In microbiology, coinfection is the simultaneous infection of a host by multiple pathogen species. In virology, coinfection includes simultaneous infection of a single cell by two or more virus particles. An example is the coinfection of liver cells with Hepatitis B virus and Hepatitis D virus, which can arise incrementally by initial infection followed by superinfection.

Global prevalence or incidence of coinfection among humans is unknown, but it is thought to be commonplace, sometimes more common than single infection. Coinfection with helminths affects around 800 million people worldwide.

Coinfection is of particular human health importance because pathogen species can interact within the host. The net effect of coinfection on human health is thought to be negative. Interactions can have either positive or negative effects on other parasites. Under positive parasite interactions, disease transmission and progression are enhanced and this is also known as syndemism. Negative parasite interactions include microbial interference when one bacterial species suppresses the virulence or colonisation of other bacteria, such as "Pseudomonas aeruginosa" suppressing pathogenic "Staphylococcus aureus" colony formation. The general patterns of ecological interactions between parasite species are unknown, even among common coinfections such as those between sexually transmitted infections. However, network analysis of a food web of coinfection in humans suggests that there is greater potential for interactions via shared food sources than via the immune system.

A globally common coinfection involves tuberculosis and HIV. In some countries, up to 80% of tuberculosis patients are also HIV-positive. The potential for dynamics of these two infectious diseases to be linked has been known for decades. Other common examples of coinfections are AIDS, which involves coinfection of end-stage HIV with opportunistic parasites and polymicrobial infections like Lyme disease with other diseases.

Signs and symptoms may include:

- fever

- severe headache

- muscle aches (myalgia)

- chills and shaking, similar to the symptoms of influenza

- nausea

- vomiting

- loss of appetite

- unintentional weight loss

- abdominal pain

- cough

- diarrhea,

- aching joints

- sensitivity to light

- weakness

- fatigue

- change in mental status (extreme confusion, memory loss, inability to comprehend environment- interaction, reading, etc.)

- temporary loss of basic motor skills

Symptoms may be minor, as evidenced by surveillance studies in high-risk areas. Gastrointestinal tract symptoms occur in less than half of patients and a skin rash is seen in less than 10% of patients. It is also characterized by a low number of platelets, a low number of white blood cells, and elevated serum transaminase levels in the majority of infected patients. Even though people of any age can get HGA, it is usually more severe in the aging or immune-compromised. Some severe complications may include respiratory failure, kidney failure, and secondary infections.

The signs and symptoms of malaria typically begin 8–25 days following infection; however, symptoms may occur later in those who have taken antimalarial medications as prevention. Initial manifestations of the disease—common to all malaria species—are similar to flu-like symptoms, and can resemble other conditions such as sepsis, gastroenteritis, and viral diseases. The presentation may include headache, fever, shivering, joint pain, vomiting, hemolytic anemia, jaundice, hemoglobin in the urine, retinal damage, and convulsions.

The classic symptom of malaria is paroxysm—a cyclical occurrence of sudden coldness followed by shivering and then fever and sweating, occurring every two days (tertian fever) in "P. vivax" and "P. ovale" infections, and every three days (quartan fever) for "P. malariae". "P. falciparum" infection can cause recurrent fever every 36–48 hours, or a less pronounced and almost continuous fever.

Severe malaria is usually caused by "P. falciparum" (often referred to as falciparum malaria). Symptoms of falciparum malaria arise 9–30 days after infection. Individuals with cerebral malaria frequently exhibit neurological symptoms, including abnormal posturing, nystagmus, conjugate gaze palsy (failure of the eyes to turn together in the same direction), opisthotonus, seizures, or coma.

Neglected tropical diseases (NTDs) are a diverse group of tropical infections which are especially common in low-income populations in developing regions of Africa, Asia, and the Americas. They are caused by a variety of pathogens such as viruses, bacteria, protozoa and helminths. These diseases are contrasted with the big three diseases (HIV/AIDS, tuberculosis, and malaria), which generally receive greater treatment and research funding. In sub-Saharan Africa, the effect of these diseases as a group is comparable to malaria and tuberculosis. NTD co-infection can also make HIV/AIDS and tuberculosis more deadly.

In some cases, the treatments are relatively inexpensive. For example, the treatment for schistosomiasis is US$0.20 per child per year. Nevertheless, in 2010 it was estimated that control of neglected diseases would require funding of between US$2 billion and US$3 billion over the subsequent five to seven years. Some pharmaceutical companies have committed to donating all the drug therapies required, and mass drug administration (for example mass deworming) has been successfully accomplished in several countries. However, preventive measures are often more accessible in the developed world, but not universally available in poorer areas.

Within developed countries, neglected tropical diseases affect the very poorest in society. In the United States, there are up to 1.46 million families including 2.8 million children living on less than two dollars a day. In countries such as these, the burdens of neglected tropical diseases are often overshadowed by other public health issues. However, many of the same issues put populations at risk in developed as developing nations. For example, from poverty stem problems such as lack of adequate housing, thus exposing individuals to the vectors of these diseases.

Twenty neglected tropical diseases are prioritized by the World Health Organization (WHO), though other organizations define NTDs differently. Chromoblastomycosis and other deep mycoses, scabies and other ectoparasites and snakebite envenoming were added to the list in 2017. These diseases are common in 149 countries, affecting more than 1.4 billion people (including more than 500 million children) and costing developing economies billions of dollars every year. They resulted in 142,000 deaths in 2013—down from 204,000 deaths in 1990. Of these 20, two were targeted for eradication (dracunculiasis (guinea-worm disease) by 2015 and yaws by 2020), and four for elimination (blinding trachoma, human African trypanosomiasis, leprosy and lymphatic filariasis by 2020).

Human granulocytic anaplasmosis (HGA) is a tick-borne, infectious disease caused by "Anaplasma phagocytophilum", an obligate intracellular bacterium that is typically transmitted to humans by ticks of the "Ixodes ricinus" species complex, including "Ixodes scapularis" and "Ixodes pacificus" in North America. These ticks also transmit Lyme disease and other tick borne diseases.

The bacteria infect white blood cells called neutrophils, causing changes in gene expression that prolong the life of these otherwise short-lived cells.

Malaria is a mosquito-borne infectious disease affecting humans and other animals caused by parasitic protozoans (a group of single-celled microorganisms) belonging to the "Plasmodium" type. Malaria causes symptoms that typically include fever, tiredness, vomiting, and headaches. In severe cases it can cause yellow skin, seizures, coma, or death. Symptoms usually begin ten to fifteen days after being bitten. If not properly treated, people may have recurrences of the disease months later. In those who have recently survived an infection, reinfection usually causes milder symptoms. This partial resistance disappears over months to years if the person has no continuing exposure to malaria.

The disease is most commonly transmitted by an infected female "Anopheles" mosquito. The mosquito bite introduces the parasites from the mosquito's saliva into a person's blood. The parasites travel to the liver where they mature and reproduce. Five species of "Plasmodium" can infect and be spread by humans. Most deaths are caused by "P. falciparum" because "P. vivax", "P. ovale", and "P. malariae" generally cause a milder form of malaria. The species "P. knowlesi" rarely causes disease in humans. Malaria is typically diagnosed by the microscopic examination of blood using blood films, or with antigen-based rapid diagnostic tests. Methods that use the polymerase chain reaction to detect the parasite's DNA have been developed, but are not widely used in areas where malaria is common due to their cost and complexity.

The risk of disease can be reduced by preventing mosquito bites through the use of mosquito nets and insect repellents, or with mosquito control measures such as spraying insecticides and draining standing water. Several medications are available to prevent malaria in travellers to areas where the disease is common. Occasional doses of the combination medication sulfadoxine/pyrimethamine are recommended in infants and after the first trimester of pregnancy in areas with high rates of malaria. Despite a need, no effective vaccine exists, although efforts to develop one are ongoing. The recommended treatment for malaria is a combination of antimalarial medications that includes an artemisinin. The second medication may be either mefloquine, lumefantrine, or sulfadoxine/pyrimethamine. Quinine along with doxycycline may be used if an artemisinin is not available. It is recommended that in areas where the disease is common, malaria is confirmed if possible before treatment is started due to concerns of increasing drug resistance. Resistance among the parasites has developed to several antimalarial medications; for example, chloroquine-resistant "P. falciparum" has spread to most malarial areas, and resistance to artemisinin has become a problem in some parts of Southeast Asia.

The disease is widespread in the tropical and subtropical regions that exist in a broad band around the equator. This includes much of Sub-Saharan Africa, Asia, and Latin America. In 2016, there were 216 million cases of malaria worldwide resulting in an estimated 731,000 deaths. Approximately 90% of both cases and deaths occurred in Africa. Rates of disease have decreased from 2000 to 2015 by 37%, but increased from 2014 during which there were 198 million cases. Malaria is commonly associated with poverty and has a major negative effect on economic development. In Africa, it is estimated to result in losses of US$12 billion a year due to increased healthcare costs, lost ability to work, and negative effects on tourism.

Lábrea fever, also known as Lábrea's black fever and Lábrea hepatitis, is a lethal tropical viral infection discovered in the 1950s in the city of Lábrea, in the Brazilian Amazon basin, where it occurs mostly in the area south of the Amazon River, in the states of Acre, Amazonas and Rondônia

. The disease has also been diagnosed in Colombia and Peru. The similar form in Colombia has been named Santa Marta fever.

Its main manifestation is a fulminant hepatitis which may kill in less than a week, and which characteristically affects children and young adults, and more males than females. It is accompanied also by an encephalitis in many cases. The disease is highly lethal: in a study carried out in 1986 at Boca do Acre, also in the Amazon, 39 patients out of 44 died in the acute phase of the disease. Survivors may develop chronic disease.

Lábrea fever has a sudden onset, with jaundice (yellowing of the skin), anorexia (lack of appetite), hematemesis (vomiting of blood), headache, fever and severe prostration. Death occurs by acute liver failure (ALF). In the last phase, neurological symptoms such as agitation, delirium, convulsions and hemorrhagic coma commonly appear.

Dientamoebiasis is a medical condition caused by infection with "Dientamoeba fragilis", a single-cell parasite that infects the lower gastrointestinal tract of humans. It is an important cause of traveler's diarrhea, chronic abdominal pain, chronic fatigue, and failure to thrive in children.

The most commonly reported symptoms in conjunction with infection with "D. fragilis" include abdominal pain (69%) and diarrhea (61%). Diarrhea may be intermittent and may not be present in all cases. It is often chronic, lasting over two weeks. The degree of symptoms may vary from asymptomatic to severe, and can include weight loss, vomiting, fever, and involvement of other digestive organs.

Symptoms may be more severe in children. Additional symptoms reported have included:

1. Weight loss

2. Fatigue

3. Nausea and vomiting

4. Fever

5. Urticaria (skin rash)

6. Pruritus (itchiness)

7. Biliary infection

Most conditions of STH have a light worm burden and usually have no discernible symptoms. Heavy infections however cause a range of health problems, including abdominal pain, diarrhoea, blood and protein loss, rectal prolapse, and physical and mental retardation.

Severe ascariasis is typically a pneumonia, as the larvae invades lungs, producing fever, cough and dyspnoea during early stage of infection.

Hookworm infections insinuate a skin reaction (dermatitis), increased white blood cells (eosinophils), a pulmonary reaction (pneumonitis), and skin rash (urticarial).

Iron deficiency anaemia due to blood loss is a common symptom.

Symptoms becomes evident only when the intensity of infection is relatively high. Thus the degree of negative outcomes is directly related to worm burden; more worms means greater severity of disease.

Secondary syphilis occurs approximately four to ten weeks after the primary infection. While secondary disease is known for the many different ways it can manifest, symptoms most commonly involve the skin, mucous membranes, and lymph nodes. There may be a symmetrical, reddish-pink, non-itchy rash on the trunk and extremities, including the palms and soles. The rash may become maculopapular or pustular. It may form flat, broad, whitish, wart-like lesions known as condyloma latum on mucous membranes. All of these lesions harbor bacteria and are infectious. Other symptoms may include fever, sore throat, malaise, weight loss, hair loss, and headache. Rare manifestations include liver inflammation, kidney disease, joint inflammation, periostitis, inflammation of the optic nerve, uveitis, and interstitial keratitis. The acute symptoms usually resolve after three to six weeks; about 25% of people may present with a recurrence of secondary symptoms. Many people who present with secondary syphilis (40–85% of women, 20–65% of men) do not report previously having had the classic chancre of primary syphilis.

Light infestations (<100 worms) frequently have no symptoms. Heavier infestations, especially in small children, can present gastrointestinal problems including abdominal pain and distension, bloody or mucus-filled diarrhea, and tenesmus (feeling of incomplete defecation, generally accompanied by involuntary straining). Mechanical damage to the intestinal mucosa may occur, as well as toxic or inflammatory damage to the intestines of the host. While appendicitis may be brought on by damage and edema of the adjacent tissue, if there are large numbers of worms or larvae present, it has been suggested that the embedding of the worms into the ileocecal region may also make the host susceptible to bacterial infection. A severe infection with high numbers of embedded worms in the rectum leads to edema, which can cause rectal prolapse, although this is typically only seen in small children. The prolapsed, inflamed and edematous rectal tissue may even show visible worms.

Growth retardation, weight loss, nutritional deficiencies, and anemia (due to long-standing blood loss) are also characteristic of infection, and these symptoms are more prevalent and severe in children. It does not commonly cause eosinophilia.

Coinfection of "T. trichiura" with other parasites is common and with larger worm burdens can cause both exacerbation of dangerous trichuriasis symptoms such as massive gastrointestinal bleeding (shown to be especially dramatic with coinfection with "Salmonella typhi") and exacerbation of symptoms and pathogenesis of the other parasitic infection (as is typical with coinfection with "Schistosoma mansoni", in which higher worm burden and liver egg burden is common). Parasitic coinfection with HIV/AIDS, tuberculosis, and malaria is also common, especially in Sub-saharan Africa, and helminth coinfection adversely affects the natural history and progression of HIV/AIDS, tuberculosis, and malaria and can increase clinical malaria severity. In a study performed in Senegal, infections of soil-transmitted helminths like "T. trichiura" (as well as schistosome infections independently) showed enhanced risk and increased the incidence of malaria.

Heavy infestations may have bloody diarrhea. Long-standing blood loss may lead to iron-deficiency anemia. Vitamin A deficiency may also result due to infection.

Primary syphilis is typically acquired by direct sexual contact with the infectious lesions of another person. Approximately 3 to 90 days after the initial exposure (average 21 days) a skin lesion, called a chancre, appears at the point of contact. This is classically (40% of the time) a single, firm, painless, non-itchy skin ulceration with a clean base and sharp borders 0.3–3.0 cm in size. The lesion may take on almost any form. In the classic form, it evolves from a macule to a papule and finally to an erosion or ulcer. Occasionally, multiple lesions may be present (~40%), with multiple lesions more common when coinfected with HIV. Lesions may be painful or tender (30%), and they may occur in places other than the genitals (2–7%). The most common location in women is the cervix (44%), the penis in heterosexual men (99%), and anally and rectally relatively commonly in men who have sex with men (34%). Lymph node enlargement frequently (80%) occurs around the area of infection, occurring seven to 10 days after chancre formation. The lesion may persist for three to six weeks without treatment.

Tropical diseases are diseases that are prevalent in or unique to tropical and subtropical regions. The diseases are less prevalent in temperate climates, due in part to the occurrence of a cold season, which controls the insect population by forcing hibernation. However, many were present in northern Europe and northern America in the 17th and 18th centuries before modern understanding of disease causation. The initial impetus for tropical medicine was to protect the health of colonialists, notably in India under the British Raj. Insects such as mosquitoes and flies are by far the most common disease carrier, or vector. These insects may carry a parasite, bacterium or virus that is infectious to humans and animals. Most often disease is transmitted by an insect "bite", which causes transmission of the infectious agent through subcutaneous blood exchange. Vaccines are not available for most of the diseases listed here, and many do not have cures.

Human exploration of tropical rainforests, deforestation, rising immigration and increased international air travel and other tourism to tropical regions has led to an increased incidence of such diseases.

Hepatitis D (hepatitis delta) is a disease caused by the "hepatitis D virus" ("HDV"), a small spherical enveloped virusoid. This is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a subviral satellite because it can propagate only in the presence of the hepatitis B virus (HBV). Transmission of HDV can occur either via simultaneous infection with HBV (coinfection) or superimposed on chronic hepatitis B or hepatitis B carrier state (superinfection).

Both superinfection and coinfection with HDV results in more severe complications compared to infection with HBV alone. These complications include a greater likelihood of experiencing liver failure in acute infections and a rapid progression to liver cirrhosis, with an increased risk of developing liver cancer in chronic infections. In combination with hepatitis B virus, hepatitis D has the highest fatality rate of all the hepatitis infections, at 20%.

Trichuriasis, also known as whipworm infection, is an infection by the parasitic worm "Trichuris trichiura" (whipworm). If infection is only with a few worms, there are often no symptoms. In those who are infected with many worms, there may be abdominal pain, tiredness and diarrhea. The diarrhea sometimes contains blood. Infections in children may cause poor intellectual and physical development. Low red blood cell levels may occur due to loss of blood.

The disease is usually spread when people eat food or drink water that contains the eggs of these worms. This may occur when contaminated vegetables are not fully cleaned or cooked. Often these eggs are in the soil in areas where people defecate outside and where untreated human feces is used as fertilizer. These eggs originate from the feces of infected people. Young children playing in such soil and putting their hands in their mouths also become infected easily. The worms live in the large bowel and are about four centimetres in length. Whipworm is diagnosed by seeing the eggs when examining the stool with a microscope. Eggs are barrel-shaped. Trichuriasis belongs to the group of soil-transmitted helminthiases.

Prevention is by properly cooking food and hand washing before cooking. Other measures include improving access to sanitation such as ensuring use of functional and clean toilets and access to clean water. In areas of the world where the infections are common, often entire groups of people will be treated all at once and on a regular basis. Treatment is with three days of the medication: albendazole, mebendazole or ivermectin. People often become infected again after treatment.

Whipworm infection affected about 464 million in 2015. It is most common in tropical countries. In the developing world, those infected with whipworm often also have hookworms and ascariasis infections. They have a large effect on the economy of many countries. Work is ongoing to develop a vaccine against the disease. Trichuriasis is classified as a neglected tropical disease.

In virology, defective interfering particles (DIPs), also known as defective interfering viruses, are spontaneously generated virus mutants in which a critical portion of the particle's genome has been lost due to defective replication. DIPs are derived from and associated with their parent virus, and particles are classed as DIPs if they are rendered non-infectious due to at least one essential gene of the virus being lost or severely damaged as a result of the defection. A DIP can usually still penetrate host cells, but requires another fully functional virus particle (the 'helper' virus) to co-infect a cell with it, in order to provide the lost factors. The existence of DIPs has been known about for decades, and they can occur within nearly every class of both DNA and RNA viruses.

There is some debate among the WHO, CDC, and infectious disease experts over which diseases are classified as neglected tropical diseases. Feasey, a researcher in neglected tropical diseases, notes 13 neglected tropical diseases: ascariasis, Buruli ulcer, Chagas disease, dracunculiasis, hookworm infection, human African trypanosomiasis, Leishmaniasis, leprosy, lymphatic filariasis, onchocerciasis, schistosomiasis, trachoma, and trichuriasis. Fenwick recognizes 12 "core" neglected tropical diseases: ascariasis, Buruli ulcer, Chagas disease, dracunculiasis, human African trypanosomiasis, Leishmaniasis, leprosy, lymphatic filariasis, onchocerciasis, schistosomiasis, trachoma, and trichuriasis.

These diseases result from four different classes of causative pathogens: (i) protozoa (for Chagas disease, human African trypanosomiasis, leishmaniases); (ii) bacteria (for Buruli ulcer, leprosy, trachoma, yaws), (iii) helminths or metazoan worms (for cysticercosis/taeniasis, dracunculiasis, echinococcosis, foodborne trematodiases, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiasis); and (iv) viruses (dengue and chikungunya, rabies).

The World Health Organization recognizes the seventeen diseases below as neglected tropical diseases.

Feline infectious anemia (FIA) is an infectious disease found in felines, causing anemia and other symptoms. The disease is caused by a variety of infectious agents, most commonly "Mycoplasma haemofelis" (which used to be called "Haemobartonella"). "Haemobartonella" and "Eperythrozoon" species were reclassified as mycoplasmas. Coinfection often occurs with other infectious agents, including: feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), "Ehrlichia" species, "Anaplasma phagocytophilum", and Candidatus "Mycoplasma haemominutum".

The illness in humans is a severe form of hemorrhagic fever. Typically, after a 1–3 day incubation period following a tick bite or 5–6 days after exposure to infected blood or tissues, flu-like symptoms appear, which may resolve after one week. In up to 75% of cases, signs of bleeding can appear within 3–5 days of the onset of illness in case of bad containment of the first symptoms: mood instability, , mental confusion and throat petechiae; and soon after nosebleeds, vomiting, and black stools. The liver becomes swollen and painful. Disseminated intravascular coagulation may occur, as well as acute kidney failure, shock, and sometimes acute respiratory distress syndrome. People usually begin to recover after 9–10 days first symptoms appeared. Up to 30% of infected people die by the end of the second week of illness.

DIPs are a naturally occurring phenomenon that can also be synthesized for experimental use. They are spontaneously produced by error-prone viral replication, something particularly prevalent in RNA viruses over DNA viruses due to the enzyme used (replicase, or RNA-dependent RNA polymerase.) DI genomes typically retain the termini sequences needed for recognition by viral polymerases, and sequences for packaging of their genome into new particles, but little else. The size of the genomic deletion event can vary greatly, with one such example in a DIP derived from rabies virus exhibiting a 6.1 kb deletion. In another example, the size of several DI-DNA plant virus genomes varied from one tenth of the size of the original genome to one half.

HIV/AIDS is a major public health concern and cause of death in many parts of Africa. Although the continent is home to about 15.2 percent of the world's population, more than two-thirds of the total, some 35 million infected, were Africans, of whom 15 million have already died. Sub-Saharan Africa alone accounted for an estimated 69 percent of all people living with HIV and 70 percent of all AIDS deaths in 2011. In the countries of sub-Saharan Africa most affected, AIDS has raised death rates and lowered life expectancy among adults between the ages of 20 and 49 by about twenty years. Furthermore, the life expectancy in many parts of Africa is declining, largely as a result of the HIV/AIDS epidemic with life-expectancy in some countries reaching as low as thirty-four years.

Countries in North Africa and the Horn of Africa have significantly lower prevalence rates, as their populations typically engage in fewer high-risk cultural patterns that have been implicated in the virus's spread in Sub-Saharan Africa. Southern Africa is the worst affected region on the continent. As of 2011, HIV has infected at least 10 percent of the population in Botswana, Lesotho, Malawi, Mozambique, Namibia, South Africa, Swaziland, Zambia, and Zimbabwe.

In response, a number of initiatives have been launched in various parts of the continent to educate the public on HIV/AIDS. Among these are combination prevention programmes, considered to be the most effective initiative, the abstinence, be faithful, use a condom campaign, and the Desmond Tutu HIV Foundation's outreach programs.

According to a 2013 special report issued by the Joint United Nations Programme on HIV/AIDS (UNAIDS), the number of HIV positive people in Africa receiving anti-retroviral treatment in 2012 was over seven times the number receiving treatment in 2005, "with nearly 1 million added in the last year alone". The number of AIDS-related deaths in Sub-Saharan Africa in 2011 was 33 percent less than the number in 2005. The number of new HIV infections in Sub-Saharan Africa in 2011 was 25 percent less than the number in 2001.

Crimean–Congo hemorrhagic fever (CCHF) is a viral disease. Symptoms may include fever, muscle pains, headache, vomiting, diarrhea, and bleeding into the skin. Onset of symptoms is less than two weeks following exposure. Complications may include liver failure. In those who survive, recovery generally occurs around two weeks after onset.

The CCHF virus is typically spread by tick bites or contact with livestock carrying the disease. Those affected are often farmers or work in slaughterhouses. It can also spread between people via body fluids. Diagnosis is by detecting antibodies, the virus's RNA, or the virus itself. It is a type of viral hemorrhagic fever.

Prevention involves avoiding tick bites. A vaccine is not commercially available. Treatment is typically with supportive care. The medication ribavirin may also help.

It occurs in Africa, the Balkans, the Middle East, and Asia. Often it occurs in outbreaks. In 2013 Iran, Russia, Turkey, and Uzbekistan documented more than fifty cases. The risk of death among those affected is between 10 and 40%. It was first detected in the 1940s.