Clinical Information

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA virus that causes COVID-19. Like other coronaviruses that infect humans, SARS-CoV-2 can cause both upper and lower respiratory tract illness. Symptoms can range from mild (ie, the common cold) to severe (ie, pneumonia) in both healthy and immunocompromised patients. SARS-CoV-2 transmission occurs primarily via respiratory droplets. During the early stages of COVID-19 disease, the symptoms may be nonspecific and resemble other common respiratory infections, such as influenza. If testing for other respiratory infections is negative, specific testing for SARS-CoV-2 (COVID-19) may be warranted.

Severe acute respiratory syndrome coronavirus 2 is likely to be at the highest concentrations in the nasopharynx during the first 3 to 5 days of symptomatic illness. As the disease progresses, the viral load tends to decrease in the upper respiratory tract, at which point lower respiratory tract specimens (eg, sputum, tracheal aspirate, bronchoalveolar fluid) may be more likely to have detectable SARS-CoV-2.

Influenza, otherwise known as the "flu," is an acute, contagious respiratory illness caused by influenza A, B, and C viruses. Of these, only influenza A and B are thought to cause significant disease, with infections due to influenza B usually being milder than infections with influenza A. Influenza A viruses are further categorized into subtypes based on the 2 major surface protein antigens: hemagglutinin (H) and neuraminidase (N).

Common symptoms of influenza infection include fever, chills, sore throat, muscle pains, severe headache, weakness, fatigue, and a nonproductive cough. Certain patients, including infants, older individuals, patients who are immunocompromised, and those with impaired lung function, are at risk for serious complications. In the United States, influenza results in 10,000 to 30,000 deaths and more than 200,000 hospitalizations each year.

In the northern hemisphere, annual epidemics of influenza typically occur during the fall or winter months. However, the peak of influenza activity can occur as late as April or May, and the timing and duration of flu seasons vary.

Influenza infection may be treated with supportive therapy as well as antiviral drugs, such as the neuraminidase inhibitors, oseltamivir (Tamiflu) and zanamivir (Relenza). These drugs are most effective when given within the first 48 hours of infection, so prompt diagnosis and treatment are essential for proper management.

Respiratory syncytial virus (RSV) is a respiratory virus that also infects the human respiratory tract, causing an influenza-like illness. Most otherwise healthy people recover from RSV infection in 1 to 2 weeks, but infection can be severe in infants, young children, and older adults. RSV is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia in children younger than 1 year in the United States. It is increasingly recognized as a frequent cause of respiratory illness in older adults.

The Influenza viruses and RSV can be detected in respiratory secretions, including upper and lower respiratory tract specimens, by molecular test methods. Nasopharyngeal swabs or aspirates are the preferred specimen types for detection of influenza A virus, influenza B virus, SARS-CoV-2, and RSV. Nasal swabs have also been shown to provide comparable yield to nasopharyngeal specimens for molecular detection of SARS-CoV-2 RNA and influenza A and B viral RNA but not RSV RNA.