but the 2020 pandemic was caused by a different kind of virus – a coronavirus.

Coronaviruses are a family of viruses, some of which cause respiratory illness in humans. The virus exhibits a crown-like halo, when viewed under an electron microscope, which is how it got its name. The viruses have been found circulating among animals, such as camels, cats, and bats and a few have jumped to people - a spread that is defined by epidemiologists as "zoonotic." Scientists believe SARS-CoV-2, the coronavirus that causes COVID-19 disease, was zoonotic and likely jumped from an animal living in China to humans at the end of 2019.

The World Health Organization declared the transmission of SARS-CoV-2 a pandemic in March 2020 and the pandemic had not yet ended, as of August 2022.

For more on the COVID-19 pandemic, see our COVID-19 section.


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.

Whooping cough is a contagious and potentially dangerous respiratory disease, especially for young children. To prevent the disease, there is a vaccine, developed in the early 20th century. The whooping cough vaccine is part of the diphtheria, tetanus and pertussis (DTaP) vaccine, given to children between 2 months and 6 years of age, according to the CDC, but people of all ages should be vaccinated against pertussis.

The history of the pertussis vaccine is important because it is one of the origins of the current state of vaccine hesitancy. A 1970’s a study in the U.K. journal Archives of Diseases of Childhood suggested that there was a connection between the whole-cell whooping cough vaccine and neurological damage in children. The report led to a steep decline in vaccine coverage in the U.K. and a rise in distrust with the medical establishment regarding vaccine safety, according to a Health Affairs report from 2005.

Researchers retooled the vaccine and adverse events declined. However, protection from the retooled vaccine — which uses parts of a pertussis bacteria cell instead of the whole cell — doesn’t last as long, and scientists are now in the process of working on developing a new vaccine.

Presumptive positive

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

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.

Prion diseases usually evolve rapidly and are 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, of which there were 538 cases reported to the CDC in 2020.

Quarantine and isolation

These are terms that are often confused by the public. A quarantine involves restricting the moment of a healthy person who is suspected of exposure to a communicable disease, even if the person isn’t experiencing symptoms or doesn’t know if they have been exposed. The person is kept apart from the community during the time the pathogen is known to incubate and then become contagious to others.

Isolation involves separating someone who is already sick and/or tested positive or a disease. The person is then kept apart from the community until they are no longer contagious.

Quarantines and isolation may take place in the home, or other locations determined by health authorities.

The history of quarantines goes back to the Middle Ages, when the plague was sweeping through Europe. Venice, a major port, tried to stop the disease from entering its city by requiring ships suspected of harboring plague to wait offshore for 40 days before people or goods could come ashore. The city also built a hospital off its coast, where sailors who came off ships with the plague were sent. The 40-day waiting period was called “quarantinario,” for the Italian word for 40. Hence the word “quarantine.”

Quarantines can be important when there is no vaccine or drug to treat a rapidly spreading disease, as was true in the early days of the COVID-19 pandemic. However, as the pandemic also demonstrated, quarantines are controversial because they involve separating healthy people from the community, and they raise civil liberties questions.

The Centers for Disease Control and Prevention has the legal authority to quarantine and isolate a person at a U.S. airport, port or the border if the person is known to be infected or possibly infected with one of nine quarantinable diseases. The nine include: cholera, diphtheria, infectious tuberculosis, smallpox, yellow fever, viral hemorrhagic fevers, severe acute respiratory syndrome, new types of flu that could cause a pandemic, or a disease that has been designated by order of the president, as was done so with the COVID-19 pandemic.

During the first year of the COVID-19 pandemic, at the order of the president, the CDC restricted and banned international travel for non-U.S. citizens from some countries to slow the spread of the SARS-CoV-2 virus that causes COVID-19 disease.

The CDC also initially asked people to isolate in their homes for up to 10 days if they had symptoms or tested positive for COVID-19 and to quarantine for up to 10 days if they had been exposed, but changed its guidelines in August 2022. Those that test positive are asked to quarantine for 5 days. For those who have been exposed, but tested negative, the CDC no longer recommends quarantining, but rather encourages those exposed to wear a mask when in public and to test 5 days after exposure.

Ring vaccination

This is a public health strategy aimed at halting the spread of a viral infection. It involves vaccinating all people in a specific area, during an outbreak, that may be susceptible to contracting the virus.

With ring vaccination, health providers identify patients that are infected and then vaccinate all those around the individuals, forming a “ring” or a kind of buffer of immune individuals to prevent the spread of the disease.

The strategy was most famously deployed to eradicate smallpox. When an infection of smallpox was identified, public health providers identified everyone who was or might have been exposed to the virus and then vaccinated those individuals. Then a second “ring” of people that might have been exposed to the first ring of people were identified and vaccinated. The last naturally occurring case of smallpox occurred in Somalia in 1977 and the World Health Organization declared smallpox eradicated in 1980.


R0 (pronounced R-naught) is a number epidemiologists use to determine the infectiousness of a disease and a community’s susceptibility to an epidemic.

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.

The “R” stands for “reproductive number” and is an epidemiological threshold. If the “R” number of a bacteria, virus, fungi or parasite, is greater than one, it means the disease may be highly contagious or an outbreak may be spreading. If it is less than one, it means the outbreak is either on the decline or isn’t likely to cause an epidemic. If you want to geek out on the mathematical formula, check out the Mathematical and Statistical Estimation Approaches in Epidemiology or this detailed description.

The “R” number for a disease is a range and changes with conditions within the community at the time. Many factors impact the “R” number including the period of time for which a disease is contagious (the longer a person is contagious, the more likely the disease is to spread), the number of people that a sick person comes in contact with (a sick person who stays home may spread the disease more slowly), how the disease is transmitted between people (diseases that spread through the air, like measles can travel quickly, while those that are sexually transmitted spread more slowly), the immunity level of the population (whether people have been vaccinated for the disease or survived a version of the disease in the past) and whether there is a strong health and legal system within the community (hospitals to treat people and law enforcement to impose quarantines can reduce spread of a disease).

Understanding the R number of a disease is important for helping public health officials determine strategies for controlling its spread, such as vaccinating the population or quarantining sick individuals if no vaccine is available.

Examples of infectious disease with R numbers above one include: measles (R12-18), Ebola (R2), Hepatitis C (R2), HIV/AIDS (R4), Severe Acute Respiratory Syndrome (SARS) (R4), mumps (R10).

COVID-19 is another disease with an R-naught above 1. In November 2020, epidemiologists estimated that the R range of SARS-CoV-2 was 1.4 to 6.68, and in May 2022, that the omicron variant’s basic and effective R range was 8.2 and 3.6.


Sepsis is an extreme bodily response to an infection.

With sepsis, the body sends a flood of chemicals to the blood stream to fight an infection, which in turn causes widespread inflammation, slowing 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 350,000 die from it, according to the Centers for Disease Control and Prevention. One in three patients that die in the hospital die from sepsis.

Serologic test

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.

With COVID-19, some people have had a serologic test to determine their antibody levels for SARS-CoV-2, the virus that causes COVID-19 disease. Those with high levels of antibodies in their blood indicate that a person may have been exposed to or recovered from COVID-19, or their body has responded to the COVID-19 vaccine. But the U.S. Food and Drug Administration says antibodies in the blood do not necessarily mean someone is protected from COVID-19 infection and therefore serologic tests are not recommended for use by the general public.

Social epidemiology

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.

For example, they look 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.

Super spreader

Someone who is infected with a particular disease and responsible for transmitting that bacteria or virus to many other people. Epidemiologists say these are often the index cases where an epidemic begins.

Why someone is a "super spreader," depends on the kind of pathogen, the infected person's biology, their environment, and their behavior at the given time. Today, with global travel, the ability to move pathogens rapidly across great distances, often before people are aware they are sick, creates environments ripe for super spreading.

Some infected people might shed more of a virus or bacteria into the environment than others because of how their immune system works. A person who is infected, but with no symptoms, may continue about their daily routines and inadvertently infect more people. A famous example of that type of person is "Typhoid Mary," a cook who supposedly infected dozens of people with typhoid, even though she wasn't sick.

Alternatively, people who are sick may be very good at transmitting a pathogen even if they reduce their contacts with others. Individuals who have more symptoms – for example, coughing or sneezing more – can spread the disease to new human hosts. During an outbreak, epidemiologists look for super spreaders, because they can accelerate the rate of new infections in people.

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 the symptomatic case-fatality rate figure helps scientists determine the danger of a particular pathogen. With a fast-moving and novel pathogen, this figure may be a moving target, because only those with illness are tested and geographic differences impact the mortality rate. 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 should caveat mortality rate figures during an outbreak with something to the effect of: "a mortality rate, based on the information that scientists have."

For COVID-19, many people don’t have symptoms and most epidemiologists are using the observed-case fatality rate, which is the number of deaths divided by the number of confirmed cases, rather than the symptomatic case fatality rate to track COVID-19’s mortality figure. As of early September 2022, the observed fatality rate for COVID-19 was 4.7% in Mexico and 1.1% in the U.S.


Vaccines are agents (usually dead or weakened microorganisms, or a genetic piece of the organism) that elicit a specific immune response protecting individuals from the pathogen should they be exposed to it later.

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, surface proteins or genetic material. 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 and prevent disease.

They are considered the most important and powerful tools for preventing the spread of infectious diseases.

The term vaccine stems from the work of Edward Jenner, an English physician, who noted in the mid-18th century that people exposed to cowpox, a mild version of smallpox, were then immune to smallpox. Smallpox, a virus that causes fever and severe and debilitating skin blisters, was killing about 400,000 Europeans annually during the 18th century. The Latin translation of cowpox was “variolae vaccinae.”

In 1796, Jenner experimented with taking a scab from a milkmaid with cowpox and inserted it into a cut on an 8-year-old boy. The boy became immune to smallpox, proving a person could be protected from smallpox without being directly exposed to it. Jenner’s method was recognized as the first scientific attempt to control an infectious disease. Breakthroughs in science after Jenner’s experiment led to the development of vaccines for rabies, plague, typhoid, cholera, diphtheria, tuberculosis, whooping cough, polio, measles, mumps and rubella, all diseases that used to kill millions of people annually.

The impact of vaccines on public health has been obvious. After vaccines became available, cancer, heart disease and strokes replaced infectious diseases as top causes of death.

The COVID-19 pandemic reversed that success, however, as COVID-19 became the third-leading cause of death in the U.S. in 2020 and 2021. With the wide availability of vaccines, public health officials hope that in the coming years, COVID-19 will drop down on the list of leading causes of death.

Vaccine hesitancy

Vaccine hesitancy is a term that has emerged as a more neutral way to discuss attitudes toward vaccines, without identifying people strictly as “anti-” or “pro-” vaccine. The term 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.

Vaccine platform

A method of manufacturing vaccines for broad use and multiple pathogens.

Most conventional vaccines contain either an inactivated pathogen or the protein made by that pathogen called an antigen.

Genetic engineering has enabled scientists to develop a new way to design, test and manufacture vaccines. The method involves taking a piece of a pathogen’s genetic material to trigger the body’s immune response.

This is what has been used with some COVID-19 vaccines. Pfizer and Moderna’s vaccines utilize RNA from the SARS-CoV-2 virus, the virus that causes COVID-19. The RNA is injected into the body to trigger the production of SARS-CoV-2 antigens. Antigens are molecules that spur the body’s immune system to recognize a biological intruder.

Once the immune system “sees” the SARS-CoV-2 antigen, the body produces antibody proteins. If the whole SARS-CoV-2 virus should enter the body, there are now existing antibodies to immediately mark the virus as an intruder, enabling the immune system to quickly mount a defense and thwart disease.

Using genetic engineering also enables scientists to quickly update vaccines. For example, both Moderna and Pfizer have developed a booster vaccine to protect against the latest omicron variant of SARS-CoV-2, months after the variant emerged.

Vector-borne diseases

Vectors are organisms that pass diseases from animals to humans or between humans.

Many vectors are insects that suck infected blood from the animal or human host and then pass the disease-causing microorganism to other animals or humans. Mosquitos are the most widely known vector. Other vectors include ticks, fleas, sand flies, freshwater snails and triatomine insects (like kissing bugs). Vector-borne diseases cause about 17 percent of infectious diseases globally and cause as many as 1 million deaths. The World Health Organization has a good primer here.

There are a number of vector-borne diseases in the U.S., including Zika, Chikungunya, and West Nile, which are spread by mosquitos. Lyme disease is spread by ticks. In May 2018, the CDC warned that illnesses caused by the bite of fleas, mosquitos and ticks tripled to 640,000 between 2004 and 2016. Nine new germs spread by mosquitos and ticks were discovered or introduced since 2004, the agency said. Among the reasons they are on the rise in the U.S. include a warming climate, travel and global trade.

Viral load

A 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 on to 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 multiply.


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 waterfowl. 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% to 75% of all new diseases that affect humans are zoonotic in origin.

Most scientists have concluded that COVID-19 is zoonotic and traced its origins to a wet animal market in Wuhan, China, though researchers have been unable to determine in which animal the reservoir for SARS-CoV-2 occurred. But, some researchers disagree with this assessment and theorize that the virus emerged from an accidental release at a Wuhan biology laboratory. In. June 2022, a World Health Organization science advisory group expressed the need for further investigation of the lab leak scenario.