Department of Health

Testing for respiratory pathogens

Health advisory

Advisory number:
Date issued:
14 Jun 2022 - update to Advisory issued 15 June 2021
Issued by:
Associate Professor Deborah Friedman, Deputy Chief Health Officer (Communicable Disease)
Issued to:
General Practitioners, respiratory clinics and Primary Health Networks

Key messages

  • Rapid testing for respiratory pathogens is critical in identifying outbreaks in the community and providing timely medical care, particularly for people at high risk of severe illness.
  • Many respiratory pathogens can cause similar symptoms early in the course of an illness. 
  • Distinguishing between influenza, COVID-19 and other respiratory pathogens is particularly important in people at high-risk of severe illness as the treatments and public health measures differ.
  • Rates of seasonal influenza and other respiratory illnesses are increasing in Victoria. 
  • In people at high-risk of severe illness presenting with respiratory illness, clinicians are asked to request a respiratory virus PCR panel, which includes influenza and respiratory syncytial virus (RSV) in addition to COVID-19. 
  • Clinicians are encouraged to provide influenza and COVID-19 vaccination to all eligible Victorians, and particularly to those at high-risk.

What is the issue?

Influenza has been steadily increasing within Victoria in 2022, with the population being largely highly susceptible given low numbers of infections over the past 2 years. There have been 23,221 cases of influenza notified this year. This compares with 64 cases at the same time in 2021, 4,576 in 2020 and 18,548 in 2019. Co-infections with COVID-19 are also increasing.

Other respiratory pathogens, such as respiratory syncytial virus (RSV), are also increasing, following lower than usual notifications throughout 2021.

Many people are only being tested for COVID-19 but may be infected with other respiratory pathogens that are spreading throughout the community. People may be infectious in the day before they develop symptoms, and depending on the severity of infection, they may remain infectious for up to a week after symptoms develop.

Specific antiviral therapy is available for influenza to reduce severe illness.

Who is at risk?

The very young, very old and people with other medical conditions are those most at risk of complications from respiratory infections, but people of all ages can become seriously ill.

People at high risk of severe illness from influenza and COVID-19, include:

  • People aged 65 years and over
  • Comorbidities at any age, including
    • Heart disease
    • Obesity
    • Chronic respiratory conditions
    • Severe neurological conditions
    • Neurodevelopmental disorders
    • Immune compromise
    • Cancer
    • Diabetes requiring medication
    • Chronic liver disease
    • Chronic kidney disease
  • Children aged 5 years and under
  • Pregnant women
  • Aboriginal and Torres Strait Islander people aged 50 years and over
  • People with disabilities with frailty or comorbidities

Recommendations for clinicians 

  • People at high risk of severe illness presenting with respiratory symptoms or influenza-like illness should be tested via a respiratory virus PCR panel. At a minimum, testing for both COVID-19 and influenza should be performed.
  • Influenza antiviral therapy should be prescribed for people at high-risk presenting with influenza-like illness, if clinically indicated, while awaiting the results of PCR testing and ceased if influenza results return negative. 
  • COVID-19 antiviral therapy can be prescribed for patients with positive COVID-19 results on rapid antigen test or PCR, if clinically indicated.
  • Advise people with mild to moderate respiratory symptoms who are not at risk of severe illness to isolate until their symptoms resolve and consider using a rapid antigen test for COVID-19.
  • Remind people of the importance of practicing good hygiene to reduce the spread of respiratory viruses including coughing or sneezing into elbows, thorough, regular hand washing, and wearing face masks in crowded indoor spaces and high-risk settings such as hospitals and aged care facilities.
  • Encourage influenza and COVID-19 vaccination to all eligible people.

The Influenza and COVID-19 vaccinations are safe to co-administer. 

Influenza vaccination is currently free for all Victorians until 30 June 2022. After this date, it will remain free for children aged 6 months to under 5 years, people over 65 years, pregnant women, or those with underlying medical conditions.

Reviewed 15 June 2022


Contact details

Communicable Disease Prevention and Control Department of Health

Was this page helpful?