Nationwide survey of testing practices for respiratory viruses in Australia in the post COVID-19 pandemic era

Abstract

Background
In the wake of the coronavirus disease 2019 (COVID-19) pandemic, there have been dramatic changes in the testing protocols for respiratory illness. Laboratory identification of respiratory pathogens causing clinical symptoms has become more important in the post-COVID-19 era, both for epidemiological and clinical reasons. This is particularly the case for respiratory syncytial virus (RSV) where a number of preventatives are at the point of clinical translation. The laboratory diagnosis is one of the critical elements in understanding the disease burden of respiratory pathogens and the effectiveness of preventatives. The aims of this study were to understand current laboratory testing and reporting practices across Australia.

Methods
We undertook a cross-sectional survey of Australian NATA (National Association of Testing Authorities) accredited laboratories to collect data on patterns of laboratory testing, the methods used and their reporting processes. The survey asked participants to report on testing of respiratory samples for 2022 as well as current respiratory multiplex testing in 2023.

Outcomes
In total, 45 out of 193 eligible laboratories (23%) completed the online survey. The majority of laboratories were from Victoria and New South Wales (31% and 27%, respectively) and most were hospital-based clinical diagnostic laboratories. Overall, 40% of responding laboratories (18/44) reported that > 80% of all tests in the molecular laboratory in 2023 were respiratory multiplex. Influenza viruses, RSV and SARS-CoV-2 were tested most frequently on respiratory multiplex PCR panels. RSV typing (RSV A or RSV B) was included in under a quarter of panels (9/43; 21%), compared to almost two-thirds for influenza typing (influenza A or influenza B: 29/44; 66%). There was considerable variability in testing platforms used, with thirty-seven laboratories using 87 different platforms (18 unique platforms). GeneXpert® (Cepheid) was the most commonly used platform; with a higher concentration of this instrument in laboratories from the eastern states (New South Wales, Queensland, Victoria). Forty percent of laboratories reported changes to respiratory testing procedures/panels in 2023 compared to the previous year. Laboratories were most likely to report results directly to the referring doctor (96–100%) followed by notifying their jurisdictional Department of Health.