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What is Influenza?

Influenza, also known as “the flu”, is an acute respiratory infection caused by a virus of the Orthomyxoviridae family. This virus can be classified into three types: influenza A, B, or C. Influenzas A and B are the most common causes of human influenza infections, with influenza A responsible for most seasonal epidemics.1,2 Influenza is characterized by a fever, headache, and cough that last an average of three days, though cough and discomfort can persist for more than 2 weeks.1

In the U.S., seasonal influenza epidemics happen between October and April, and their severity varies widely depending on the characteristics of the viruses, timing of the season, vaccine efficacy, and percentage of vaccinated people. According to the Center for Disease Control and Prevention (CDC), since 2010, the U.S. has seen an estimated 9.2-35.6 million cases of influenza, between 140,000-710,000 hospitalizations, and 12,000-56,000 deaths each year.3

Because influenza virus strains can mutate rapidly, the circulating strains and the protection covered by influenza vaccines can vary each year. A yearly influenza vaccination is recommended, particularly for people who are at high risk for an influenza infection, such as children, the elderly, and people with underlying health conditions.

What are the symptoms?

Influenza has an incubation period of 2-5 days and the onset of symptoms is usually rapid. Common symptoms of influenza are (in order of frequency)4:

  • Fever or chills
  • Cough
  • Headaches
  • Runny or stuffy nose
  • Sore throat
  • Body aches
  • Fatigue and lethargy

These symptoms can be more severe and lead to complications in children, the elderly, and immunocompromised patients. Influenza complications may include (in order of frequency)1,2:

  • Otitis media (middle ear inflammation)
  • Bacterial sinusitis
  • Bacterial pneumonia
  • Sepsis
  • Exacerbations of chronic respiratory disease such as asthma or COPD
  • Febrile convulsions
  • Reye’s syndrome in children (severe tissue damage in liver and brain)
  • Myocarditis (inflammation of the heart muscle)

 What are the causes?

The influenza virus is most commonly transmitted via air droplets – produced by sneezing or coughing by an infected patient – that enter the body through the respiratory tract. In the respiratory tract, the virus binds to epithelial cells in both the upper and lower airways (binding in the lower airways leads to more severe complications). Then, the virus enters the cell, and its RNA is replicated in the cell within hours, producing numerous virus particles (virions). These virions break out of the cell and spread throughout the body, infecting neighbouring cells.5

In the lower respiratory tract, these cycles of viral infection and breaking-out-of-cells destroy epithelial cells, resulting in shedding of layers of epithelium in a variety of places until only the basal layer remains. As a result, the surfaces in the respiratory tract, such as the trachea and bronchi, redden and swell, limiting the flow of air in and out of the lungs.6

The main risk factors for influenza are4,6:

  • Age: infants and the elderly
  • Immunosuppression
  • Living in a care facility, such as a nursing home
  • Pregnancy
  • Prevalence of chronic disease, such as chronic pulmonary or cardiac disease, or diabetes mellitus

How does this topic relate to my microbiome?

Generally, a healthy upper airway microbiome in humans protects the body by preventing respiratory viral infections from spreading to the lower airways. For example, the sinuses of healthy individuals have many beneficial microbes in comparison to subjects with chronic rhinosinusitis, whose sinuses are home to pathogenic species such as Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumonia.7,8 Lactobacillus may also protect the respiratory mucosa of the upper respiratory tract by helping the immune system respond to viruses.9

The health of a person’s respiratory microbiome can influence their susceptibility to influenza, and the influenza virus can negatively affect a person’s respiratory microbiome. For example, several animal models show that a viral infection like influenza can encourage the growth of bacterial pathogens in the respiratory tract, lungs, or even the spleen.10 This has also been found in humans. During influenza infection, the layers of cells that line the airways become damaged, leaving them more susceptible to infection with pathogenic bacteria. This can lead to “secondary bacterial pneumonia”, a bacterial infection of the lungs that follows a primary viral infection.5

Patients infected with H1N1 influenza A virus were found to have increased numbers of Pseudomonas and Acinetobacter – and reduced numbers of Prevotella, Veillonella, and Neisseria – in their oropharyngeal (throat) microbiota. This finding demonstrated that the influenza virus disturbs the respiratory microbiome, which makes it easier for the virus to further infect the lower airways and cause severe complications.5,10,11

Additionally, in studies conducted with mice, the presence of certain bacteria in their lung microbiota – such as Staphylococcus aureus, Streptomyces griseus, and Aerococcus viridans – made them more susceptible to the influenza virus.10

Which diseases/topics are related to influenza?

Comorbid conditions related to influenza are (in order of frequency)12,13:

  • Respiratory diseases – such as asthma
  • Cardiovascular diseases
  • Diabetes
  • Cancers
  • Obesity
  • Other immunosuppression

How can people take action?

If you feel sick and suspect you might have an influenza infection, you should stay home and avoid contact with other people to prevent spread of the virus. Most people have mild symptoms and don’t need medical care. However, if your illness worsens or you have any comorbidity, contact your healthcare provider to get the right treatment. The CDC recommends these “Take 3” actions to fight and prevent influenza14:

  1. Vaccinate: a yearly flu vaccine is recommended, especially for high-risk people
  2. Stop germs:
    • Avoid contact with sick people
    • While sick, avoid contact with healthy people
    • Cover nose and mouth when sneezing and coughing
    • Wash hands often with soap and water, or with an alcohol-based hand sanitizer
  3. Take antiviral drugs if your doctor prescribes them: they can reduce disease symptoms and shorten the length of your sickness


1. Demicheli, V., Jefferson, T., Al-Ansary, L. A., Ferroni, E., Rivetti, A., & Di Pietrantonj, C. (2014). Vaccines for preventing influenza in healthy adults. Cochrane Database of Systematic Reviews.

2. Lynch, J., & Walsh, E. (2007). Influenza: evolving strategies in treatment and prevention. Seminars in Respiratory and Critical Care Medicine, 28(2), 144–157.

3. Center for Disease Control and Prevention (2018a). Disease Burden of Influenza.

4. Clark, N., & Lynch, J. (2011). Influenza: Epidemiology, Clinical Features, Therapy, and Prevention. Seminars in Respiratory and Critical Care Medicine, 32(04), 373–392.

5. Behrens, G., & Stoll, M. (2006). Pathogenesis and Immunology. In B. S. Kamps, C. Hoffmann, & W. Preiser (Eds.), Influenza Report 2006 (p. 225). Paris: Flying Publisher.

6. Taubenberger, J. K., & Morens, D. M. (2008). The Pathology of Influenza Virus Infections. Annual Review of Pathology: Mechanisms of Disease, 3(1), 499–522.

7. Healy, D. Y., Leid, J. G., Sanderson, A. R., & Hunsaker, D. H. (2008). Biofilms with fungi in chronic rhinosinusitis. Otolaryngology – Head and Neck Surgery, 138(5), 641–647.

8. Sanderson, A. R., Leid, J. G., & Hunsaker, D. (2006). Bacterial Biofilms on the Sinus Mucosa of Human Subjects With Chronic Rhinosinusitis. The Laryngoscope, 116(7), 1121–1126.

9. Tomosada, Y., Chiba, E., Zelaya, H., Takahashi, T., Tsukida, K., Kitazawa, H., … Villena, J. (2013). Nasally administered Lactobacillus rhamnosus strains differentially modulate respiratory antiviral immune responses and induce protection against respiratory syncytial virus infection. BMC Immunology, 14(1).

10. Lynch, S. V. (2014). Viruses and microbiome alterations. Annals of the American Thoracic Society, 11(SUPPL. 1), 57–60.

11. Leung, R. K. K., Zhou, J. W., Guan, W., Li, S. K., Yang, Z. F., & Tsui, S. K. W. (2013). Modulation of potential respiratory pathogens by pH1N1 viral infection. Clinical Microbiology and Infection, 19(10), 930–935.

12. DiazGranados, C. A., Dunning, A. J., Robertson, C. A., Talbot, H. K., Landolfi, V., & Greenberg, D. P. (2015). Efficacy and immunogenicity of high-dose influenza vaccine in older adults by age, comorbidities, and frailty. Vaccine, 33(36), 4565–4571.

13. Jain, S., & Chaves, S. S. (2011). Obesity and Influenza. Clinical Infectious Diseases, 53(5), 422–424.

14. Center for Disease Control and Prevention (2018b). Preventive Steps.