Some cases of pharyngitis are caused by fungal infection such as Candida albicans causing oral thrush.

Pharyngitis may also be caused by mechanical, chemical or thermal irritation, for example cold air or acid reflux. Some medications may produce pharyngitis such as pramipexole and antipsychotics.

There are three main viruses that have been studied and confirmed as the agents responsible for AHC, including enterovirus 70, coxsakievirus A24 variant (CA24v) and adenovirus 11.

AHC can only exist in a human host and is transmitted through human contact with an infected individual or object, such as a towel used by an infected person. It is also easily communicable through fecal-oral pathways, thus allowing for its abundance in areas of the world with low levels of hygiene. Within one to two days of infection, symptoms will begin to become apparent.

Enterovirus 70 is a member of the genus of viruses called Enterovirus and family of the viruses Picornaviridae. Usually very small (about 30 nm in diameter), it is non-enveloped (meaning it only has a nucleic acid core and protein capsid) and has a single-stranded positive-sense RNA genome; the protein capsid the virus itself is surrounded by is icosahedral. It is known as one of the more new enteroviruses within this category. It spreads easily from one person’s eyes to another’s through contact with infected objects, like fingers, or through the eye secretion itself. Enterovirus 70 infrequently causes polio-like permanent paralysis.

Most household disinfectants will inactivate FHV-1. The virus can survive up to 18 hours in a damp environment, but less in a dry environment and only shortly as an aerosol.

FVR is transmitted through direct contact only. It replicates in the nasal and nasopharyngeal tissues and the tonsils. Viremia (the presence of the virus in the blood) is rare. The virus is shed in saliva and eye and nasal secretions, and can also be spread by fomites. FVR has a two- to five-day incubation period. The virus is shed for one to three weeks postinfection. Latently infected cats (carriers) will shed FHV-1 intermittently for life, with the virus persisting within the trigeminal ganglion. Stress and use of corticosteroids precipitate shedding. Most disinfectants, antiseptics and detergents are effective against the virus.

Adenovirus can cause severe necrotizing pneumonia in which all or part of a lung has increased translucency radiographically, which is called Swyer-James Syndrome. Severe adenovirus pneumonia also may result in bronchiolitis obliterans, a subacute inflammatory process in which the small airways are replaced by scar tissue, resulting in a reduction in lung volume and lung compliance.

Viruses that may cause adenoiditis include adenovirus, rhinovirus and paramyxovirus. Bacterial causes include Streptococcus pyogenes, Streptococcus pneumoniae, Moraxella catarrhalis and various species of Staphylococcus including Staphylococcus aureus.

Adenoiditis occurs mainly in childhood, often associated with acute tonsillitis. Incidence decreases with age, with adenoiditis being rare in children over 15 years due to physiological atrophy of the adenoid tissue.

Although epidemiologic characteristics of the adenoviruses vary by type, all are transmitted by direct contact, fecal-oral transmission, and occasionally waterborne transmission. Some types are capable of establishing persistent asymptomatic infections in tonsils, adenoids, and intestines of infected hosts, and shedding can occur for months or years. Some adenoviruses (e.g., serotypes 1, 2, 5, and 6) have been shown to be endemic in parts of the world where they have been studied, and infection is usually acquired during childhood. Other types cause sporadic infection and occasional outbreaks; for example, epidemic keratoconjunctivitis is associated with adenovirus serotypes 8, 19, and 37. Epidemics of febrile disease with conjunctivitis are associated with waterborne transmission of some adenovirus types, often centering on inadequately chlorinated swimming pools and small lakes. ARD is most often associated with adenovirus types 4 and 7 in the United States. Enteric adenoviruses 40 and 41 cause gastroenteritis, usually in children. For some adenovirus serotypes, the clinical spectrum of disease associated with infection varies depending on the site of infection; for example, infection with adenovirus 7 acquired by inhalation is associated with severe lower respiratory tract disease, whereas oral transmission of the virus typically causes no or mild disease. Outbreaks of adenovirus-associated respiratory disease have been more common in the late winter, spring, and early summer; however, adenovirus infections can occur throughout the year.

"Ad14 (for adenovirus serotype 14), has caused at least 140 illnesses in New York, Oregon, Texas and Washington, according to a report from the Centers for Disease Control and Prevention. The illness made headlines in Texas in September 2007, when a so-called "boot camp flu" sickened hundreds at Lackland Air Force Base in San Antonio. A 19-year-old trainee died."

Several adenoviruses, including Ad5, Ad9, Ad31, Ad36, Ad37, and SMAM1, have at least some evidence of causation of obesity in animals, adipogenesis in cells, and/or association with human obesity. To date, the most thorough investigations have been conducted for adenovirus serotype 36 (Adv36).

The most common causes of acute bacterial conjunctivitis are "Staphylococcus aureus", "Streptococcus pneumoniae", and "Haemophilus influenzae". Though very rare, hyperacute cases are usually caused by "Neisseria gonorrhoeae" or "N. meningitidis". Chronic cases of bacterial conjunctivitis are those lasting longer than 3 weeks, and are typically caused by "Staphylococcus aureus", "Moraxella lacunata", or gram-negative enteric flora.

Adenoviruses is the most common cause of viral conjunctivitis (adenoviral keratoconjunctivitis). Herpetic keratoconjunctivitis (caused by herpes simplex viruses) can be serious and requires treatment with acyclovir. Acute hemorrhagic conjunctivitis is a highly contagious disease caused by one of two enteroviruses, Enterovirus 70 and Coxsackievirus A24. These were first identified in an outbreak in Ghana in 1969, and have spread worldwide since then, causing several epidemics.

The risk factors associated with BPF are not well known. However, it has been suggested that children under 5 years of age are more susceptible to BPF since they lack serum bactericidal activity against the infection. Older children and adults have much higher titers of bactericidal antibodies, which serve as a protective measure. Also children residing in warmer geographic areas have been associated with a higher risk of BPF infection.

Long-term antibiotics, while they decrease rates of infection during treatment, have an unknown effect on long-term outcomes such as hearing loss. This method of prevention has been associated with emergence of antibiotic-resistant otitic bacteria. They are thus not recommended.

Pneumococcal conjugate vaccines (PCV) in early infancy, decreases the risk of acute otitis media in healthy infants. PCV is recommended for all children, and, if implemented broadly, PCV would have a significant public health benefit. Influenza vaccine is recommended annually for all children. PCV does not appear to decrease the risk of otitis media when given to high-risk infants or for older children who have previously experienced otitis media.

Risk factors such as season, allergy predisposition and presence of older siblings are known to be determinants of recurrent otitis media and persistent middle-ear effusions (MEE). History of recurrence, environmental exposure to tobacco smoke, use of daycare, and lack of breastfeeding have all been associated with increased risk of development, recurrence, and persistent MEE. Thus, cessation of smoking in the home should be encouraged, daycare attendance should be avoided or daycare facilities with the fewest attendees should be recommended, and breastfeeding should be promoted.

There is some evidence that breastfeeding for the first year of life is associated with a reduction in the number and duration of OM infections. Pacifier use, on the other hand, has been associated with more frequent episodes of AOM.

Evidence does not support zinc supplementation as an effort to reduce otitis rates except maybe in those with severe malnutrition such as marasmus.

An oncovirus is a virus that can cause cancer. This term originated from studies of acutely transforming retroviruses in the 1950–60s, often called oncornaviruses to denote their RNA virus origin.

It now refers to any virus with a DNA or RNA genome causing cancer and is synonymous with "tumor virus" or "cancer virus". The vast majority of human and animal viruses do not cause cancer, probably because of longstanding co-evolution between the virus and its host. Oncoviruses have been important not only in epidemiology, but also in investigations of cell cycle control mechanisms such as the Retinoblastoma protein.

The World Health Organization's International Agency for Research on Cancer estimated that in 2002, infection caused 17.8% of human cancers, with 11.9% caused by one of seven viruses. These cancers might be easily prevented through vaccination (e.g., papillomavirus vaccines), diagnosed with simple blood tests, and treated with less-toxic antiviral compounds.

Several aetiologies are suggested, and any combination of these may be present in any given case.

- Vitamin deficiency (A, B or C)

- Viral infection

- Bacterial infection

- "Leptospira

- "Streptococcus

- "Brucella

- Parasitic infection

- Strongyle

- "Onchocerca cervicalis"

- Autoimmune disease

The disease has been suggested to be primarily autoimmune in nature, being a delayed hypersensitivity reaction to any of the above agents.

Adhesive otitis media occurs when a thin retracted ear drum becomes sucked into the middle-ear space and stuck (i.e., adherent) to the ossicles and other bones of the middle ear.

There is low or very-low quality evidence that probiotics may be better than placebo in preventing acute URTIs. Vaccination against influenza viruses, adenoviruses, measles, rubella, "Streptococcus pneumoniae", "Haemophilus influenzae", diphtheria, "Bacillus anthracis", and "Bordetella pertussis" may prevent them from infecting the URT or reduce the severity of the infection.

Dogs will typically recover from kennel cough within a few weeks. However, secondary infections could lead to complications that could do more harm than the disease itself. Several opportunistic invaders have been recovered from the respiratory tracts of dogs with kennel cough, including Streptococcus, Pasteurella, Pseudomonas, and various coliforms. These bacteria have the potential to cause pneumonia or sepsis, which drastically increase the severity of the disease. These complications are evident in thoracic radiographic examinations. Findings will be mild in animals affected only by kennel cough, while those with complications may have evidence of segmental atelectasis and other severe side effects.

A vaccine is available in the UK and Europe, however in laboratory tests it is not possible to distinguish between antibodies produced as a result of vaccination and those produced in response to infection with the virus. Management also plays an important part in the prevention of EVA.

In terms of pathophysiology, rhino virus infection resembles the immune response. The viruses do not cause damage to the cells of the upper respiratory tract but rather cause changes in the tight junctions of epithelial cells. This allows the virus to gain access to tissues under the epithelial cells and initiate the innate and adaptive immune responses.

Up to 15% of acute pharyngitis cases may be caused by bacteria, most commonly "Streptococcus pyogenes", a group A streptococcus in streptococcal pharyngitis ("strep throat"). Other bacterial causes are "Streptococcus pneumoniae", "Haemophilus influenzae", "Corynebacterium diphtheriae", "Bordetella pertussis", and "Bacillus anthracis".

Sexually transmitted infections have emerged as causes of oral and pharyngeal infections.

HSV is a double-stranded DNA virus that has icosahedral capsid. HSV-1 infections are found more commonly in the oral area and HSV-2 in the genital area.

Estimated percent of new cancers attributable to the virus worldwide in 2002. NA indicates not available.

The association of other viruses with human cancer is continually under research.

Viral infections such as canine parainfluenza or canine coronavirus are only shed for roughly 1 week following recovery; however, respiratory infections involving "Bordetella bronchiseptica" can be transmissible for several weeks longer. While there was early evidence to suggest that "B. bronchiseptica" could be shed for many months post-infection, a more recent report places detectable nasal and pharyngeal levels of "B. bronchiseptica" in 45.6% of all clinically healthy dogs. This has potentially expanded the vector from currently or recently infected dogs to half the dog population as carriers. To put the relative levels of shedding bacteria into perspective, a study analyzing the shedding kinetics of "B. bronchiseptica" presents the highest levels of bacterial shedding one week post-exposure, with an order of magnitude decrease in shedding observed every week. This projection places negligible levels of shedding to be expected 6 weeks post-exposure (or ~5 weeks post-onset of symptoms). Dogs which had been administered intranasal vaccine 4 weeks prior to virulent "B. bronchiseptica" challenge displayed little to no bacterial shedding within 3 weeks of exposure to the virulent strain.

Chemical irritants such as silver nitrate can cause chemical conjunctivitis, usually lasting 2–4 days. Thus, prophylaxis with a 1% silver nitrate solution is no longer in common use. In most countries neomycin and chloramphenicol eye drops are used instead. However, it is possible for newborns to suffer from neonatal conjunctivitis due to reactions with chemicals in these common eye drops. Additionally, a blocked tear duct may be another non-infectious cause of neonatal conjunctivitis.