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By Mary-Lou Considine 4 September 2020 5 min read

Scientists now know that the genetic signature of SARS-CoV-2 – the virus that causes COVID-19 – can be detected in sewage samples.

In fact, sewage analysis can detect the virus’ presence in a population days before positive cases or clusters show up in results of public screening programs.

Sewage sampling can detect virus levels within a wastewater catchment, the rate of increase over time, whether the virus is mutating out from epicentres, or if new strains are being introduced from outside the catchment.

This timeline provides a guide to the COVID-19 sewage testing process.

Dr Paul Bertsch is a member of a joint CSIRO–University of Queensland team that’s been at the forefront of research into the use of wastewater surveillance for detecting SARS-CoV-2 in the population.

Here, he explains how the method works, and why it’s becoming a critical part of our public health response toolkit.

ECOS: Why sample raw sewage? And how do you detect coronavirus?

Paul Bertsch: We now know that people start shedding the virus in their faeces about two to three days after first being infected with SARS-CoV-2 – well before they show symptoms of COVID-19, if they notice any symptoms at all.

After it’s flushed into the sewerage system, the virus gradually disintegrates, leaving behind fragments of its unique RNA signature.

Our approach is like the one used in TV shows, where forensics teams use genetic ‘fingerprinting’ to solve crimes. The RNA encoded gene fragments we recover from sewage are the unique fingerprint of the SARS-CoV2 virus.

We use filtration techniques to separate out the nano-scale viral and gene fragments from untreated wastewater, then ‘amplify’ the fragments, enabling us to isolate and confirm the virus’s fingerprint over any other genetic material present in the sample.

The process is called reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

PCR is the molecular amplification or ‘molecular photocopying’ part – you make millions of copies of the gene fragments. The RT refers to reverse transcription, where you encode the virus’s single-strand RNA into complementary double-stranded DNA to produce the millions of copies of SARS-CoV-2 gene fragments. The amplified product is then sequenced to confirm it is the SARS-CoV-2 gene fragments.

RT-PCR is the standard way of testing for SARS-CoV-2, whether it involves samples of saliva, nasal mucus, or wastewater. So we’re simply applying a similar diagnostic testing approach used in individual testing to the collective SARS-CoV-2 ‘signature’ of entire communities.

Lead researcher Dr Warish Ahmed in the CSIRO laboratory where testing occurs.

Why has CSIRO’s Queensland study attracted attention?

The joint University of Queensland and CSIRO team produced the world’s first peer reviewed journal article documenting a proof-of-concept study on the use of wastewater analysis for detecting SARS-CoV-2 in the population.

The team sampled two wastewater treatment plants in the Brisbane region early in 2020, when Australia experienced its first wave of COVID-19. From the sampling, the team found the intensity of the SARS-CoV-2 signal in Brisbane’s wastewater was tracking clinical screening results in the community.

So the clinical testing results confirmed the wastewater methodology.

Is sampling wastewater for coronavirus safe?

Coronavirus is fragile and quickly rendered unviable, that is, not contagious, by detergents and the other surfactants in wastewater, and by typical water-treatment processes.

The UQ and CSIRO team members are trained to collect and analyse wastewater samples safely, using correct handling procedures and PPE equipment.

It’s also important to note that research to date suggests that drinking water is safe.

We constantly see news images of people being swabbed at testing points – isn’t clinical testing enough, in terms of tracing the virus’s spread through the community?

I should point out that wastewater sampling can’t replace individual sampling – it should be seen as complementary, providing unique information.

It’s not feasible for everyone in a community to be tested individually. Wastewater sampling is like an early warning system that covers an entire community. Especially in the early stages of COVID-19, many people will be asymptomatic. Some may never show symptoms and others may not want to be tested.

Researchers in the US recently did some modelling showing that up to 2.5 billion people globally could be monitored using wastewater surveillance, through regular sampling of 105,000 wastewater facilities.

The US study also suggested billions of dollars could be saved globally through reducing the need for individual testing and reducing the cost of across-the-board restrictions and economic shutdowns.

How accurate is wastewater sampling for coronavirus?

The US study estimated wastewater surveillance could detect one SARS-CoV-2 infection for every 100 people at the very least, in a monitored water-treatment catchment. At best, it could detect up to one infection per two million people.

The University of Arizona has used wastewater-based epidemiology at the individual dormitory level to manage the risk of COVID-19 among the returning student population. Early detection of SARS-CoV-2 in wastewater from one dormitory led to immediate individual testing of all 311 dormitory residents, with two asymptomatic students testing positive. These two were immediately isolated, preventing further spread of the virus and demonstrating the effectiveness of the approach.

Our own researchers have also confirmed that SARS-CoV-2 RNA seems to persist long enough in warmer conditions to permit detection – in other words, wastewater testing for the virus is reliable across a range of temperatures.

How long does it take to get a result?

SARS-CoV-2 can appear in faeces within two or three days of infection. Wastewater samples can be analysed within one to two days.

By contrast, it usually takes from five days to two weeks for people to develop symptoms severe enough for them to be tested.

In another recent study, our team was able to identify the most cost-effective and rapid sampling approach, which takes only 15–30 minutes per sample. We’re continuing to refine our sampling and analysis methods to improve their accuracy.

What about the future?

Some experts say we’re a long way from having a vaccine. So a national wastewater surveillance program or network could help Australian authorities detect and contain emerging COVID-19 clusters faster and more cost-effectively.

The technique can also be used to detect the virus in smaller populations, like aged-care facilities, schools and prisons, where COVID-19 prevention is particularly critical.

We recently demonstrated the effectiveness of on-board testing of wastewater on cruise ships for detecting SARS-CoV-2 before passengers disembark. This could play an important role in the resumption of cruises in future.

With biosecurity, nations tend to be reactive rather than proactive. Scientists, disease ecologists, and epidemiologists have been predicting the emergence of other pandemics following the SARS and MERS outbreaks earlier this century.

We need to prepare for future pandemics. The economics of permanent sewage surveillance stacks up – it costs very little in comparison to closing down entire economies.

As a leading public official in the US commented recently, if investing in sewage surveillance enabled his county to open even half a day earlier, it would be the best investment he ever made.

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