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.

Deworming treatments in infected children may have some nutritional benefit, as worms are often partially responsible for malnutrition. However, in areas where these infections are common, there is strong evidence that mass deworming campaigns do not have a positive effect on children's average nutritional status, levels of blood haemoglobin, cognitive abilities, performance at school or survival. To achieve health gains in the longer term, improvements in sanitation and hygiene behaviours are also required, together with deworming treatments.

Coinfection is a major concern with neglected tropical diseases, making NTDs more damaging than their mortality rates might portray. Because the factors that support neglected tropical diseases (poverty, inadequate healthcare, inadequate sanitation practices etc.) support all NTDs, they are often found in overlapping distributions. Helminth infections, as the most common infection of humans, are often found to be in multi-infection systems. For example, in Brazil, low socioeconomic status contributes to overcrowded housing. In these same areas, connection by "Necator americanus" and "Schistosoma mansoni" is common. The effect of each worm weakens the immune system of those infected, making infection from the other easier and more severe. For this reason, coinfection carries a higher risk of mortality. NTDs may also play a role in infection with other diseases, such as malaria, HIV/AIDS, and tuberculosis. The ability of helminths to manipulate the immune system may create a physiological environment that could exacerbate the progression of HIV/AIDS. Some evidence from Senegal, Malawi, and Thailand has shown that helminth infections raise the risk of malarial infection.

Much of the deadliness of the epidemic in Sub-Saharan Africa is caused by a deadly synergy between HIV and tuberculosis, termed a "co-epidemic". The two diseases have been "inextricably bound together" since the beginning of the HIV epidemic. "Tuberculosis and HIV co-infections are associated with special diagnostic and therapeutic challenges and constitute an immense burden on healthcare systems of heavily infected countries like Ethiopia." In many countries without adequate resources, the tuberculosis case rate has increased five to ten-fold since the identification of HIV. Without proper treatment, an estimated 90 percent of persons living with HIV die within months after contracting tuberculosis. The initiation of highly active antiretroviral therapy in persons coinfected with tuberculosis can cause an immune reconstitution inflammatory syndrome with a worsening, in some cases severe worsening, of tuberculosis infection and symptoms.

An estimated 874,000 people in Sub-Saharan Africa were living with both HIV and tuberculosis in 2011, with 330,000 in South Africa, 83,000 in Mozambique, 50,000 in Nigeria, 47,000 in Kenya, and 46,000 in Zimbabwe. In terms of cases per 100,000 population, Swaziland's rate of 1,010 was by far the highest in 2011. In the following 20 African countries, the cases-per-100,000 coinfection rate has increased at least 20 percent between 2000 and 2011: Algeria, Angola, Chad, Comoros, Republic of the Congo, Democratic Republic of the Congo, Equatorial Guinea, The Gambia, Lesotho, Liberia, Mauritania, Mauritius, Morocco, Mozambique, Senegal, Sierra Leone, South Africa, Swaziland, Togo, and Tunisia.

Since 2004, however, tuberculosis-related deaths among people living with HIV have fallen by 28 percent in Sub-Saharan Africa, which is home to nearly 80 percent of the people worldwide who are living with both diseases.

Some of the strategies for controlling tropical diseases include:

- Draining wetlands to reduce populations of insects and other vectors, or introducing natural predators of the vectors.

- The application of insecticides and/or insect repellents) to strategic surfaces such as clothing, skin, buildings, insect habitats, and bed nets.

- The use of a mosquito net over a bed (also known as a "bed net") to reduce nighttime transmission, since certain species of tropical mosquitoes feed mainly at night.

- Use of water wells, and/or water filtration, water filters, or water treatment with water tablets to produce drinking water free of parasites.

- Sanitation to prevent transmission through human waste.

- In situations where vectors (such as mosquitoes) have become more numerous as a result of human activity, a careful investigation can provide clues: for example, open dumps can contain stagnant water that encourage disease vectors to breed. Eliminating these dumps can address the problem. An education campaign can yield significant benefits at low cost.

- Development and use of vaccines to promote disease immunity.

- Pharmacologic pre-exposure prophylaxis (to prevent disease before exposure to the environment and/or vector).

- Pharmacologic post-exposure prophylaxis (to prevent disease after exposure to the environment and/or vector).

- Pharmacologic treatment (to treat disease after infection or infestation).

- Assisting with economic development in endemic regions. For example, by providing microloans to enable investments in more efficient and productive agriculture. This in turn can help subsistence farming to become more profitable, and these profits can be used by local populations for disease prevention and treatment, with the added benefit of reducing the poverty rate.

- Hospital for Tropical Diseases

- Tropical medicine

- Infectious disease

- Neglected diseases

- List of epidemics

- Waterborne diseases

- Globalization and disease

When properly treated, people with malaria can usually expect a complete recovery. However, severe malaria can progress extremely rapidly and cause death within hours or days. In the most severe cases of the disease, fatality rates can reach 20%, even with intensive care and treatment. Over the longer term, developmental impairments have been documented in children who have suffered episodes of severe malaria. Chronic infection without severe disease can occur in an immune-deficiency syndrome associated with a decreased responsiveness to "Salmonella" bacteria and the Epstein–Barr virus.

During childhood, malaria causes anemia during a period of rapid brain development, and also direct brain damage resulting from cerebral malaria. Some survivors of cerebral malaria have an increased risk of neurological and cognitive deficits, behavioural disorders, and epilepsy. Malaria prophylaxis was shown to improve cognitive function and school performance in clinical trials when compared to placebo groups.

Nearly 200 parasitic "Plasmodium" species have been identified that infect birds, reptiles, and other mammals, and about 30 species naturally infect non-human primates. Some malaria parasites that affect non-human primates (NHP) serve as model organisms for human malarial parasites, such as "P. coatneyi" (a model for "P. falciparum") and "P. cynomolgi" ("P. vivax"). Diagnostic techniques used to detect parasites in NHP are similar to those employed for humans. Malaria parasites that infect rodents are widely used as models in research, such as "P. berghei". Avian malaria primarily affects species of the order Passeriformes, and poses a substantial threat to birds of Hawaii, the Galapagos, and other archipelagoes. The parasite "P. relictum" is known to play a role in limiting the distribution and abundance of endemic Hawaiian birds. Global warming is expected to increase the prevalence and global distribution of avian malaria, as elevated temperatures provide optimal conditions for parasite reproduction.

"A. phagocytophilum" is transmitted to humans by "Ixodes" ticks. These ticks are found in the US, Europe, and Asia. In the US, "I. scapularis" is the tick vector in the East and Midwest states, and "I. pacificus" in the Pacific Northwest. In Europe, the "I. ricinus" is the main tick vector, and "I. persulcatus" is the currently known tick vector in Asia.

The major mammalian reservoir for "A. phagocytophilum" in the eastern United States is the white-footed mouse, "Peromyscus leucopus". Although white-tailed deer and other small mammals harbor "A. phagocytophilum", evidence suggests that they are not a reservoir for the strains that cause HGA. A tick that has a blood meal from an infected reservoir becomes infected themselves. If an infected tick then latches onto a human the disease is then transmitted to the human host and "A." "phagocytophilum" symptoms can arise.

"Anaplasma phagocytophilum" shares its tick vector with other human pathogens, and about 10% of patients with HGA show serologic evidence of coinfection with Lyme disease, babesiosis, or tick-borne meningoencephalitis.

Additional neglected tropical diseases include:

Some tropical diseases are very rare, but may occur in sudden epidemics, such as the Ebola hemorrhagic fever, Lassa fever and the Marburg virus. There are hundreds of different tropical diseases which are less known or rarer, but that, nonetheless, have importance for public health.

Latest estimates indicate that the total annual death toll which is directly attributable is as high as 135,000. The death toll due to the malnutrition link is likely to be much higher.

HIV infection rates in central Africa are generally moderate to high.

The World Health Organization estimates that globally more than 1.5 billion people (24% of the total population) have a soil-transmitted helminth infection. Over 270 million preschool-age children and over 600 million school-age children live in areas where these parasites are intensively transmitted, and are in need of treatment and preventive interventions. Latest estimates indicate that more than 880 million children are in need of treatment from STH infections.

By type of parasitic worm the breakdown is:

- approximately 807-1,121 million with ascaris

- approximately 576-740 million with hookworm

- approximately 604-795 million with whipworm

Currently, there is no vaccine against human granulocytic anaplasmosis, so antibiotics are the only form of treatment. The best way to prevent HGA is to prevent getting tick bites.

The routes of transmission of hepatitis D are similar to those for hepatitis B. Infection is largely restricted to persons at high risk of hepatitis B infection, particularly injecting drug users and persons receiving clotting factor concentrates. Worldwide more than 15 million people are co-infected. HDV is rare in most developed countries, and is mostly associated with intravenous drug use. However, HDV is much more common in the immediate Mediterranean region, sub-Saharan Africa, the Middle East, and the northern part of South America. In all, about 20 million people may be infected with HDV.

Rates of infection increase in conditions of crowding and poor sanitation, and are higher in military personnel and mental institutions.

The true extent of disease has yet to emerge, as most laboratories do not use techniques to adequately identify this organism. An Australian study identified a large number of patients, considered to have irritable bowel syndrome, who were actually infected with "Dientamoeba fragilis".

Although "D. fragilis" has been described as an infection "emerging from obscurity", it has become one of the most prevalent gastrointestinal infections in industrialized countries, especially among children and young adults. A Canadian study reported a prevalence of around 10% in boys and girls aged 11–15 years, a prevalence of 11.5% in individuals aged 16–20, and a lower incidence of 0.3–1.9% in individuals over age 20.

Infection of "T. trichiura" is most frequent in areas with tropical weather and poor sanitation practices. Trichuriasis occurs frequently in areas in which untreated human feces is used as fertilizer or where open defecation takes place. Trichuriasis infection prevalence is 50 to 80 percent in some regions of Asia (noted especially in China and Korea) and also occurs in rural areas of the southeastern United States.

Treatment is similar to hepatitis B, but due to its high lethality, more aggressive therapeutic approaches are recommended in the acute phase. In absence of a specific vaccine against delta virus, the vaccine against HBV must be given soon after birth in risk groups.

Condom use reduces the likelihood of transmission during sex, but does not completely eliminate the risk. The Centers for Disease Control and Prevention (CDC) states, "Correct and consistent use of latex condoms can reduce the risk of syphilis only when the infected area or site of potential exposure is protected. However, a syphilis sore outside of the area covered by a latex condom can still allow transmission, so caution should be exercised even when using a condom."

Abstinence from intimate physical contact with an infected person is effective at reducing the transmission of syphilis. The CDC states, "The surest way to avoid transmission of sexually transmitted diseases, including syphilis, is to abstain from sexual contact or to be in a long-term mutually monogamous relationship with a partner who has been tested and is known to be uninfected."

Organisms similar to "D. fragilis" are known to produce a cyst stage that is able to survive outside the host and facilitate infection of new hosts. However, the exact manner in which it is transmitted is not yet known, as the organism is unable to survive outside its human host for more than a few hours after excretion, and no cyst stage has been found.

Early theories of transmission suggested "D. fragilis" was unable to produce a cyst stage in infected humans, but some animal existed that in which it did produce a cyst stage, and this animal was responsible for spreading it. However, no such animal has ever been discovered. A later theory suggested the organism was transmitted by pinworms, which provided protection for the parasite outside the host. DNA has been detected in surface-sterilized eggs of "Enterobius vermicularis" eggs, thus suggesting the latter may harbor the former. Experimental ingestion of pinworm eggs established infection in two investigators. Numerous studies reported high rates of coinfection with helminthes. However, recent study has failed to show any association between "D. fragilis" infection and pinworm infection. Parasites similar to "D. fragilis" are transmitted by consuming water or food contaminated with feces. The high rate (40%) of concomitant infection with other protozoa reported by at St. Vincent's Hospital, Sydney, Australia, supports the oral-fecal route of transmission.

, there is no vaccine effective for prevention. Several vaccines based on treponemal proteins reduce lesion development in an animal model, and research is ongoing.

Lábrea fever is a coinfection or superinfection of hepatitis D or delta virus and hepatitis B (HBV). The infection by delta virus may occur in a patient who already has the HBV, or both viruses may infect at the same time a previously uninfected patient. Delta virus can only multiply in the presence of HBV, therefore vaccination against HBV prevents infection. Thus, American and Brazilian scientists have determined that the delta virusa, virus, which is a small circular RNA virus, is normally unable to cause illness by itself, due to a defect. When it is combined with HBV, Lábrea hepatitis may ensue. The main discovery of delta virus and HBV association was done by Dr. Gilberta Bensabath, a leading tropical virologist of the Instituto Evandro Chagas, of Belém, state of Pará, and her collaborators.

Infected patients show extensive destruction of liver tissue, with steatosis of a particular type (microsteatosis, characterized by small fat droplets inside the cells), and infiltration of large numbers of inflammatory cells called "morula cells", comprised mainly by macrophages containing delta virus antigens.

In the 1987 Boca do Acre study, scientists did an epidemiological survey and reported delta virus infection in 24% of asymptomatic HBV carriers, 29% of acute nonfulminant hepatitis B cases, 74% of fulminant hepatitis B cases, and 100% of chronic hepatitis B cases. The delta virus seems to be endemic in the Amazon region.

"T. trichiura" is the third most common nematode (roundworm) infecting humans. Infection is most prevalent among children, and in North America, infection occurs frequently in immigrants from tropical or sub-tropical regions. It is estimated that 600-800 million people are infected worldwide with 3.2 billion individuals at risk because they live in regions where this intestinal worm is common.

The vaccine for hepatitis B protects against hepatitis D virus because of the latter's dependence on the presence of hepatitis B virus for it to replicate.

Latest evidence suggests that Pegylated interferon alpha is effective in reducing the viral load and the effect of the disease during the time the drug is given, but the benefit generally stops if the drug is discontinued. The efficiency of the pegylated interferon treatment does not usually exceed ~20%.

The drug myrcludex B, which inhibits virus entry into hepatocytes, is in clinical trials .

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.

Recent work has been done by virologists to learn more about the interference in infection of host cells and how DI genomes could potentially work as antiviral agents. The Dimmock & Easton, 2014 article explains that pre-clinical work is being done to test their effectiveness against influenza viruses. DI-RNAs have also been found to aid in the infection of fungi via viruses of the family "Partitiviridae" for the first time, which makes room for more interdisciplinary work.