Testing and Management Considerations for Nursing Home Residents with Acute Respiratory Illness Symptoms when SARS-CoV-2 and Influenza Viruses are Co-circulating

The following practices should be considered when SARS-CoV-2 and Influenza viruses are found to be co-circulating based upon local public health surveillance data and testing at local healthcare facilities. While these considerations are specific to care of residents residing in nursing homes, some practices could be adapted for use in other long-term care settings (e.g. assisted living communities).

  1. Place symptomatic residents in Transmission-Based Precautions using all recommended PPE for care of a resident with suspected SARS-CoV-2 infection1

    Because some of the symptoms of influenza and COVID-19 are similar, it may be difficult to tell the difference between these two respiratory diseases based on symptoms alone. Residents in the facility who develop symptoms of acute illness consistent with influenza or COVID-19 should be moved to a single room, if available, or remain in current room, pending results of viral testing. They should not be placed in a room with new roommates nor should they be moved to a COVID-19 care unit (if one exists) unless they are confirmed to have COVID-19 by SARS-CoV-2 testing.

    Nursing home residents, including older adults, those who are medically fragile and those with neurological or neurocognitive conditions, may manifest atypical signs and symptoms of influenza virus infection and may not have fever.

    Older adults with COVID-19 may not always manifest fever or respiratory symptoms. Less common symptoms can include new or worsening malaise, headache, or new dizziness, nausea, vomiting, diarrhea, and loss of taste or smell.

  2. Test any resident with symptoms of COVID-19 or influenza for both viruses

    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.

    Stay connected with the healthcare-associated infection program in your state health department, as well as your local health department, and their notification requirements. The local public health and state health departments should be notified of every suspected or confirmed influenza outbreak in a long-term care facility, especially if a resident develops influenza while on or after receiving antiviral chemoprophylaxis.

    A) Obtain respiratory specimens for influenza and SARS-CoV-2 testing2

    Check the manufacturer’s package insert for approved respiratory specimens. There are no FDA-cleared influenza diagnostic assays that utilize saliva specimens.

    If available, multiplex nucleic acid detection assay for SARS-CoV-2, influenza A and B viruses can be performed onsite, or at an offsite clinical laboratory.3

    Two different specimens may need to be collected if a multiplex nucleic acid detection assay including both influenza viruses and SARS-CoV-2 is unavailable.2,3

    B) Test for SARS-CoV-2 by nucleic acid detection4 OR by SARS-CoV-2 antigen detection assay.5,6

    Because antigen detection assays have lower sensitivity than nucleic acid detection assays for detecting SARS-CoV-2 in upper respiratory tract specimens, a negative SARS-CoV-2 antigen detection assay result in a symptomatic person does not exclude SARS-CoV-2 infection and should be confirmed by either a negative result from a SARS-CoV-2 nucleic acid detection assay or a second negative antigen test result on an upper respiratory tract specimen collected 48 hours after the first negative test result. 1

    New SARS-CoV-2 infection identified in HCP or nursing home-onset infection in a resident should prompt additional testing in the facility.1

    C) Test for influenza by rapid influenza nucleic acid detection assay6; if a rapid influenza nucleic acid detection assay is not available, perform rapid influenza antigen detection assay.9 Because of lower sensitivities to detect influenza viruses, confirm negative rapid influenza antigen detection test results in a symptomatic person by influenza nucleic acid detection assay.

    D) Test for other respiratory pathogens; if residents with acute respiratory illness test negative for both influenza and SARS-CoV-2 consider additional viral or bacterial testing based on respiratory pathogens known or suspected of circulating in the community.

  3. Placement Decisions

    A) Residents confirmed to have SARS-CoV-2 infection should be placed in a single room, if available, or housed with other residents with only SARS-CoV-2 infection. If unable to move a resident, he or she could remain in the current room with measures in place to reduce transmission to roommates (e.g., optimizing ventilation).

    Residents found to have SARS-CoV-2 and influenza virus co-infection should be placed in a single room or housed with other co-infected residents. These residents should continue to be cared for using all recommended PPE for the care of a resident with SARS-CoV-2 infection.1

    If single room isolation or cohorting of residents with SARS-CoV-2 and influenza virus co-infection is not possible, consult with public health authorities for guidance on other management options (e.g., transferring the resident; placing physical barriers between beds in shared rooms and initiating antiviral chemoprophylaxis for roommates to reduce their risk of acquiring influenza).

    B) Residents confirmed with influenza only should be placed in a single room, if available, or housed with other residents with only influenza. If unable to move a resident, he or she could remain in the current room with measures in place to reduce transmission to roommates (e.g., optimizing ventilation, antiviral chemoprophylaxis).

    Residents with only influenza should be placed in Droplet Precautions, in addition to Standard Precautions. As part of Standard Precautions, eye protection should be worn if splashes or sprays are anticipated (e.g., the resident is coughing or sneezing). Because it can be difficult to anticipate potential for coughs and sneezes, facilities might consider having healthcare personnel routinely wear eye protection for the care of residents with influenza.

    C) Residents with symptoms of acute respiratory illness who are determined to have neither SARS-CoV-2 infection nor influenza should be cared for using Standard Precautions and any additional Transmission-Based Precautions based on their suspected or confirmed diagnosis.8

  4. Clinical management9

    A) Prescribe antiviral treatment as soon as possible if influenza testing is positive OR prescribe empiric antiviral treatment based upon a clinical suspicion of influenza while test results are pending for symptomatic residents.9-12

    Antiviral treatment for influenza should be administered as soon as possible following clinical diagnosis.

    B) Properly manage residents with SARS-CoV-2 infection.

    Recommendations for treatment of persons with COVID-19 are available from the National Institutes of Health COVID-19 Treatment Guidelines Panel. Treatment should be administered as soon as possible for nursing home residents with mild-to-moderate COVID-19 because they are at high risk of progression to severe COVID-19.  See the latest recommendations on treatment of nonhospitalized persons with mild-to-moderate COVID-19, and Therapeutic Management of Nonhospitalized Adults With COVID-19. Medicare Monoclonal Antibody COVID-19 Infusion Program Instruction [1 MB, 4 Pages] is also available.

    C) 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.13

    D) SARS-CoV-2 post-exposure prophylaxis considerations

    For recommendations on post-exposure prophylaxis following close exposure to a person with SARS-CoV-2 infection, visit the latest recommendations from the NIH COVID-19 Treatment Guidelines Panel.

    E) Influenza antiviral chemoprophylaxis considerations.9-14

    The facility should promptly initiate antiviral chemoprophylaxis with oral oseltamivir to all exposed individuals (e.g., roommates) of residents with confirmed influenza. When at least 2 residents are ill within 72 hours of each other with laboratory-confirmed influenza, the facility should expand antiviral chemoprophylaxis to non-ill residents living on the same unit as the residents with influenza (outbreak affected units), regardless of influenza vaccination status.

    Persons receiving antiviral chemoprophylaxis who develop signs or symptoms should be tested (see above) and switched to antiviral treatment doses pending results.

    F) Encourage influenza vaccination for unvaccinated residents and HCP.

    For newly vaccinated individuals with exposure, antiviral chemoprophylaxis can be considered for up to 2 weeks following inactivated influenza vaccination until vaccine-induced immunity is acquired.

    G) Encourage residents and HCP to remain up to date with recommended COVID-19 vaccine doses.

    The facility should encourage all individuals to be up to date with all recommended COVID-19 vaccine doses, based upon the latest recommendations.


  1. CDC. Interim Infection Prevention and Control Recommendations for Healthcare Personnel During the COVID-19 Pandemic: https://www.cdc.gov/coronavirus/2019-ncov/hcp/infection-control-recommendations.html;
  2. CDC. Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens for COVID-19. https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html.
  3. CDC. Multiplex Assays Authorized for Simultaneous Detection of Influenza Viruses and SARS-CoV-2 by FDA Emergency Use Authorization. https://www.cdc.gov/flu/professionals/diagnosis/table-flu-covid19-detection.html
  4. FDA. Individual EUAs for Molecular Diagnostic Tests for SARS-CoV-2. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas#individual-molecular
  5. FDA. Individual EUAs for Antigen Diagnostic Tests for SARS-CoV-2. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas#individual-antigenhttps://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas#individual-antigenNote: Because antigen detection assays have lower sensitivity than nucleic acid detection assays, a negative result does not exclude SARS-CoV-2 infection and should be confirmed by nucleic acid detection assay.
  6. CDC. FDA-cleared Nucleic Acid Detection Based Tests for Influenza Viruses. https://www.cdc.gov/flu/professionals/diagnosis/table-nucleic-acid-detection.html
  7. CDC. Available FDA-Cleared Rapid Influenza Diagnostic Tests (Antigen Detection Only). https://www.cdc.gov/flu/professionals/diagnosis/table-ridt.html Note: Because rapid influenza antigen detection assays have lower sensitivity than molecular assays, a negative result does not exclude influenza virus infection.
  8. CDC. Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings (2007). Appendix A: https://www.cdc.gov/infectioncontrol/guidelines/isolation/appendix/type-duration-precautions.html
  9. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza. https://academic.oup.com/cid/article/68/6/895/5369363
  10. CDC. Influenza Antiviral Medications: Summary for Clinicians. https://www.cdc.gov/flu/professionals/antivirals/summary-clinicians.htm. Note: For non-high-risk persons who present within 2 days of onset of influenza-like illness (fever and either cough or sore throat), antiviral treatment of influenza can be prescribed based upon clinical judgement.
  11. CDC. People at High Risk for Flu Complications. https://www.cdc.gov/flu/highrisk/index.htm. For a list of People with Certain Medical Conditions who are at increased risk for severe illness from COVID-19, see: https://www.cdc.gov/coronavirus/2019-ncov/need-extra-precautions/people-with-medical-conditions.html
  12. NIH. COVID-19 Treatment Guidelines: Influenza and COVID-19. https://www.covid19treatmentguidelines.nih.gov/special-populations/influenza/
  13. 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. https://www.atsjournals.org/doi/10.1164/rccm.201908-1581ST
  14. CDC. Interim Guidance for Influenza Outbreak Management in Long-Term Care and Post-Acute Care Facilities. https://www.cdc.gov/flu/professionals/infectioncontrol/ltc-facility-guidance.htm