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]
Patients with Acute Respiratory Illness Symptoms Requiring Hospital Admission (With or Without Fever)
- Specimen collection
- Implement recommended infection prevention and control measures and collect respiratory specimens for influenza and SARS-CoV-2 testing.1 (Two different respiratory specimens may need to be collected if multiplex testing is unavailable).
- SARS-CoV-2 and Influenza Testing
- Order multiplex nucleic acid detection assay for influenza A/B/SARS-CoV-2.2,3 If not available, order SARS-CoV-2 nucleic acid detection assay3 and influenza nucleic acid detection assay4 (If a SARS-CoV-2 nucleic acid detection assay is not available on-site and a SARS-CoV-2 antigen detection assay is used,5 confirm negative SARS-CoV-2 antigen detection assay results by SARS-CoV-2 nucleic acid detection assay at an outside laboratory). (Note: Rapid influenza antigen detection assays are not recommended due to lower sensitivities compared with rapid influenza nucleic acid detection assays.)
(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.)
- In critically ill intubated and mechanically ventilated patients who are suspected to have COVID-19 or influenza without a confirmed diagnosis, including when upper respiratory tract specimens are negative, lower respiratory tract (e.g. endotracheal aspirate) specimens should be collected for SARS-CoV-2 and influenza virus testing by nucleic acid detection assay per NIH COVID-19 Treatment Guidelines,6 and Infectious Diseases Society of America Influenza Clinical Practice Guidelines.7
- 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 Guidelines,8 and administer supportive care and treatment for suspected or confirmed COVID-19 patients per NIH COVID-19 Treatment Guidelines.6 (Note: community-acquired bacterial co-infections can occur with COVID-19 but appear to be uncommon,9,10,11 and may be more common with influenza.7)
- 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-2external icon.
- CDC. FDA-cleared Nucleic Acid Detection Based Tests for Influenza Viruses.
- FDA. Individual EUAs for Antigen Diagnostic Tests for SARS-CoV-2external icon. 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.
- NIH Coronavirus Disease 2019 (COVID-19) Treatment Guidelinesexternal icon.
- Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaexternal icon.
- 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.
- 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. doi: 10.1016/S2666-5247(20)30036-7. Epub 2020 Jun 8.
- 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. Online ahead of print.
- CDC. Influenza Antiviral Medications: Summary for Clinicians.