Department of Health

Testing for respiratory pathogens

Health advisory

Advisory number:
Date issued:
14 Jun 2021
Issued by:
Adjunct Clinical Professor Brett Sutton, Chief Health Officer
Issued to:
General practitioners and laboratories

Key messages

  • Rapid testing for respiratory pathogens is critical in identifying outbreaks in the community, particularly in vulnerable groups and settings such as aged care.
  • Many respiratory pathogens can cause similar symptoms early in the course of an illness but may require different public health and infection control measures once identified by laboratory testing.
  • Distinguishing between influenza, COVID-19 and other respiratory pathogens is particularly important in vulnerable groups such as aged care residents.
  • Although rates of seasonal influenza are currently low, there are a range of other respiratory pathogens circulating.
  • Many laboratories can perform multiplex assays on symptomatic patients which will identify influenza and respiratory syncytial virus (RSV) in addition to COVID-19. 
  • Clinicians are specifically requested to add influenza testing to patients in whom COVID-19 tests are also being performed in the aged care setting.
  • Clinicians are encouraged to provide influenza vaccination to vulnerable patients and populations, including aged care residents and staff.

What is the issue?

Although local and international rates of influenza are currently low, there have been influenza cases detected in recently returned overseas travellers.

Low numbers of influenza infections in 2020 have led to a potentially highly susceptible population.

There were increased numbers of emergency department presentations and hospital admissions due to RSV in the first few months of 2021. 

Many people are only being tested for COVID-19 but may be infected with other respiratory pathogens. They may be unknowingly spreading these infections throughout the community, so testing for these pathogens is a vital step in outbreak control.

Who is at risk?

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


Respiratory viruses are usually spread by droplets when an infectious person coughs or sneezes.

They may be spread through touching surfaces when the infected droplets have landed.

The incubation period for many respiratory infections may be up to five days.

As with COVID-19, people may be infectious in the day before they develop symptoms, and depending on severity of infection, they may remain infectious for up to a week after symptoms develop.


  • Consider testing for other respiratory pathogens in addition to COVID-19 in persons who present with respiratory illness.
  • Advise people with respiratory symptoms to isolate, even if their COVID-19 test result is negative.
  • Remind people of the importance of practicing good hygiene to reduce spread of respiratory viruses including coughing or sneezing into elbows, and thorough, regular hand washing.
  • Encourage influenza vaccination.

Note: There should be at least 7 days between doses of influenza and COVID-19 vaccination. Influenza vaccination is free for children aged 6 months to under 5 years, people over 65 years, pregnant women, or those with underlying medical conditions.

More information

Clinical information

Department of Health: Croup or bronchiolitis

Consumer information

Better Health Channel: Flu (influenza)

FluTracking is an online surveillance system monitoring influenza-like illness in the community. Find out more and register.


For more information please contact the Communicable Disease Prevention and Control section at the Department of Health on 1300 651 160 (24 hours). 

Reviewed 15 June 2021


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