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 infection. 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, symptoms maybe nonspecific and resemble other common respiratory tract infections, such as influenza. If testing for other respiratory tract pathogens is negative, specific testing for SARS-CoV-2 may be warranted.

SARS-CoV-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) would be more likely to have detectable SARS-CoV-2.

Influenza, also 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, the elderly, the immunocompromised, and those with impaired lung function, are at risk for serious complications. 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 an infectious pathogen that infects the human respiratory tract causing an influenza-like illness. Most healthy people spontaneously recover from RSV infection in 1 to 2 weeks, but infection can be severe in infants, young children, and older adults. The virus is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia in children under 1 year of age in the United States, and it is recognized increasingly as a frequent cause of respiratory illnesses in older adults.

RSV can be detected by polymerase chain reaction in the human upper and lower respiratory tract specimens. Nasopharyngeal swabs or aspirates are the preferred specimen types for detection of RSV RNA. Nasal swabs may not yield as high detection rate as those of nasopharyngeal specimens for molecular detection of RSV RNA.