Detecting multiple respiratory viruses with a single qRT-PCR assay

MARCH 11, 2022. Reviewed May 7, 2024

Why a negative COVID test result doesn't always give the full picture of viral infection.


As some of the symptoms of COVID-19 overlap with influenza and respiratory syncytial virus (RSV), a negative COVID test result doesn't always give the full picture of infection. Testing for multiple respiratory viruses in one simple qRT-PCR test could be the answer:

Why test for COVID, flu and RSV?

The similarity of the symptoms between COVID-19, flu and RSV like a cough, high temperature and a headache, means that symptoms alone cannot be used to diagnose the infection. As the risk profiles, treatments available and incubation and infectious timeframes are different for each viral infection, knowing which virus is present avoids misdiagnosis and inappropriate prescriptions (including antibiotics). It also allows hospitals and businesses where staff absences are disruptive, better assess risk of transmission.

This is especially important for businesses deemed critical (like defence or power companies) where having large numbers of staff off sick or isolating is disruptive for the community as well as the business itself. Or industries like film and sport where the absence of one individual has far reaching impact.

Seasonal fluctuations in respiratory infection

The incidence of infections caused by respiratory viruses tends to follow a cyclic pattern, characterized by high incidence during winter in temperate regions. This winter, measures put in place to reduce COVID-19 infections have also been effective at reducing the transmission of influenza viruses and RSV. Consequently, the number of cases of flu has not been as high as normal or expected.1

Although lockdowns and social distancing have kept respiratory viruses at bay this winter, there is concern that lack of exposure to them has reduced our natural immunity. In Scotland, it is thought this led to an unseasonably early surge in RSV cases in September 2021.2

As the weather warms up, public health guidance is changing; measures are being lifted and social mixing is increasing. Circulation of respiratory viruses is also likely to increase inevitably leading to increase in transmission, increase in cases and increase in the risk of co-infection (infection with more than one respiratory virus has been shown to be  associated with worse outcomes for severe COVID-19).3

This has ongoing implications not just for hospitals and healthcare providers but any businesses keen to protect their staff from infection, isolation and ill health and maintain business as normal.


Testing for multiple respiratory viruses

Since the start of the pandemic, tests for SARS-CoV-2, Influenza viruses and RSV have been carried out separately but as these tests use the same technique - qRT-PCR - combining them into one test makes sense. Laboratories currently offering COVID-19 testing can add influenza and RSV to their menu of services with minimal changes to their set up, saving time and money and conserving reagents that have been in short supply during the pandemic.

As seasonal virus testing evolves, the MHRA has outlined a desirability for COVID-19 tests to include targets for RSV and influenza and the CDC are recommending providers switch to combined testing.4

Protecting business and critical industries

During the pandemic, routine COVID-19 testing, and the isolation of COVID-19 cases kept many industries, including those deemed critical like defence and power companies, operational.

As daily life resumes, many companies whose business is heavily impacted by staff illness and absence, not only want to protect their employees and minimise business interruption from COVID-19 but from influenza and RSV too.