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?
- 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).
- 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.)
- 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.7 (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)
Follow recommended infection prevention and control measures1
- SARS-CoV-2 Testing
Test for SARS-CoV-2 by nucleic acid detection2,3; OR 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
- 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 assay2,3,4,11; if 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.11,12,14
- 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
- SARS-CoV-2 Testing
- 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.)
- 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.
- CDC. Multiplex Assays Authorized for Simultaneous Detection of Influenza Viruses and SARS-CoV-2 by FDA Emergency Use Authorization.
- FDA. Individual EUAs for Molecular Diagnostic Tests for SARS-CoV-2.
- CDC. FDA-cleared Nucleic Acid Detection Based Tests for Influenza Viruses. https://www.cdc.gov/flu/professionals/diagnosis/table-nucleic-acid-detection.html
- 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.
- 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.
- NIH Coronavirus Disease 2019 (COVID-19) Treatment Guidelines.
- 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.
- 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.
- 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.
- Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza.
- CDC. Influenza Antiviral Medications: Summary for Clinicians.
- 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.
- CDC. People at High Risk for Flu Complications. People with Certain Medical Conditions who are at increased risk for severe illness from COVID-19.
- 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