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)*

Does the Patient Require Hospital Admission?



  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 is unavailable).
  1. SARS-CoV-2 and Influenza Testing
    a) Order multiplex nucleic acid detection assay for influenza A/B/SARS-CoV-2.2,3OR
    b) If multiplex nucleic acid detection assay is not available, order SARS-CoV-2 nucleic acid detection assay3 and Influenza nucleic acid detection assay.4   (If SARS-CoV-2 nucleic acid detection assay is not available on-site and SARS-CoV-2 antigen detection assay is used,5 confirm negative SARS-CoV-2 antigen detection results by SARS-CoV-2 nucleic acid detection assay at an outside laboratory). (Note: Rapid influenza antigen detection assays are not recommended for hospitalized patients due to low sensitivities.)

(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 COVID-19, and a positive SARS-CoV-2 test result without influenza testing does not exclude influenza.)

  1. Treatment
  • If bacterial pneumonia or sepsis is suspected, consider testing recommendations and empiric antibiotic treatment per American Thoracic Society-Infectious Diseases Society of America Adult Community-acquired Pneumonia Guidelines6, and administer supportive care and treatment for suspected or confirmed COVID-19 patients per NIH COVID-19 Treatment Guidelines.(Note: community-acquired bacterial co-infections can occur but appear to be uncommon with COVID-19,8,9,10 and may be more common with influenza.11)
  • Start empiric oseltamivir treatment for suspected influenza as soon as possible regardless of illness duration, without waiting for influenza testing results, per Infectious Diseases Society of America Influenza Guidelines11,12, and administer supportive care.

Follow recommended infection prevention and control measures1

    1. SARS-CoV-2 Testing
      Test for SARS-CoV-2 by nucleic acid detection2,3OR if not available, by SARS-CoV-2 antigen detection assay.5
      a) If SARS-CoV-2 Test result is positive, administer supportive care. If the patient is at high risk for progression to severe COVID-19, prescribe treatment for nonhospitalized patients as recommended per NIH COVID-19 Treatment Guidelines.7
    2. Influenza Testing and Treatment
      a) 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
      2,3,4,11if rapid influenza nucleic acid detection assay is not available on-site, order rapid influenza antigen assay13; prescribe antiviral treatment if positive.11,12OR
      b) Prescribe empiric antiviral treatment as soon as possible without influenza testing based on 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.
      • For adult patients with suspected community-acquired pneumonia who do not require admission, see American Thoracic Society-Infectious Diseases Society of America Adult Community-acquired Pneumonia Guidelines6
      • 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 can be prescribed based upon clinical judgement.11,12
      • 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.11
    1. Follow isolation and quarantine recommendations for SARS-CoV-215

Footnotes (*Separate algorithms are also available for patients being admitted to hospital, and for patients not requiring hospitalization.)

  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-2.
  4. CDC. FDA-cleared Nucleic Acid Detection Based Tests for Influenza Viruses. https://www.cdc.gov/flu/professionals/diagnosis/table-nucleic-acid-detection.html
  5. FDA. Individual EUAs for Antigen Diagnostic Tests for SARS-CoV-2. Use within five days of illness onset. Note: Because antigen detection assays have lower sensitivity than nucleic acid detection assays, a negative result does not necessarily exclude SARS-CoV-2 infection and should be confirmed by nucleic acid detection assay.
  6. Diagnosis and Treatment of Adults with Community-acquired Pneumonia. An Official Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of America.
  7. NIH Coronavirus Disease 2019 (COVID-19) Treatment Guidelines.
  8. Langford BJ, So M, Raybardhan S, Leung V, Westwood D, MacFadden DR, Soucy JR, Daneman N. Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis. Clin Microbiol Infect. 2020 Jul 22:S1198-743X(20)30423-7. doi: 10.1016/j.cmi.2020.07.016. Online ahead of print.
  9. Adler H, Ball R, Fisher M, Mortimer K, Vardhan MS. Low rate of bacterial co-infection in patients with COVID-19. Lancet Microbe. 2020 Jun;1(2):e62.
  10. Vaughn VM, Gandhi T, Petty LA, Patel PK, Prescott HC, Malani AN, Ratz D, McLaughlin E, Chopra V, Flanders SA. Empiric Antibacterial Therapy and Community-onset Bacterial Co-infection in Patients Hospitalized with COVID-19: A Multi-Hospital Cohort Study. Clin Infect Dis. 2020 Aug 21:ciaa1239. doi: 10.1093/cid/ciaa1239.
  11. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza.
  12. CDC. Influenza Antiviral Medications: Summary for Clinicians.
  13. 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.
  14. CDC. People at High Risk for Flu Complications. People with Certain Medical Conditions who are at increased risk for severe illness from COVID-19.
  15. CDC. 3 Key Steps to Take While Waiting for Your COVID-19 Test Result [230 KB, 2 pages]; When You Can be Around Others After You Had or Likely Had COVID-19;
    Discontinuation of Isolation for Persons with COVID-19 Not in Healthcare Settings; When to Quarantine