Tracking COVID-19: SA's sewage surveillance strategy

The Australian Water Quality Centre (AWQC) has rapidly developed and deployed a monitoring tool capable of detecting future outbreaks of COVID-19 using South Australia’s sewage.

The team of AWQC scientists developed a specialised molecular technique to identify the virus’s genetic signature — viral RNA — and established methodology to determine how much of it is present in sewage.

Low levels of RNA from SARS-CoV-2 were successfully detected in samples taken at the state’s major metropolitan and regional wastewater treatment plants earlier this year, when there was a greater number of active cases in the state.

Recent laboratory testing returned a positive result at two of SA Water’s treatment facilities, prompting the local health authority to deploy a mobile clinical testing unit to Angaston in the state’s Barossa region.

AWQC Senior Manager Water Expertise and Research Dr Daniel Hoefel said monitoring sewage provides a unique mechanism for public health clinicians to detect COVID-19 on an ongoing basis and build an even clearer picture of the virus in the community.

“Our cutting-edge laboratory is at the forefront of water quality science and the protection of public health, and our scientists share an abundance of experience which allowed them to quickly shift their focus and forge a new line of defence in the fight against COVID-19,” Dr Hoefel said.

“Detecting the virus in wastewater is more complex when compared to clinical samples such as a patient swab, as the number of virus particles present in a wastewater catchment consisting of 700,000 people are minuscule in comparison — particularly during a period of low case numbers.

“To use a familiar term, it’s like we’re looking for a tiny needle in a large haystack. However, our sophisticated monitoring tool is capable of detecting very low levels of this virus in sewage samples, down to as few as four individual virus particles with each typically around 0.1 µm in size.

“Working together with SA Health, we overlaid our wastewater treatment plant catchment areas with a heat map identifying infection ‘hotspots’ within the community to determine suitable sampling locations for affected communities, along with parts of the state where the virus was yet to be detected.

“We collected 500 mL samples using a combination of composite samplers and manual sampling over a 24-hour period to provide a snapshot of the wastewater’s content for the entire day.

“Sewage samples are concentrated in our purpose-built virus laboratory using centrifugation, before being filtered through a negatively charged membrane. Once the sample concentrate is processed, we’re able to extract all of the RNA present.

“Our team applies a specialised method, reverse transcription–polymerase chain reaction, to detect traces of the virus’s RNA, using two separate assays targeting two different parts of its genome for confidence in our detection results.

“With our monitoring tool active across multiple metropolitan and regional areas, we’ll keep a keen eye on South Australia’s sewage for any early warning signs of the virus re-emerging and continue to optimise our methodology.”

Weekly testing of untreated sewage is in place across metropolitan treatment plants, with testing of Mount Gambier’s sewage occurring twice a week due to an increased risk posed by the region’s border with Victoria.

Dr Hoefel said sewage surveillance ultimately enhances the state’s scientific prowess amid the pandemic.

“By combining the collective knowledge of South Australia’s water and public health experts, we’ve created a non-invasive community surveillance tool to supplement clinical testing,” Dr Hoefel said.

“Normally, developing a methodology such as this would require a year of research and testing. Our team of expert scientists have truly demonstrated their capabilities, overcoming several challenges to design a robust technique in less than 12 weeks.

“Through research and innovative thinking, we identified a method to concentrate the virus which differed to our method for standard gastroenteritis viruses and trialled multiple assays to avoid PCR inhibition, before finding a reliable commercial test kit.

“Our sampling and testing process is more complex than the equivalent for clinic testing; therefore, it was important to create several quality control steps and criteria for interpreting results to ensure accuracy.

“We’re already helping several laboratories across the country with monitoring programs given our expertise and success to date, by carrying out testing and sharing knowledge to improve method performance.

“Our work also forms part of a broader national initiative coordinated by Water Research Australia, championing the Australian water industry’s collaborative spirit to design a nationwide program supporting infection control strategies.

“During times of emergency, the water and health industry often goes above and beyond to protect the health of our communities and we’re proud to play a vital role in our state’s response to the pandemic.”

Image caption: AWQC conducts all of its testing and analytics for South Australia’s COVID-19 wastewater monitoring program at its Adelaide-based laboratories.