For Providers: Respiratory Infection Testing
This clinical tool is intended to be used as a training tool for providers and also as a resource for primary care physicians during clinic.
Respiratory Infection Testing
This tool is designed to help clinicians determine when respiratory testing is appropriate, which test to order and how results may affect patient management during respiratory season (typically around November to March). Because influenza, SARS-CoV-2 and other viral and bacterial respiratory infections can present with similar symptoms, this tool covers a risk-based approach to testing rather than routine testing for every patient.
Testing is most appropriate when results may influence antiviral treatment, infection prevention, public health decisions or other aspects of care. Refer to the guideline for specifics on management for hospitalized patients, high-risk outpatients, otherwise healthy patients with mild illness and patients with suspected pertussis or Mycoplasma pneumoniae. A broader respiratory infection array may be useful and outlines specimen requirements and test limitations.
What Causes Respiratory Illnesses?
Acute respiratory illnesses are caused by a range of viral and bacterial pathogens rather than a single respiratory infection. Common causes include:
- Influenza
- SARS-CoV-2, RSV
- Adenovirus
- Human Metapneumovirus
- Parainfluenza viruses
- Rhinovirus/Enterovirus
- Selected bacterial pathogens.
Because these infections often cause overlapping clinical presentations, symptoms alone may not reliably identify the specific pathogen.
The clinical question may not simply whether a patient has a respiratory infection, but whether identifying the specific causative pathogen would change care. The respiratory infection array is a multiplex nucleic acid amplification test that can detect multiple respiratory pathogens from a single nasopharyngeal specimen, including 17 viral targets and four bacterial targets.
For suspected pertussis or Mycoplasma pneumoniae, targeted PCR testing may be preferred because the broader array has lower sensitivity for these organisms.
What Are the Signs and Symptoms of Respiratory Infections?
Respiratory infections caused by different viral and bacterial pathogens frequently produce similar symptoms. Common presentations may include fever or chills, cough, sore throat, congestion, fatigue, shortness of breath, headache, muscle or body aches, and new loss of taste or smell.
Because these symptoms overlap considerably, clinical presentation alone may not distinguish influenza, COVID-19 or other respiratory infections. Testing decisions should instead consider the patient’s overall clinical status, risk for severe disease and whether identifying the pathogen is likely to change treatment or infection-control decisions.
Risk factors for more severe influenza or COVID-19 illness can include young age, chronic medical conditions, immunocompromising conditions and other factors that increase the potential benefit of identifying the infection promptly. Otherwise healthy outpatients with mild illness generally do not require routine testing unless clinical judgment indicates that the result would affect management.
How Can Testing Help Treatment Decisions?
Testing may be most effective when results can meaningfully guide treatment decisions. For patients at increased risk of complications, identifying influenza or SARS-CoV-2 can support timely consideration of antiviral therapy and appropriate infection-prevention measures.
For hospitalized patients with acute respiratory illness, influenza and SARS-CoV-2 testing is recommended, with broader respiratory pathogen testing considered when the result may affect clinical management. In otherwise healthy patients with mild outpatient illness, supportive management may proceed without testing when identifying the specific pathogen would not change care.
Appropriate testing can also help reduce unnecessary antibiotic use, support antimicrobial stewardship, identify patients who require isolation precautions and improve diagnostic clarity in hospitalized or high-risk patients.
When to Refer
There are certain situations in which additional clinical or laboratory consultation may be appropriate.
Consider consultation when:
- The patient is seriously ill and broader or confirmatory testing is needed.
- A negative respiratory infection array conflicts with strong clinical suspicion for pertussis or Mycoplasma pneumoniae.
- There are questions about the most appropriate respiratory test, specimen type or interpretation of results.
- A patient’s clinical course or risk factors suggest that infectious disease expertise may influence management.
For suspected pertussis, a dedicated Bordetella pertussis/parapertussis PCR may be recommended because it is more sensitive than the respiratory infection array. A targeted Mycoplasma pneumoniae PCR is similarly preferred when that infection is strongly suspected.
Nationwide Children's Hospital | Clinical Practice Tool
Clinical Reviewers: Amy Leber, PhD – Laboratory Services & Matthew Washam, MD, MPH – Infectious Diseases
Date Last Reviewed: October 2026
