The Pathogens That Cause a Primary Infection

HIV virus infection particle

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A primary infection is the first time you are exposed to and infected by a pathogen. During a primary infection, your body has no innate defenses against the organism, such as antibodies, which can be developed through exposure or vaccination.

Pathogens that can cause primary infections include viruses, bacteria, parasites, and fungi. These pathogens lead to different symptoms, types of health conditions, and treatments.

This article discusses the pathogens that lead to primary infections, including examples such as sexually transmitted illnesses (STIs). It will help you to know more about why specific infections occur.

Causes of Primary Infection

A primary infection occurs when you are initially exposed to a pathogen. For example, genital herpes occurs when you are exposed to the herpes simplex virus, even though infection persists in the body.

There are four different types of pathogens that can lead to a primary infection:

  • Viruses: These enter the body and spread to other cells, and can be mild like the common cold, or life-threatening, such as HIV or hepatitis-C. 
  • Fungi (singular: fungus): Yeast, mold, and mushrooms can cause allergic reactions and related illnesses. They're difficult to eliminate once they've entered the body, and often the treatment, which may include antibiotics or antifungal medications, can have detrimental effects on the body as well. Ringworm and vaginal yeast infections are examples of fungal infections. 
  • Bacteria: While they can lead to primary infections, bacteria tend to be secondary infections, which enter the body after it's been weakened by a virus. Strep throat and botulism are examples of bacterial infections. 
  • Parasites: These enter a host body and drain energy from the host. Tapeworm, which wreaks havoc on the digestive system, and Lyme-carrying are two examples of parasites that can make people sick. 

Virus Infections

Viruses are pathogens that lead to an array of illnesses, from the common cold to COVID-19. The viral microorganisms can affect your respiratory system, digestive tract, neurological function and more.

Common illnesses caused by a virus also include:

Some viral infections, like influenza, are easily spread but comparatively mild though they may cause serious illness or even death in some people. Good hygiene practices may limit their spread. Some viruses also may be prevented with vaccines.

Other viruses may lead to severe and often fatal illness, as is the case with Ebola virus and human immunodeficiency virus (HIV) that are not properly treated.

Treatment for a viral infection may be as simple as taking over-the-counter medication for symptom relief until the infection clears. Antiviral drugs, like those used to treat Hepatitis C infections, may be prescribed. In cases that require hospitalization, you may need:

Viruses and Cancer

Researchers who study viruses have found that in some cases, there are links to specific types of cancer. For example, the human papillomavirus (HPV) is the most common type of sexually transmitted infection.It's implicated in cervical cancer, anal cancer, head and neck cancers, and more.

Fungal Infections

A fungal infection, formally called mycosis, is caused by a fungus. Fungi are a type of organism that lives in the environment—air, soil, and water—as well as in human and animal bodies. In some cases, the illnesses they cause can be contagious and spread.

Common fungal infections include:

  • Yeast infections (for example, affecting the mouth or vagina)
  • Aspergillosis, a type of lung infection
  • Meningitis, caused by infection with Cryptococcus neoformans 

Many fungal infections affect the skin, as with athlete's foot or ringworm, and are treated with antifungal medication. Others pose a deadly threat.

In October 2022, the World Health Organization identified 19 fungal pathogens that are a priority for researchers. This is because of increasing resistance to antifungal medications, and because more people appear to be affected by fungal infections. That's especially true for people living with:

  • Chronic obstructive pulmonary disease (COPD)
  • Liver disease
  • Chronic kidney disease

Bacterial Infections

Bacteria are single-celled organisms that exist everywhere. Some, however, can lead to illness. Bacterial infections can be responsible for cases of:

Bacterial infections, like those that cause strep throat, often lead to the same kind of symptoms seen in viral infections, including a fever, sore throat, and sinus congestion. Other symptoms are more specific to the illness, as with the headache and stiff neck associated with meningitis (which also can be caused by viral infection).

It's important to have an accurate diagnosis of any bacterial infection because your healthcare provider can treat these infections with an antiobiotic. That's not the case for a viral infection.

Keep in mind that some bacterial infections can be prevented through vaccination. For example, Prevnar 20 is used in older adults to prevent pneumococcal disease including pneumonia, while a tetanus shot limits the potentially life-threatening impacts of a Clostridium tetani infection.

Parasite Infections

Infections caused by parasites do happen in the United States, although certain illnesses caused by parasites (like roundworms) are more prevalent around the world.

The single-celled protozoa are the most common type of parasite in the U.S. These parasites can cause toxoplasmosis, as is the case with Toxoplasma gondii infection.

Other types of parasites can lead to:

  • Giardiasis, an intestinal disease tied to water that's contaminated with the Giardia lamblia or Giardia duodenalis parasites
  • Trichinosis, an infection caused by ingesting Trichinella spiralis roundworms found in improperly cooked meats, especially pork

Symptoms of parasitic infection depend on the type of parasite and what's affected. Flu-like symptoms of fever, swollen lymph nodes, and fatigue may occur, along with diarrhea, vomiting, and other effects on the gastrointestinal system.

Most parasite infections can be treated, in some cases with natural remedies. But some infections can lead to life-threatening complications, as can occur with toxoplasmosis.Be sure to see a healthcare provider for an accurate diagnosis and treatment.

Secondary Infections

It's important to note that the phrase "secondary infection" does not refer to the second time a person becomes infected with the same illness. Secondary infection is a different infection altogether, which can thrive in a person who has a primary infection.

Sometimes called "opportunistic infections," secondary infections in HIV patients are able to do more damage because HIV weakens the immune system. Many patients who do not have HIV can fight off other viral and fungal infections that are potentially life-threatening to HIV patients.


Primary infections can be caused by pathogens entering your body, whether  viruses, bacteria, parasites, or fungi. Sometimes the symptoms of these illnesses may be similar, but the pathogens have different characteristics and pathways for causing illness.

Some of these infections are common viral illnesses that affect nearly everyone, like influenza. Others are more rare, with greater impact on those with higher exposure (traveling outside the U.S., for example) or in people who are more vulnerable because they live with a weakened immune system.

Most infections can be diagnosed and treated with success, but it's important to be sure about the infection. Antibiotics, for example, won't help with a viral infection, while antifungal drugs are designed to target fungi that cause infection.

Frequently Asked Questions

  • Is athlete's foot a fungal infection?

    Yes, athlete's foot (tinea pedis) is caused by a fungus that affects the foot and toes. Most people can treat this type of infection at home with over-the-counter products. When symptoms are severe or long-lasting, or they affect someone with special foot care concerns, it's best to see a healthcare provider.

  • Can a primary infection have no symptoms?

    It's possible. For example, about 80% of people who have a bacterial Helicobacter pylori (H. pylori) infection don't have symptoms, even though half of the global population is affected, typically in childhood. Many people living with a primary Epstein-Barr virus (EBV) infection are asymptomatic, too.

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Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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By Elizabeth Boskey, PhD
Elizabeth Boskey, PhD, MPH, CHES, is a social worker, adjunct lecturer, and expert writer in the field of sexually transmitted diseases.