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Coronavirus Disease 2019

Testing & Isolation/Quarantine for Influenza in the Context of COVID-19: Principles & Framework for Skilled Nursing Facilities

Testing & Isolation/Quarantine for Influenza in the Context of COVID-19: Principles & Framework for Skilled Nursing Facilities


During the viral respiratory illness season that typically begins in late Fall and continues through early Spring, Facilities experience an increase in the number of residents experiencing respiratory symptoms. There are many viruses that can cause respiratory illness, but this season, both influenza and SARS-CoV-2 will most likely be associated with the greatest morbidity and are of highest concern in skilled nursing facilities (SNFs).

Optimal management of potential viral respiratory illnesses in SNFs will depend on many factors, such as detection of single or concurrent viruses and a Facility’s ability to separate persons with confirmed/suspected infection(s). It can be challenging to appropriately cohort symptomatic residents and their close contacts if private rooms are not available. Managing a resident who develops acute symptoms compatible with a viral respiratory illness can be further complicated if timely access to influenza and COVID-19 testing is not available. It is not possible to provide prescriptive or standard recommendations that can be applied across all settings. Therefore, Facilities must understand and adapt the principles and framework described in this document for testing and managing persons with an acute respiratory illness of suspected infectious etiology.

All outbreaks of respiratory illness are reportable to the Los Angeles County Department of Public Health (Public Health). Reporting will allow for assigning a public health team to provide consultation and tailored recommendations for outbreak management within the facility.

Testing Principles and Strategies

All LA County SNFs are required to conduct screening and response-driven testing for COVID-19. Information and guidance on testing for COVID-19 is available in the Public Health Guidelines for Preventing and Managing COVID-19 in SNFs. This document focuses on testing for influenza in SNFs in the context of the current COVID-19 pandemic.

Although influenza activity typically peaks on or after January in most seasons, it is possible to encounter local outbreaks early in the season. For that reason, starting in October, SNFs should test for influenza (in addition to COVID-19) in all residents and staff with acute respiratory symptoms. Promptly identifying influenza or COVID-19 will inform outbreak management decisions such as the appropriate isolation or cohorting of infected residents, quarantining exposed residents, and starting influenza antiviral therapy. If two or more residents are diagnosed with influenza, Facilities should consider adding regular influenza testing to ongoing COVID-19 screening or response-testing activities until no new cases of influenza are identified for 7 days.

Influenza Diagnostic Tests

A variety of influenza diagnostic tests are available. It is important to understand the limitations of influenza virus tests and how to properly interpret the results. There are two categories of diagnostic tests for the detection of influenza viruses in respiratory specimens:

  1. Molecular assays (including rapid molecular assays and reverse transcription polymerase chain reaction [RT-PCR]).
  2. Antigen detection tests (including rapid influenza diagnostic tests [RIDTs] and immunofluorescence assays).

CDC recommends using RT-PCR or other molecular assays for diagnostic testing in institutional outbreaks because of the low to moderate sensitivity of antigen detection assays. Antigen tests can result in false positives when the prevalence of circulating influenza viruses is low and false negatives when the prevalence is high.

Influenza Outbreak Management

Containing an influenza outbreak and mitigating morbidity depends on three key activities: 1) early identification of infected residents and staff, 2) early initiation of antiviral therapy for infected residents and chemoprophylaxis for exposed residents, and 3) optimal isolation of residents with suspected/confirmed influenza and quarantine of exposed persons.

Early identification of influenza

All SNFs should be conducting daily symptom screening of staff and residents as required for COVID-19 active surveillance. All residents with acute respiratory symptoms should be tested for COVID-19 and for influenza using a molecular test as described in the testing section above.

When there are confirmed influenza infections among two or more residents who are not roommates, consider also collecting specimens for influenza testing during the ongoing screening or response testing for COVID-19.

Early initiation of antiviral therapy

Any resident with influenza should be started on antiviral therapy. Influenza should be strongly suspected in a resident with acute respiratory symptoms if 1) there are other persons with confirmed influenza at the facility or 2) LA County influenza surveillance data indicate that >5% of respiratory specimens tested Countywide are positive for influenza. If influenza is suspected, then antiviral therapy should be started immediately while waiting for the test results, irrespective of vaccination history. Oseltamivir is the most commonly used antiviral medication, but other options include oral baloxavir, inhaled zanamivir, and intravenous peramivir. See CDC, Influenza Antiviral Medications for more information.

  • All of the roommates of a resident with confirmed influenza infection should be started on oseltamivir chemoprophylaxis.
  • If influenza infection is confirmed in a second resident who was not a roommate of the first case, antiviral chemoprophylaxis should be started for all residents in the outbreak-affected unit/wing regardless of vaccination history.
  • If there are cases in multiple units/wings, then chemoprophylaxis should be provided for all residents in the facility regardless of vaccination history.
  • Antiviral chemoprophylaxis can be considered for healthcare personnel if they are unvaccinated, if they received an inactivated influenza vaccine within 14 days prior, or if evidence indicates that the circulating influenza viruses are not well-matched to the seasonal influenza vaccine.
Optimal isolation of residents with suspected/confirmed influenza and quarantine of exposed persons

Appropriate isolation of residents with suspected/confirmed influenza and quarantine of exposed residents can be logistically challenging given the multiple permutations of residents who could have influenza, COVID-19, coinfection with both viruses, and/or infection with some other respiratory virus.

For confirmed cases of COVID-19 in residents, isolation in a physically separated Red Cohort is recommended; all residents on the unit or wing where COVID-19 was identified in a resident or healthcare worker should be considered exposed and remain in their current rooms unless sufficient private rooms are available. See Cohorting section of the SNF COVID-19 Guidelines for more information.

The guidance for isolation and quarantine for influenza differs from COVID-19 because there are interventions to mitigate influenza spread (vaccination and antiviral chemoprophylaxis) and the morbidity is lower for influenza than for COVID-19.

For confirmed cases of influenza in residents, unlike COVID-19, it is not necessary to dedicate a physically separated space for isolation. Facilities should consider isolating residents with confirmed influenza in a private room, if possible. However, if a private room is unavailable, then the resident with influenza and their roommates should remain in their current rooms. Ensure spatial separation of at least 6 feet and privacy curtain between residents. In facilities that do not have 6 feet of space between residents, separation should be as close to 6 feet as possible, but no less than 3 feet.

Symptomatic residents who are waiting for both COVID-19 and influenza testing results should be in quarantine in a private room in the Yellow Cohort, if possible. However, if a private room is unavailable, then the symptomatic resident and their roommates should remain in their current rooms with appropriate transmission based precautions as appropriate for the Yellow Cohort. Subsequent management will follow either the COVID-19 or influenza guidance as indicated by the testing results.

Avoid moving residents with suspected or confirmed influenza between COVID-19 cohorts.

Other Influenza Outbreak Control Measures
Managing Healthcare Personnel During an Influenza Outbreak

Facilities should encourage staff to get the influenza vaccine if they have not already received it. Influenza infected staff should be excluded from work for at least 7 days after symptom onset or >24 hours after fever resolution (without antipyretics) and improvement of respiratory symptoms. Staff should be offered antiviral therapy if indicated as described above.

Personal Protective Equipment (PPE)

In the context of the current COVID-19 pandemic, standard and droplet precautions are recommended for caring for all SNF residents, regardless of the presence of influenza. When caring for residents with a new acute respiratory illness, an N95 respirator should be worn until test results are returned and COVID-19 is excluded. See Infection Prevention and Control Considerations section of the SNF COVID-19 Guidelines for more information


If an influenza outbreak occurs in a facility without a COVID-19 outbreak, then non-essential visitation should be restricted. If the facility has a concurrent influenza and COVID-19 outbreak, then the facility should adhere to the visitation restrictions during a COVID-19 outbreak.

Concurrent COVID-19 and Influenza Outbreak Management

If there is a concurrent COVID-19 and influenza outbreak, then the Facility should prioritize implementing cohorting, PPE use, and other infection control precautions as recommended for COVID-19. If a resident is concurrently diagnosed with COVID-19 and influenza by molecular testing for both viruses, then the resident should ideally be placed in a private room in the COVID-19 Red Cohort. The rationale behind prioritization of cohorting of residents and staff by COVID-19 status over influenza status is that treatment is available for influenza and because the morbidity/mortality is lower for influenza compared with COVID-19.

Please refer to the Los Angeles County Department of Public Health Influenza Toolkit for additional information on managing influenza outbreaks in SNFs.

Influenza Vaccination

Facilities should ensure that all residents have received the influenza vaccine for the current season or have documentation indicating reason for declination. Facilities should establish policies and procedures to ensure that staff have received the influenza vaccine as outlined by the Health Officer Order. Vaccination is recommended to be offered by the end of October. Ensuring high facility-wide influenza vaccine coverage among residents and staff can substantially reduce the risk for experiencing an influenza outbreak.

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Public Health has made reasonable efforts to provide accurate translation. However, no computerized translation is perfect and is not intended to replace traditional translation methods. If questions arise concerning the accuracy of the information, please refer to the English edition of the website, which is the official version.

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