Influenza and COVID-19: antiviral windows and the AU general practice approach

What influenza and COVID-19 are, and why they matter together

Influenza and COVID-19 are both acute viral respiratory infections with overlapping presentations, similar at-risk populations, and parallel antiviral management pathways — making them natural companions for a single AU general practice reference.

Influenza is caused by orthomyxovirus types A (H1N1, H3N2 and other subtypes) and B. It produces a seasonal winter epidemic in Australia, accounting for approximately 3,000 deaths per year. H3N2 tends to cause more severe illness than H1N1.

COVID-19 is caused by SARS-CoV-2 (a betacoronavirus), which transitioned from pandemic to endemic. Omicron sub-lineages have dominated since 2022. Approximately 14,000 Australians died with COVID-19 between 2020 and 2024. Long COVID — symptoms persisting ≥3 months post-acute — affects an estimated 5–15% of infected individuals and represents a significant burden on Australian general practice.

RSV (respiratory syncytial virus) is an increasingly recognised co-pathogen in winter respiratory illness, particularly severe in infants and older adults. New RSV vaccines are now available in Australia.

Management of both influenza and COVID-19 rests on three clinical decisions: (1) symptomatic care for all; (2) antiviral therapy for eligible patients within the treatment window; and (3) vaccination as the primary prevention strategy.

A. Core clinical — the AU general-practice framework

Clinical features and differentiation

Typical influenza — abrupt onset with high fever, severe myalgia (“truck-hit” feeling), headache, dry cough, and marked fatigue lasting more than one week. GI symptoms occur but are less prominent in adults.

Typical COVID-19 — more variable; fever, cough, sore throat, headache, myalgia, and fatigue are common. Loss of smell and taste (anosmia/ageusia) was characteristic of earlier variants but is less specific with Omicron. GI symptoms, including diarrhoea, occur in a minority.

Clinical differentiation is unreliable. A combined respiratory PCR panel testing influenza A/B, COVID-19, and RSV is the definitive test when the result will change management.

History and assessment

Per eTG and the Department of Health annual influenza statement:

• Symptom onset, duration, and trajectory.
• High-risk status (see Section B below) — this drives the antiviral decision.
• Vaccination status — current influenza season, COVID-19 boosters per ATAGI.
• Medication history — especially for nirmatrelvir/ritonavir interaction assessment.
• Pregnancy status.
• Contact history — household, aged care, healthcare setting.
• Travel.

Investigations

Mild illness in low-risk adults: clinical diagnosis is sufficient; no tests required.

When testing changes management: combined respiratory PCR (influenza A/B + SARS-CoV-2 ± RSV) for high-risk patients, antiviral candidates, hospitalisation, or institutional outbreak management. COVID-19 RAT (over-the-counter) has ~70% sensitivity — acceptable for screening but PCR is preferred for antiviral candidacy decisions given false-negative risk.

Additional bloods for moderate-to-severe illness: FBC (MBS 65070), UEC (MBS 66500), CRP (MBS 66509), troponin if chest pain (myocarditis), D-dimer if VTE is in the differential, LFTs. Pulse oximetry for all moderate and high-risk presentations. CXR (MBS 58500 range) if pneumonia is suspected or oxygen saturation is below normal.

B. Evidence — antiviral windows and who benefits most

Influenza: oseltamivir within 48 hours

Per eTG, AMH, and ATAGI:

Oseltamivir (Tamiflu) 75 mg orally twice daily for 5 days for adults. Paediatric weight-based dosing: <15 kg = 30 mg twice daily; 15–23 kg = 45 mg twice daily; 23–40 kg = 60 mg twice daily; >40 kg = 75 mg twice daily. Renal dose adjustment required for eGFR <30.

The 48-hour window is critical. Starting within 48 hours of symptom onset provides the greatest reduction in severity, duration, and complications including hospitalisation. Starting later still offers modest benefit in hospitalised or severely ill patients.

PBS Authority Required (Streamlined) for high-risk patients meeting current season criteria — eligible groups include: age ≥65, age <5 years, ATSI people, pregnant women, people with chronic cardiac, respiratory, renal, liver, or neurological disease, BMI ≥40, immunocompromised, and residential aged care residents.

Alternative: zanamivir inhaler (bronchospasm risk — avoid in asthma/COPD unless no alternative). Baloxavir single dose is newer with some resistance concerns; not currently PBS-listed routinely in Australia.

COVID-19: nirmatrelvir/ritonavir within 5 days

Per Department of Health COVID-19 oral antivirals guidance and PBS Authority criteria:

Nirmatrelvir/ritonavir (Paxlovid) 300/100 mg orally twice daily for 5 days — within 5 days of symptom onset.

PBS Authority Required for: age ≥70; age ≥50 with additional risk factors; ATSI people aged ≥30; immunocompromised patients (including transplant recipients, haematological malignancy, on immunosuppressants, HIV with CD4 count <200). Verify current PBS criteria at every prescribing event — they are updated periodically.

Renal dose adjustment: eGFR 30–60 → reduce to 150/100 mg twice daily; eGFR <30 → avoid.

Drug interactions: ritonavir is a potent CYP3A4 inhibitor. Key interactions that require action before prescribing per the Liverpool COVID-19 Drug Interaction Checker:

• Statins: simvastatin and lovastatin — withhold for 5 days; atorvastatin — reduce dose significantly; rosuvastatin and pravastatin are the safer alternatives.
• Anticoagulants: warfarin — INR will rise significantly, increased monitoring required; DOACs (apixaban, rivaroxaban, dabigatran) — dose adjustments required; rivaroxaban is contraindicated at full anticoagulation doses.
• Immunosuppressants: tacrolimus, cyclosporin, sirolimus — levels rise dramatically; specialist input is essential and doses must be held.
• Calcium channel blockers, amiodarone, methadone, some antipsychotics, and opioids — require dose review.
• Contraindicated: rifampicin, St John’s wort (rapid ritonavir metabolism → antiviral failure), and high-dose rivaroxaban.

Pharmacist review of the full medication list before dispensing is strongly recommended and is standard of care.

Molnupiravir (Lagevrio) has been withdrawn from the PBS as of 2024. The PANORAMIC trial (Lancet 2023) showed no reduction in hospitalisation in a vaccinated population. Per TGA, molnupiravir should not be prescribed.

Vaccination: the most effective strategy

Per Australian Immunisation Handbook and ATAGI:

Influenza vaccine is reformulated annually. NIP-funded for: all people aged ≥65; all ATSI people ≥6 months; pregnant women; all children 6 months to <5 years; people with qualifying chronic medical conditions. All other individuals are encouraged to self-fund annual vaccination.

COVID-19 booster — ATAGI updates recommendations as new variant-adapted vaccines become available and as population immunity evolves. Check current ATAGI recommendations; NIP funding for eligible high-risk groups.

RSV vaccines — Abrysvo (for adults ≥60, and in pregnancy) and Arexvy (for adults ≥60) are TGA-approved and funded through the NIP for eligible older adults.

C. Long COVID and post-acute sequelae

Long COVID (also called post-acute sequelae of SARS-CoV-2, PASC) is defined by the National COVID-19 Clinical Evidence Taskforce Living Guidelines as symptoms persisting for ≥3 months post-acute infection that cannot be explained by an alternative diagnosis.

Common presentations in general practice: fatigue and post-exertional malaise (PEM), brain fog and cognitive difficulties, dyspnoea and breathlessness without identifiable structural lung cause, palpitations and dysautonomia (including POTS-like syndrome), sleep disturbance, anosmia and ageusia, and psychological symptoms including anxiety and depression.

The pacing principle. Unlike post-viral fatigue following other respiratory infections, long COVID with PEM follows a pattern similar to ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome): exertion beyond the patient’s energy envelope worsens and prolongs symptoms. Traditional graded exercise therapy (GET) can deteriorate patients with significant PEM. Pacing — working within the current energy envelope and gradually, carefully expanding it — is the recommended approach per the National COVID-19 Clinical Evidence Taskforce.

Multidisciplinary management:

• GP as coordinator and for investigation of treatable alternatives (TSH, iron studies, B12, FBC, cardiac screening, sleep study if indicated).
• Physiotherapy with energy conservation and pacing guidance.
• Occupational therapy for activity pacing and return-to-work planning.
• Psychology via a Mental Health Care Plan (MBS 2715/2717, up to 10 sessions/year under Better Access) for anxiety and depression that often co-occur.
• GPCCMP (MBS 965/967) for long COVID with comorbid chronic conditions — allows allied health referrals under the chronic condition management plan.

Post-COVID cardiovascular risk: thromboembolism risk is elevated 3–6 times in the acute illness period. VTE prophylaxis is not routinely indicated outpatient, but VTE should be considered in any patient presenting with breathlessness, chest pain, or leg swelling post-COVID.

D. Australian operations

Key MBS items:

• Standard GP consultations: items 23 (Level B), 36 (Level C), 44 (Level D).
• Telehealth: video and phone equivalents (existing-relationship 12-month rule — patient must have had face-to-face consult within 12 months).
• GPCCMP: MBS 965/967 for long COVID with chronic comorbidity — enables allied health referrals.
• Mental Health Care Plan: MBS 2700/2701 for long COVID psychological burden.
• Heart Health Check: MBS 699 for post-COVID cardiovascular risk reassessment.
• Pathology: combined respiratory PCR (influenza/COVID/RSV); FBC MBS 65070; UEC MBS 66500; CRP MBS 66509; troponin MBS 66512; D-dimer.
• CXR: MBS 58500 range.
• Vaccination: practice nurse items MBS 10987/10997; GP vaccination consultation.
• ATSI Health Assessment: MBS 715 (every 9 months).

PBS-listed antivirals:

• Oseltamivir (Tamiflu) — Authority Required (Streamlined) for high-risk influenza per current seasonal criteria.
• Zanamivir — Authority Required.
• Nirmatrelvir/ritonavir (Paxlovid) — Authority Required for high-risk COVID-19 per current criteria.
• Molnupiravir (Lagevrio) — withdrawn from PBS 2024; do not prescribe.
• Remdesivir — Section 100 Authority for hospitalised patients; specialist prescribing.

Notifiable diseases: both influenza and COVID-19 are notifiable in Australian jurisdictions. Aged care or hospital outbreaks require public health unit notification, PPE, isolation, and cohorting. Influenza outbreak in aged care or institutional setting may warrant oseltamivir chemoprophylaxis (75 mg daily for 7–10 days) for non-vaccinated or high-risk contacts — per state public health guidance.

E. Special populations

Pregnancy. Both influenza and COVID-19 carry elevated risk of severe maternal illness, preterm labour, and perinatal complications. Oseltamivir Category B1 — use in pregnancy is appropriate for high-risk illness; do not delay. Nirmatrelvir/ritonavir has limited pregnancy data; specialist input is appropriate but pregnancy itself qualifies as a high-risk condition for COVID-19 antivirals. Annual influenza vaccination and COVID-19 booster are strongly recommended throughout pregnancy.

Children. Oseltamivir is weight-based from 1 year of age. Nirmatrelvir/ritonavir is currently approved for patients aged ≥12 years (>40 kg) — check current PBS eligibility. Annual influenza vaccination from 6 months of age. Young children may present with febrile seizures in influenza; oseltamivir is appropriate for high-risk children and severe illness.

Older adults (≥65 years). Highest risk of severe influenza and COVID-19. Annual vaccination is a priority. Annual influenza vaccination reduces hospitalisation and all-cause mortality in this group. Antiviral threshold lower — treat promptly within the window. Drug interactions with Paxlovid are more common in this age group given polypharmacy.

Immunocompromised patients. Prolonged viral shedding, higher risk of severe disease, increased risk of complications including bacterial superinfection. Lower threshold for antiviral treatment — consider even if outside the typical window. Transplant recipients and those on immunosuppressants need specialist input before Paxlovid due to critical drug-drug interactions.

ATSI communities. Disproportionate burden of severe influenza and COVID-19. Targeted vaccination catch-up and outreach programs are a health equity priority. Lower age thresholds for antiviral eligibility apply (ATSI people ≥30 for Paxlovid).

When to escalate

Emergency department immediately for:

• Severe respiratory distress — respiratory rate >25, SpO₂ <92% on room air, accessory muscle use, cyanosis.
• Sepsis — fever with hypotension, tachycardia, altered mental state.
• Suspected secondary bacterial pneumonia — biphasic illness (improvement then worsening after day 3–5), productive cough, focal chest signs.
• Myocarditis — chest pain with elevated troponin, arrhythmia, haemodynamic compromise.
• MIS-C in children — post-COVID multi-system inflammatory syndrome with fever, abdominal pain, rash, and cardiac involvement.
• Thromboembolism — chest pain, leg swelling, or haemoptysis with risk factors post-COVID.
• Unable to maintain oral hydration, medications, or breathing.

Same-week: high-risk patients not improving on antivirals, long COVID requiring multidisciplinary assessment, significant comorbidity decompensation.

What this article is and is not

This is general health information drawn from current Australian general practice guidelines — Therapeutic Guidelines, ATAGI, Department of Health COVID-19 oral antivirals guidance, National COVID-19 Clinical Evidence Taskforce Living Guidelines, and AMH. It does not constitute personal medical advice and does not create a doctor–patient relationship. Antiviral prescribing decisions, including PBS eligibility and drug interaction review, are made with your own GP and pharmacist.

For Australian consumer resources: HealthDirect — Influenza, HealthDirect — COVID-19, HealthDirect — Long COVID, Better Health Channel — Influenza.

---

Sources cited

1. Department of Health — Annual influenza statement
2. Department of Health — COVID-19 oral antivirals
3. ATAGI
4. Australian Immunisation Handbook
5. Therapeutic Guidelines — eTG Antibiotic
6. Australian Medicines Handbook
7. National COVID-19 Clinical Evidence Taskforce — Living Guidelines
8. PANORAMIC trial — Lancet 2023
9. Liverpool COVID-19 Drug Interaction Checker
10. TGA — Molnupiravir cancellation
11. HealthDirect — Influenza
12. HealthDirect — COVID-19
13. Better Health Channel — Influenza
14. HealthDirect — Long COVID