Respiratory Virus Testing and Treatment for Healthcare Professionals

While respiratory infections have unique characteristics, it is often difficult to identify respiratory viruses based on symptoms alone. Only testing for these viruses can confirm the diagnosis. In patients with signs and symptoms of respiratory virus illness, especially those that are at risk for severe disease, act fast to test for flu, RSV, and COVID-19 and discuss treatment options.

Clinician Alert: Severe Influenza Complications Reported This Season

CDPH has received recent reports of patients with influenza and severe and fatal methicillin-resistant Staphylococcus aureus (MRSA) pneumonia, acute respiratory distress syndrome (ARDS) and/or myocarditis/pericarditis. Community-associated (CA) MRSA strains often carry the gene for the Panton-Valentine leukocidin (PVL) toxin. The PVL toxin is associated with increased S. aureus virulence and causes leukocyte destruction and necrotizing pneumonia, an aggressive and often fatal condition.
Clinicians should consider the possibility of MRSA in influenza patients with necrotizing or severe pneumonia. Antibiotic coverage should either include vancomycin or linezolid. Linezolid may be preferred because of additional activity as a toxin inhibitor. Also, vancomycin monotherapy may be insufficient to treat critically ill children with influenza and invasive MRSA.
To assist us in better understanding the epidemiology of this condition, clinicians are encouraged to report such cases to the local health department of the patient’s residence and to retain S. aureus isolates from such patients for possible characterization.
Methicillin-sensitive Staphylococcus aureus (MSSA) as well as group A Streptococcus invasive co-infection with influenza can also result in fulminant/severe/fatal illness, and Streptococcus pneumoniae invasive co-infection may be more common than either MSSA/MRSA/GAS with influenza. Influenza without invasive bacterial co-infection can also result in severe/critical illness.
For information and testing and antiviral treatment for influenza, please see the January 5 health advisory. It's not too late to encourage unvaccinated patients aged 6 months and older, especially those at increased risk for influenza complications, to get influenza vaccination now.

Testing

Because respiratory symptoms can indicate multiple viral and bacterial etiologies, diagnostic testing for respiratory pathogens can guide clinical management, antimicrobial treatment when appropriate, and infection prevention and control measures.

Clinical testing when multiple respiratory viruses are co-circulating

While COVID-19 is common during the summer and winter months, influenza and RSV activity typically starts increasing in the fall and peaks during winter months. When respiratory viruses are co-circulating, clinicians should test using multiplex panels for influenza, RSV, and COVID-19. If patients test negative for influenza, RSV, and COVID-19, additional testing with a respiratory pathogen panel can be performed if clinically indicated.

Rapid molecular tests are recommended over rapid antigen tests due to their higher sensitivities to detect respiratory viruses. However, rapid antigen tests for influenza and COVID-19 are FDA approved and available for over-the-counter purchase. Rapid antigen tests can be used if molecular testing is unavailable. A positive result from an at-home antigen test is likely to be a true positive. If negative, consider in-clinic testing if indicated. Patients reporting influenza A positive results from at-home tests who are severely ill (hospitalized/ICU) should be re-tested with an influenza rRT-PCR test and influenza A positive samples should be sent for subtyping.

In addition, influenza testing by rRT-PCR should be encouraged in situations where sequencing or subtyping may be needed, including:

Severe cases, such as hospitalized, intensive care unit (ICU), and/or fatal cases.
Acute respiratory illness outbreaks of public health concern.
Persons with recent close contact or exposures within 10 days of symptom onset that are concerning for avian, variant, or novel influenza infection (e.g., variant influenza A (H3N2)v, (H1N2)v, or (H1N1)v, or avian influenza H5N1 or H7N9).

For more information, see the October 14, 2025 CDPH Health Advisory:
Administer Immunizations in Preparation for Respiratory Virus Season (Influenza, RSV, and COVID-19)

Treatment

Influenza and COVID-19 antiviral treatment can decrease the risk of serious illness and hospitalization in those at higher risk for severe disease. The greatest benefits are observed when starting antivirals as soon as possible. Pre-exposure prophylaxis (prevention) medication is also available for some people who are moderately or severely immunocompromised and at risk of transmission. For disease specific information, please see the following on Influenza, COVID-19, and RSV:

Influenza:

Antiviral medications can be used to treat influenza, and some can be used to prevent influenza. Influenza antivirals are recommended in hospitalized patients, patients at higher risk for severe disease, and patients who may transmit the virus to high-risk contacts. Evaluate and treat eligible symptomatic patients as soon as possible (ideally at the point of care and within the first 24 hours). Starting antiviral treatment within 12 hours of symptom onset can shorten illness by approximately 3 days compared to starting treatment at 36-48 hours.
There are currently four FDA-approved influenza antivirals recommended, which are: oseltamivir phosphate (available orally as a generic version or under the trade name Tamiflu®), zanamivir (available inhaled, trade name Relenza®), peramivir (available IV, trade name Rapivab®), and baloxavir marboxil (available orally, trade name Xofluza®).
Do not delay treatment while waiting for test results if influenza is suspected. Treat immediately with oseltamivir or single-dose baloxavir based on recommendations for use; consider in-clinic administration where possible.
See the Don't Delay, Start Antiviral for Suspected Influenza Immediately in Outpatients clinical flow chart below when to start oseltamivir or baloxavir antivirals for suspected or confirmed influenza cases in the outpatient setting, which includes guidance to treat:

Outpatients with increased risk for severe disease: oseltamivir* or baloxavir^†, as soon as possible and within 48 hours of symptom onset
Patients with progressive or severe disease (such as pneumonia or exacerbation of chronic underlying medical conditions): oseltamivir, regardless of time since onset
Hospitalized patients: oseltamivir, as soon as possible

In addition, providers should consider additional preventative therapeutics in higher-risk patients for seasonal influenza pre-exposure (PrEP) and post-exposure (PEP) prophylaxis for influenza in institutional and household contacts who are at higher risk of severe infection.

For more information, see:

*Initial doses of oseltamivir may cause nausea and/or emesis. Administer with food if possible.
†Clinical trials demonstrated that one dose of baloxavir is effective at reducing influenza hospitalization risk, symptom duration, hospitalization duration, and household transmission. Baloxavir has fewer side effects than oseltamivir, which is taken twice a day for 5 days, and greater clinical efficacy in influenza B illness. While the upfront cost of baloxavir is higher than that of oseltamivir, modeling studies indicate that it is cost-effective compared with oseltamivir. However, baloxavir has been associated with treatment-emergent antiviral resistance. In addition, baloxavir is not recommended for those under 5 years of age, pregnant or ≤2 week postpartum individuals, breast-feeding individuals, immunocompromised patients, or hospitalized or severe cases; oseltamivir is first line treatment in such patients.

Don't Delay, Start Antiviral for Suspected Influenza Immediately in Outpatients

Chart with timeline of when to start antiviral treatment

COVID-19:

In individuals who are at high risk for severe disease, prescription COVID-19 antiviral treatment can prevent serious illness, including hospitalization and death.

There are three FDA-approved antivirals for COVID-19 in outpatient settings, which are nirmatrelvir-ritonavir (available orally, trade name Paxlovid), Remdesivir (available IV, trade name Veklury), and Molnupiravir (available orally, trade name Lagrevio).

CDPH recommends that providers prescribe nirmatrelvir/ritonavir (Paxlovid) to non-hospitalized, symptomatic, and eligible patients.

Remdesivir (Veklury) should be considered when nirmatrelvir/ritonavir (Paxlovid) is clinically contraindicated, and molnupiravir (Lagevrio) may be considered if remdesivir is impractical and Paxlovid is clinically contraindicated.
In addition, providers should consider additional preventative therapeutics in higher-risk patients, such as pemivibart (Pemgarda) for COVID-19 prevention, an authorized monoclonal antibody for pre-exposure prophylaxis (PrEP) in moderately-to-severely immunocompromised individuals who may not mount an adequate immune response to COVID-19 vaccination. PrEP with Pemgarda is not a substitute for vaccination and all individuals who can receive vaccination should do so.

For more information, including information on treatment in inpatient settings, see:

RSV:

While there is no specific treatment for RSV, there are various therapeutics for RSV prevention, especially in infants and young children, pregnant people, and older adults. For more information, see CDPH's Immunization Recommendations for RSV.

Cost and coverage

For patients without insurance or those whose insurance plan does not cover the cost of antivirals for influenza or COVID-19, there may be patient assistance programs, discount programs, and other plans to help support access to medications at low cost or no cost.

Offer your patients support programs for covering costs of treatment:

For influenza:

GSK Patient Assistance Program - for zanamivir (Relenza)

For RSV:

For more information on RSV, see CDC's Clinical Overview of RSV.

For COVID-19:

In addition to vaccination, testing, and treatment, talk to your patients about respiratory virus season and advise patients to continue to follow the additional core prevention strategies found at CDPH's Respiratory Viruses Hub for the public.

For more information on infection control and prevention in various healthcare settings and return to work guidance for healthcare personnel, see: