Technically, any clinical diagnosis of influenza is a diagnosis of ILI, not of influenza. This distinction usually is of no great concern because, regardless of cause, most cases of ILI are mild and self-limiting. Furthermore, except perhaps during the peak of a major outbreak of influenza, most cases of ILI are not due to influenza. ILI is very common: in the United States each adult can average 1–3 episodes per year and each child can average 3–6 episodes per year.

Influenza in humans is subject to clinical surveillance by a global network of more than 110 National Influenza Centers. These centers receive samples obtained from patients diagnosed with ILI, and test the samples for the presence of an influenza virus. Not all patients diagnosed with ILI are tested, and not all test results are reported. Samples are selected for testing based on severity of ILI, and as part of routine sampling, and at participating surveillance clinics and laboratories. The United States has a general surveillance program, a border surveillance program, and a hospital surveillance program, all devoted to finding new outbreaks of influenza.

In most years, in the majority of samples tested, the influenza virus is not present (see figure). In the United States during the 2008–9 influenza season through 18 April, out of 183,839 samples tested and reported to the CDC, only 25,925 (14.1%) were positive for influenza. The percent positive reached a maximum of about 25%. The percent positive increases with the incidence of infection, peaking with the peak incidence of influenza (see figure). During an epidemic, 60–70% of patients with a clear influenza-like illness actually have influenza.

Samples are respiratory samples, usually collected by a physician, nurse, or assistant, and sent to a hospital laboratory for preliminary testing. There are several methods of collecting a respiratory sample, depending on requirements of the laboratory that will test the sample. A sample may be obtained from around the nose simply by wiping with a dry cotton swab.

Infectious diseases causing ILI include malaria, acute HIV/AIDS infection, herpes, hepatitis C, Lyme disease, rabies, myocarditis, Q fever, dengue fever, poliomyelitis, pneumonia, measles, and many others.

Pharmaceutical drugs that may cause ILI include many biologics such as interferons and monoclonal antibodies. Chemotherapeutic agents also commonly cause flu-like symptoms. Other drugs associated with a flu-like syndrome include bisphosphonates, caspofungin, and levamisole. A flu-like syndrome can also be caused by an influenza vaccine or other vaccines, and by opioid withdrawal in addicts.

Influenza's effects are much more severe and last longer than those of the common cold. Most people will recover completely in about one to two weeks, but others will develop life-threatening complications (such as pneumonia). Thus, influenza can be deadly, especially for the weak, young and old, or chronically ill. People with a weak immune system, such as people with advanced HIV infection or transplant patients (whose immune systems are medically suppressed to prevent transplant organ rejection), suffer from particularly severe disease. Pregnant women and young children are also at a high risk for complications.

The flu can worsen chronic health problems. People with emphysema, chronic bronchitis or asthma may experience shortness of breath while they have the flu, and influenza may cause worsening of coronary heart disease or congestive heart failure. Smoking is another risk factor associated with more serious disease and increased mortality from influenza.

According to the World Health Organization: "Every winter, tens of millions of people get the flu. Most are only ill and out of work for a week, yet the elderly are at a higher risk of death from the illness. We know the worldwide death toll exceeds a few hundred thousand people a year, but even in developed countries the numbers are uncertain, because medical authorities don't usually verify who actually died of influenza and who died of a flu-like illness." Even healthy people can be affected, and serious problems from influenza can happen at any age. People over 65 years old, pregnant women, very young children and people of any age with chronic medical conditions are more likely to get complications from influenza, such as pneumonia, bronchitis, sinus, and ear infections.

In some cases, an autoimmune response to an influenza infection may contribute to the development of Guillain–Barré syndrome. However, as many other infections can increase the risk of this disease, influenza may only be an important cause during epidemics. This syndrome has been believed to also be a rare side effect of influenza vaccines. One review gives an incidence of about one case per million vaccinations. Getting infected by influenza itself increases both the risk of death (up to 1 in 10,000) and increases the risk of developing GBS to a much higher level than the highest level of suspected vaccine involvement (approx. 10 times higher by recent estimates).

In the United States, the annual incidence is 18 cases of acute pancreatitis per 100,000 population, and it accounts for 220,000 hospitalizations in the US. In a European cross-sectional study, incidence of acute pancreatitis increased from 12.4 to 15.9 per 100,000 annually from 1985 to 1995; however, mortality remained stable as a result of better outcomes. Another study showed a lower incidence of 9.8 per 100,000 but a similar worsening trend (increasing from 4.9 in 1963-74) over time.

In Western countries, the most common cause is alcohol, accounting for 65 percent of acute pancreatitis cases in the US, 20 percent of cases in Sweden, and 5 percent of those in the United Kingdom. In Eastern countries, gallstones are the most common cause of acute pancreatitis. The causes of acute pancreatitis also varies across age groups, with trauma and systemic disease (such as infection) being more common in children. Mumps is a more common cause in adolescents and young adults than in other age groups.

Little is known on the prognosis of achlorhydria, although there have been reports of an increased risk of gastric cancer.

A 2007 review article noted that non-"Helicobacter" bacterial species can be cultured from achlorhydric (pH > 4.0) stomachs, whereas normal stomach pH only permits the growth of "Helicobacter" species. Bacterial overgrowth may cause false positive H. Pylori test results due to the change in pH from urease activity.

Small bowel bacterial overgrowth is a chronic condition. Retreatment may be necessary once every 1–6 months. Prudent use of antibacterials now calls for an antibacterial stewardship policy to manage antibiotic resistance.

The influenza vaccine is recommended by the World Health Organization and United States Centers for Disease Control and Prevention for high-risk groups, such as children, the elderly, health care workers, and people who have chronic illnesses such as asthma, diabetes, heart disease, or are immuno-compromised among others. In healthy adults it is modestly effective in decreasing the amount of influenza-like symptoms in a population. Evidence is supportive of a decreased rate of influenza in children over the age of two. In those with chronic obstructive pulmonary disease vaccination reduces exacerbations, it is not clear if it reduces asthma exacerbations. Evidence supports a lower rate of influenza-like illness in many groups who are immunocompromised such as those with: HIV/AIDS, cancer, and post organ transplant. In those at high risk immunization may reduce the risk of heart disease. Whether immunizing health care workers affects patient outcomes is controversial with some reviews finding insufficient evidence and others finding tentative evidence.

Due to the high mutation rate of the virus, a particular influenza vaccine usually confers protection for no more than a few years. Every year, the World Health Organization predicts which strains of the virus are most likely to be circulating in the next year (see Historical annual reformulations of the influenza vaccine), allowing pharmaceutical companies to develop vaccines that will provide the best immunity against these strains. The vaccine is reformulated each season for a few specific flu strains but does not include all the strains active in the world during that season. It takes about six months for the manufacturers to formulate and produce the millions of doses required to deal with the seasonal epidemics; occasionally, a new or overlooked strain becomes prominent during that time. It is also possible to get infected just before vaccination and get sick with the strain that the vaccine is supposed to prevent, as the vaccine takes about two weeks to become effective.

Vaccines can cause the immune system to react as if the body were actually being infected, and general infection symptoms (many cold and flu symptoms are just general infection symptoms) can appear, though these symptoms are usually not as severe or long-lasting as influenza. The most dangerous adverse effect is a severe allergic reaction to either the virus material itself or residues from the hen eggs used to grow the influenza; however, these reactions are extremely rare.

The cost-effectiveness of seasonal influenza vaccination has been widely evaluated for different groups and in different settings. It has generally been found to be a cost-effective intervention, especially in children and the elderly, however the results of economic evaluations of influenza vaccination have often been found to be dependent on key assumptions.

A post-viral cough is a lingering cough that follows a viral respiratory tract infection, such as a common cold or flu and lasting up to eight weeks. Post-viral cough is a clinically recognized condition represented within the European medical literature. Patients usually experience repeated episodes of post-viral cough. The heightened sensitivity in the respiratory tract is demonstrated by inhalation cough challenge.

Post-viral cough can be resistant to treatment. Post-viral cough usually goes away on its own; however, cough suppressants containing codeine may be prescribed. A study has claimed theobromine in dark chocolate is more effective.

Ehrlichiosis is a nationally notifiable disease in the United States. There have been cases reported in every month of the year, but most cases are reported during April–September. These months are also the peak months for tick activity in the United States.

From 2008-2012, the average yearly incidence of ehrlichiosis was 3.2 cases per million persons. This is more than twice the estimated incidence for the years 2000-2007. The incidence rate increases with age, with the ages of 60–69 years being the highest age-specific years. Children of less than 10 years and adults aged 70 years and older, have the highest case-fatality rates. There is a documented higher risk of death among persons who are immunosuppressed.

Treatment focuses on addressing the underlying cause of symptoms.

Treatment of gastritis that leads to pernicious anemia consists of parenteral vitamin B-12 injection. Associated immune-mediated conditions (e.g., insulin dependent diabetes mellitus, autoimmune thyroiditis) should also be treated. However, treatment of these disorders has no known effect in the treatment of achlorhydria.

Achlorhydria associated with "Helicobacter pylori" infection may respond to H pylori eradication therapy, although resumption of gastric acid secretion may only be partial and it may not always reverse the condition completely.

Antimicrobial agents, including metronidazole, amoxicillin/clavulanate potassium, ciprofloxacin, and rifaximin, can be used to treat bacterial overgrowth.

Achlorhydria resulting from long-term proton-pump inhibitor (PPI) use may be treated by dose reduction or withdrawal of the PPI.

Locoregional complications include pancreatic pseudocyst (Most common, occurring in up to 25% of all cases) and phlegmon / abscess formation, splenic artery pseudoaneurysms, hemorrhage from erosions into splenic artery and vein, thrombosis of the splenic vein, superior mesenteric vein and portal veins (in descending order of frequency), duodenal obstruction, common bile duct obstruction, progression to chronic pancreatitis, pancreatic ascites, pleural effusion, sterile/infected pancreatic necrosis.

Although there is no formal national surveillance system in the United States to determine what viruses are circulating in pigs, an informal surveillance network in the United States is part of a world surveillance network.

Prevention of swine influenza has three components: prevention in pigs, prevention of transmission to humans, and prevention of its spread among humans.

Prevention and control programs must take into account local understandings of people-poultry relations. In the past, programs that have focused on singular, place-based understandings of disease transmission have been ineffective. In the case of Northern Vietnam, health workers saw poultry as commodities with an environment that was under the control of people. Poultry existed in the context of farms, markets, slaughterhouses, and roads while humans were indirectly the primary transmitters of avian flu, placing the burden of disease control on people. However, farmers saw their free ranging poultry in an environment dominated by nonhuman forces that they could not exert control over. There were a host of nonhuman actors such as wild birds and weather patterns whose relationships with the poultry fostered the disease and absolved farmers of complete responsibility for disease control.

Attempts at singular, place-based controls sought to teach farmers to identify areas where their behavior could change without looking at poultry behaviors. Behavior recommendations by Vietnam's National Steering Committee for Avian Influenza Control and Prevention (NSCAI) were drawn from the FAO Principles of Biosecurity. These included restrictions from entering areas where poultry are kept by erecting barriers to segregate poultry from non-human contact, limits on human movement of poultry and poultry-related products ideally to transporters, and recommendations for farmers to wash hands and footwear before and after contact with poultry. Farmers, pointed to wind and environmental pollution as reasons poultry would get sick. NSCAI recommendations also would disrupt longstanding livestock production practices as gates impede sales by restricting assessment of birds by appearance and offend customers by limiting outside human contact. Instead of incorporating local knowledge into recommendations, cultural barriers were used as scapegoats for failed interventions. Prevention and control methods have been more effective when also considering the social, political, and ecological agents in play.

Doxycycline and minocycline are the medications of choice. For people allergic to antibiotics of the tetracycline class, rifampin is an alternative. Early clinical experience suggested that chloramphenicol may also be effective, however, in vitro susceptibility testing revealed resistance.

People who do not regularly come into contact with birds are not at high risk for contracting avian influenza. Those at high risk include poultry farm workers, animal control workers, wildlife biologists, and ornithologists who handle live birds. Organizations with high-risk workers should have an avian influenza response plan in place before any cases have been discovered. Biosecurity of poultry flocks is also important for prevention. Flocks should be isolated from outside birds, especially wild birds, and their waste; vehicles used around the flock should be regularly disinfected and not shared between farms; and birds from slaughter channels should not be returned to the farm.

With proper infection control and use of personal protective equipment (PPE), the chance for infection is low. Protecting the eyes, nose, mouth, and hands is important for prevention because these are the most common ways for the virus to enter the body. Appropriate personal protective equipment includes aprons or coveralls, gloves, boots or boot covers, and a head cover or hair cover. Disposable PPE is recommended. An N-95 respirator and unvented/indirectly vented safety goggles are also part of appropriate PPE. A powered air purifying respirator (PAPR) with hood or helmet and face shield is also an option.

Proper reporting of an isolated case can help to prevent spread. The Centers for Disease Control and Prevention (US) recommendation is that if a worker develops symptoms within 10 days of working with infected poultry or potentially contaminated materials, they should seek care and notify their employer, who should notify public health officials.

For future avian influenza threats, the WHO suggests a 3 phase, 5 part plan.

- Phase: Pre-pandemic

- Reduce opportunities for human infection

- Strengthen the early warning system

- Phase: Emergence of a pandemic virus

- Contain or delay spread at the source

- Phase: Pandemic declared and spreading internationally

- Reduce morbidity, mortality, and social disruption

- Conduct research to guide response measures

Vaccines for poultry have been formulated against several of the avian H5N1 influenza varieties. Control measures for HPAI encourage mass vaccinations of poultry though The World Health Organization has compiled a list of known clinical trials of pandemic influenza prototype vaccines, including those against H5N1. In some countries still at high risk for HPAI spread, there is compulsory strategic vaccination though vaccine supply shortages remain a problem.

Cat flu is the common name for a feline upper respiratory tract disease. While feline upper respiratory disease can be caused by several different pathogens, there are few symptoms that they have in common.

While Avian Flu can also infect cats, Cat flu is generally a misnomer, since it usually does not refer to an infection by an influenza virus. Instead, it is a syndrome, a term referring to the fact that patients display a number of symptoms that can be caused by one or more of the following infectious agents (pathogens):

1. Feline herpes virus causing feline viral rhinotracheitis (cat common cold, this is the disease that is closely similar to cat flu)

2. Feline calicivirus—(cat respiratory disease)

3. "Bordetella bronchiseptica"—(cat kennel cough)

4. "Chlamydophila felis"—(chlamydia)

In South Africa the term cat flu is also used to refer to Canine Parvo Virus. This is misleading, as transmission of the Canine Parvo Virus rarely involves cats.

In June 2009, the United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) approved the first canine influenza vaccine. This vaccine must be given twice initially with a two-week break, then annually thereafter.

Influenza A viruses are enveloped, negative sense, single-stranded RNA viruses. Genome analysis has shown that H3N8 was transferred from horses to dogs and then adapted to dogs through point mutations in the genes. The incubation period is two to five days, and viral shedding may occur for seven to ten days following the onset of symptoms. It does not induce a persistent carrier state.

Aspergillosis is the name given to a wide variety of diseases caused by infection by fungi of the genus "Aspergillus". The majority of cases occur in people with underlying illnesses such as tuberculosis or chronic obstructive pulmonary disease (COPD), but with otherwise healthy immune systems. Most commonly, aspergillosis occurs in the form of chronic pulmonary aspergillosis (CPA), aspergilloma or allergic bronchopulmonary aspergillosis (ABPA). Some forms are intertwined; for example ABPA and simple aspergilloma can progress to CPA.

Other, non-invasive manifestations include fungal sinusitis (both allergic in nature and with established fungal balls), otomycosis (ear infection), keratitis (eye infection) and onychomycosis (nail infection). In most instances these are less severe, and curable with effective antifungal treatment.

People with deficient immune systems—such as patients undergoing hematopoietic stem cell transplantation, chemotherapy for leukaemia, or AIDS—are at risk of more disseminated disease. Acute invasive aspergillosis occurs when the immune system fails to prevent "Aspergillus" spores from entering the bloodstream via the lungs. Without the body mounting an effective immune response, fungal cells are free to disseminate throughout the body and can infect major organs such as the heart and kidneys.

The most frequently identified pathogen is "Aspergillus fumigatus"—a ubiquitous organism that is capable of living under extensive environmental stress. It is estimated that most humans inhale thousands of "Aspergillus" spores daily, but they do not affect most people’s health due to effective immune responses. Taken together, the major chronic, invasive and allergic forms of aspergillosis account for around 600,000 deaths annually worldwide.

The mechanism of subacute bacterial endocarditis could be due to malformed stenotic valves which in the company of bacteremia, become infected, via adhesion and subsequent colonization of the surface area. This causes an inflammatory response, with recruitment of matrix metalloproteinases, and destruction of collagen.

Underlying structural valve disease is usually present in patients before developing subacute endocarditis, and is less likely to lead to septic emboli than is acute endocarditis, but subacute endocarditis has a relatively slow process of infection and, if left untreated, can worsen for up to one year before it is fatal. In cases of subacute bacterial endocarditis, the causative organism (streptococcus viridans) needs a previous heart valve disease to colonize. On the other hand, in cases of acute bacterial endocarditis, the organism can colonize on the healthy heart valve, causing the disease.

It is usually caused by a form of streptococci viridans bacteria that normally live in the mouth ("Streptococcus mutans, mitis, sanguis "or "milleri").

Other strains of streptococci can also cause subacute endocarditis, streptococcus intermedius:

acute and subacute infection ( can causes about 15% of cases pertaining to infective endocarditis). Additional enterococci (urinary tract infections) and coagulase negative staphylococci can also be causative agents.

Outbreaks of zoonoses have been traced to human interaction with and exposure to animals at fairs, petting zoos, and other settings. In 2005, the Centers for Disease Control and Prevention (CDC) issued an updated list of recommendations for preventing zoonosis transmission in public settings. The recommendations, developed in conjunction with the National Association of State Public Health Veterinarians, include educational responsibilities of venue operators, limiting public and animal contact, and animal care and management.

Contact with farm animals can lead to disease in farmers or others that come into contact with infected animals. Glanders primarily affects those who work closely with horses and donkeys. Close contact with cattle can lead to cutaneous anthrax infection, whereas inhalation anthrax infection is more common for workers in slaughterhouses, tanneries and wool mills. Close contact with sheep who have recently given birth can lead to clamydiosis, or enzootic abortion, in pregnant women, as well as an increased risk of Q fever, toxoplasmosis, and listeriosis in pregnant or the otherwise immunocompromised. Echinococcosis is caused by a tapeworm which can be spread from infected sheep by food or water contaminated with feces or wool. Bird flu is common in chickens. While rare in humans, the main public health worry is that a strain of bird flu will recombine with a human flu virus and cause a pandemic like the 1918 Spanish flu. In 2017, free range chickens in the UK were temporarily ordered to remain inside due to the threat of bird flu. Cattle are an important reservoir of cryptosporidiosis and mainly affects the immunocompromised.

Prevention of aspergillosis involves a reduction of mold exposure via environmental infection-control. Anti-fungal prophylaxis can be given to high-risk patients. Posaconazole is often given as prophylaxis in severely immunocompromised patients.