Infectious Disease · Topic 9 of 10

Influenza, COVID-19 & Respiratory Viruses

Infectious disease · respiratory viruses

Influenza, COVID-19 & Respiratory Viruses

Test with PCR, isolate, and treat: oseltamivir for every hospitalized flu patient at any point; dexamethasone and remdesivir for hypoxemic COVID-19.

Key numbers

Dexamethasone 6 mg for hypoxemic COVID-19 only6 mg × 10 days

Remdesivir 5 days for hypoxemic inpatients5 days

Best within 48 hours — but inpatients always≤ 48 h best

Oseltamivir 75 mg twice daily75 mg BID

Influenza: droplet precautions for at least 7 days7 d or 24 h well

01 · DoOseltamivir for every hospitalized flu patient

Give oseltamivir as soon as possible to every hospitalized patient with suspected or confirmed influenza, regardless of how long symptoms have lasted — do not wait for laboratory confirmation.

02 · GiveDexamethasone 6 mg for hypoxemic COVID-19 only

COVID-19 with SpO₂ ≤ 94% on room air, supplemental oxygen or ventilation: dexamethasone 6 mg IV or PO daily for 10 days or until discharge. Do not give glucocorticoids to inpatients who need no oxygen.

03 · GiveRemdesivir 5 days for hypoxemic inpatients

Remdesivir for hospitalized COVID-19 with SpO₂ ≤ 94% or on oxygen: 200 mg IV on day 1, then 100 mg daily, 5 days total; not routinely started on invasive ventilation or ECMO.

Causes & risk factors

Why it happens

Older adults, pregnancy, chronic disease are high-riskInfluenza complications are most likely in adults over 65, children under 5, pregnancy (second and third trimesters), chronic medical disorders (cardiopulmonary, diabetes, renal, hepatic, immunodeficiency) and conditions that impair handling of respiratory secretions.

Diagnosis & monitoring

Work-up

Molecular (RT-PCR) testing on admission must knowDuring flu season, test every patient admitted with acute respiratory illness using RT-PCR or another molecular assay, not a rapid antigen test; in ventilated patients, test endotracheal aspirate or BAL fluid.

Do right now

In this order

First moves

Influenza: droplet precautions for at least 7 days7 d or 24 h well

→

Molecular (RT-PCR) testing on admission

→

Oseltamivir for every hospitalized flu patient

→

Dexamethasone 6 mg for hypoxemic COVID-19 only6 mg × 10 days

Why each step

Influenza: droplet precautions for at least 7 daysPlace inpatients with suspected or confirmed influenza on droplet precautions (facemask, private room when possible) for 7 days after onset or until 24 hours after fever and respiratory symptoms resolve, whichever is longer.

Molecular (RT-PCR) testing on admissionDuring flu season, test every patient admitted with acute respiratory illness using RT-PCR or another molecular assay, not a rapid antigen test; in ventilated patients, test endotracheal aspirate or BAL fluid.

Oseltamivir for every hospitalized flu patientGive oseltamivir as soon as possible to every hospitalized patient with suspected or confirmed influenza, regardless of how long symptoms have lasted — do not wait for laboratory confirmation.

Dexamethasone 6 mg for hypoxemic COVID-19 onlyCOVID-19 with SpO₂ ≤ 94% on room air, supplemental oxygen or ventilation: dexamethasone 6 mg IV or PO daily for 10 days or until discharge. Do not give glucocorticoids to inpatients who need no oxygen.

Management

Orders

Oseltamivir 75 mg twice dailyAdult oseltamivir is 75 mg orally or enterically twice daily (5 days for uncomplicated illness); reduce the dose for creatinine clearance 10–60 mL/min, and consider longer courses in severe illness or immunocompromise.

No baloxavir, zanamivir or peramivir routinely inpatientInhaled zanamivir, oral baloxavir and IV peramivir are not recommended routinely for hospitalized influenza, and neuraminidase inhibitors are never combined; single-dose baloxavir is an option for uncomplicated outpatients within 48 hours.

Progressing COVID-19: add tocilizumab or baricitinibAdd tocilizumab (IL-6 inhibitor) or baricitinib (JAK inhibitor) to dexamethasone for progressive severe or critical COVID-19 with elevated inflammatory markers such as CRP; sarilumab or tofacitinib are the alternatives.

COVID-19: contact and airborne precautions, eye protectionFor suspected or confirmed COVID-19, clinicians use standard, contact and airborne precautions (N95 respirator) with eye protection; airborne precautions matter most during aerosol-generating procedures.

Aerosol-generating procedures: N95 and airborne isolation roomDuring aerosol-generating procedures on a patient with influenza, wear a fitted N95 respirator, gown, gloves and eye protection, and use an airborne infection isolation room when feasible.

High-risk outpatient COVID: nirmatrelvir/ritonavir within 5 daysHigh-risk outpatients with mild to moderate COVID-19 within 5 days of onset: nirmatrelvir 300 mg/ritonavir 100 mg every 12 hours for 5 days (reduce if eGFR < 60), after a CYP3A interaction check; 3-day IV remdesivir is the alternative.

Red flags & don'ts

Avoid harm

Fever returning after improvement: bacterial pneumonia complicationSuspect secondary bacterial pneumonia when fever and cough persist or return after initial improvement; investigate and empirically treat bacterial coinfection in severe presentations or in patients who deteriorate on antivirals.

No adjunctive corticosteroids for influenza avoidDo not give corticosteroids as adjunctive treatment of influenza or influenza pneumonia unless they are indicated for another reason (eg, asthma or COPD exacerbation, septic shock).

The rules

Know these

Best within 48 hours — but inpatients alwaysAntiviral benefit is greatest when treatment starts within 48 hours of onset, but hospitalized patients and those with severe, complicated, progressive or high-risk illness are treated even after 48 hours.

Hospitalized with influenza or COVID-19?

Commonly confused

Antiviral	Oseltamivir for every inpatient, any day of illness
Corticosteroids	No (unless another indication)
Immunomodulator	None
Isolation	Droplet precautions (facemask)

More detail

Reference

Show 7 reference facts

Give pharmacologic VTE prophylaxis to hospitalized COVID-19 patients; therapeutic heparin may be considered for non-ICU patients on oxygen with elevated D-dimer and low bleeding risk, but not for critically ill patients.

In COVID-19 on mechanical ventilation or ECMO, continue dexamethasone and consider tocilizumab within 24 hours of ICU admission; remdesivir has not shown benefit at this stage.

Remdesivir is not recommended when eGFR is < 30 mL/min (monitor renal function), and IDSA lists elevated aminotransferases as a contraindication to remdesivir and IL-6 inhibitors.

SARS-CoV-2 PCR can stay positive for at least 3 months, yet replication-competent virus is rarely cultured after 10 days of illness — a persistent positive PCR does not by itself mean ongoing infectiousness.

When influenza and SARS-CoV-2 co-circulate, multiplex molecular assays that detect both viruses help direct antiviral therapy.

Molnupiravir is considered only when neither nirmatrelvir/ritonavir nor remdesivir can be used, with counseling about uncertain benefit; it is not used in pregnancy.

RSV and human metapneumovirus are treated supportively (oxygen, fluids); nebulized ribavirin is reserved for severely immunocompromised patients, such as stem cell transplant recipients.

Pearl

Flu in the hospital? Oseltamivir now — the 48-hour window is an outpatient rule.

Sources · CDC — Influenza Antiviral Medications: Summary for Clinicians (updated March 10, 2026) · Uyeki TM et al. Clinical Practice Guidelines by the IDSA: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza. Clin Infect Dis 2019;68(6):e1–e47 · IDSA Guidelines on the Treatment and Management of Patients with COVID-19 (living guideline; page published September 23, 2026) · Merck Manual Professional — COVID-19 · Merck Manual Professional — Influenza · CDC — Infection Control in Healthcare Settings: Seasonal Influenza (updated September 29, 2026) · Merck Manual Professional — Respiratory Syncytial Virus (RSV) and Human Metapneumovirus Infections · Starter sheet built from the verified AGACNP fact map (facts reviewed 2026-10-15).