Testing Guidance for Clinicians When SARS-CoV-2 and Influenza Viruses are Co-circulating

[Based upon local public health surveillance data and testing at local healthcare facilities]

Outpatient Clinic or Emergency Department Patients with Acute Respiratory Illness Symptoms (With or Without Fever) Not Requiring Hospital Admission

Follow recommended infection prevention and control measures 1

  1. Specimen Collection
  • Implement recommended infection prevention and control measures and collect respiratory specimens for influenza and SARS-CoV-2 testing.1 (Two different specimens may need to be collected if multiplex testing for influenza viruses and SARS-CoV-2 is unavailable on-site.2,3)
  1. SARS-CoV-2 and Influenza Testing
    A) Test for SARS-CoV-2 by nucleic acid detection 2,3; OR if not available, by SARS-CoV-2 antigen detection assay.4 (Note: Because antigen detection assays have lower sensitivity than nucleic acid detection assays, a negative SARS-CoV-2 antigen detection assay result does not necessarily exclude SARS-CoV-2 infection and should be confirmed by SARS-CoV-2 nucleic acid detection assay, especially if suspicion for COVID-19 is high – such as high SARS-CoV-2 community prevalence or recent close exposure to a person with COVID-19.)
    B) Test for influenza if results will change clinical management or for infection control decisions (e.g. long-term care facility resident returning to a facility, or a person of any age returning to a congregate setting): order rapid influenza nucleic acid detection assay 5,6;
    if rapid influenza nucleic acid detection assay is not available on-site, order rapid influenza antigen detection assay. 7 (If available, multiplex nucleic acid detection assay for SARS-CoV-2, influenza A and B viruses can be performed on-site, or at an offsite clinical laboratory.2,3)
    (Note: Because SARS-CoV-2 and influenza virus co-infection can occur, a positive influenza test result without SARS-CoV-2 testing does not exclude SARS-CoV-2 infection, and a positive SARS-CoV-2 test result without influenza testing does not exclude influenza virus infection).
  2. Treatment
  • Prescribe antiviral treatment if on-site influenza testing is positive OR prescribe empiric antiviral treatment without influenza testing based upon a clinical diagnosis of influenza for patients of any age with progressive disease of any duration, and for children and adults at high risk for influenza complications with illness.6,8,9 (encourage patients to start antiviral treatment as soon as possible)
  • For adult patients with suspected community-acquired pneumonia who do not require hospitalization, see antibiotic treatment recommendations from the American Thoracic Society-Infectious Diseases Society of America Adult Community-acquired Pneumonia Guidelines.10
  • For otherwise healthy non-high-risk persons with influenza-like illness (fever and either cough or sore throat) with illness ≤2 days, empiric antiviral treatment of suspected influenza can be prescribed based upon clinical judgement. 6,8
  • For otherwise healthy non-high-risk persons without influenza-like illness or with illness duration >2 days, antiviral treatment of influenza is unlikely to provide significant clinical benefit.6
  1. Follow isolation and quarantine recommendations for SARS-CoV-2,11 and arrange follow-up for any pending testing results.


  1. Implement recommended infection prevention and control measures; including while collecting respiratory specimens. Check the manufacturer’s package insert for approved respiratory specimens. Note: there are no FDA-cleared influenza diagnostic assays that utilize saliva specimens.
  2. CDC. Multiplex Assays Authorized for Simultaneous Detection of Influenza Viruses and SARS-CoV-2 by FDA Emergency Use Authorization.
  3. FDA. Individual EUAs for Molecular Diagnostic Tests for SARS-CoV-2external icon.
  4. FDA. Individual EUAs for Antigen Diagnostic Tests for SARS-CoV-2external icon.
  5. CDC. FDA-cleared Nucleic Acid Detection Based Tests for Influenza Viruses.
  6. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaexternal icon.
  7. CDC. Available FDA-Cleared Rapid Influenza Diagnostic Tests (Antigen Detection Only). Note: Because rapid influenza antigen detection assays have lower sensitivity than influenza nucleic acid detection assays, a negative result does not necessarily exclude influenza virus infection, particularly when local influenza activity is high.
  8. CDC. Influenza Antiviral Medications: Summary for Clinicians.
  9. CDC. People at High Risk for Flu Complications. A list of People with Certain Medical Conditions who are at increased risk for severe illness from COVID-19.
  10. Diagnosis and Treatment of Adults with Community-acquired Pneumonia. An Official Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of Americaexternal icon.
  11. CDC. 3 Key Steps to Take While Waiting for Your COVID-19 Test Resultpdf iconWhen You Can be Around Others After You Had or Likely Had COVID-19;
    Discontinuation of Isolation for Persons with COVID-19 Not in Healthcare SettingsWhen to Quarantine