Sewage testing through the water flushed down our toilets can help track the spread of SARS-CoV-2, the virus causing COVID-19.
A wastewater plant for sewage testing

Sewage testing can help us track the spread of SARS-CoV-2. But how does it work? Dr Paul Bertsch answers some questions.

Who would have thought the water flushed down our toilets can help track the spread of the virus that causes COVID-19? Sewage testing is proving to be a quick and early way to identify infection hotspots in communities around Australia and the world.

So, how does it work? And why is it becoming a critical part of our public health response toolkit?

Dr Paul Bertsch is part of a joint CSIRO and The University of Queensland (UQ) team at the forefront of the research.

He answers the top questions about how testing our sewage water can help track the spread of the virus.

1. Why sample raw sewage?

Scientists have found the genetic signature of SARS-CoV-2, the virus that causes COVID-19, can be detected in sewage water. This is because infected people shed virus fragments when washing and toileting.

In fact, sewage analysis can detect the virus in a population days before it shows up in individual screening programs. Additionally, it can detect levels of the virus within a wastewater catchment, and how levels may change over time.

2. How do you detect the virus?

People start shedding the virus in their faeces about two to three days after first being infected. And this is 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. It leaves behind fragments of its unique genetic signature, or RNA.

The gene fragments we recover from sewage are the unique fingerprint of the SARS-CoV-2 virus. In other words, it’s like in TV shows where forensics teams use genetic ‘fingerprinting’ to solve crimes.

In a lab, the nano-scale fragments are filtered from untreated wastewater and amplified. Consequently, this enables researchers to isolate and confirm the virus’s fingerprint.

3. Is sampling wastewater for COVID-19 safe?

A man smiling at the camera. He is leading the sewage testing team.

Dr Paul Bertsch is part of a joint CSIRO–University of Queensland team looking at sewage testing.

The coronavirus is fragile. And just like washing our hands, it’s broken down by all the detergents in wastewater and through the wastewater treatment process. Therefore, the good news is that while it may no longer be infectious, it can still be detected.

Drinking water is safe as it’s treated before it reaches your tap. So there is no risk in watering your garden or swimming.

4. Isn’t clinical testing enough?

Wastewater sampling can’t replace individual sampling. However, it provides complementary information about what’s happening at a larger scale.

Additionally, it’s not feasible to test everyone in a community individually through clinical testing. For example, recent US research found that up to 2.5 billion people globally could be monitored using wastewater surveillance. It estimated billions of dollars in global savings by less need for individual testing. And a lower cost from restrictions and economic shutdown.

5. How effective is sewage sampling for COVID-19?

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

Here’s one example. The University of Arizona has used wastewater-based testing to manage COVID-19 infection risks to returning students in one dormitory. Early detection of the virus in the dormitory’s wastewater led to immediate individual testing of all 311 dormitory residents. As a result, two students, who hadn’t shown symptoms, tested positive. The staff then immediately isolated the students, stopping further virus spread.

6. How long does it take to get a result?

SARS-CoV-2 can appear in faeces within two or three days of infection. Scientists can analyse wastewater samples 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.

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7. What are we working on?

Our joint team with UQ has produced the world’s first peer-reviewed journal article documenting a proof-of-concept study on using wastewater to detect SARS-CoV-2 in the population.

The team sampled two Brisbane wastewater treatment plants in early 2020, during Australia’s first COVID-19 wave. Their results aligned with the numbers captured through individual clinical testing. As a result, this confirmed the accuracy of the sewage testing methods.

A pilot research program testing sewage for traces of COVID-19 began sampling at several locations across Queensland in mid-July. This is a joint project with Queensland Health, UQ and us.

8. What about the future of sewage testing?

As we think about opening up economies, sewage surveillance can help authorities detect and contain emerging COVID-19 clusters faster and more cost-effectively.

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

We’ve also demonstrated the effectiveness of on-board testing of wastewater on cruise ships before passengers disembark. Consequently, this could play an important role in the resumption of cruises in future.

Ultimately, with scientists predicting the emergence of future pandemics, the economics of permanent sewage surveillance stacks up.

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.


  1. I can’t imagine this is actually even possible, whatever they claim.
    Imagine the amount of sewage, the huge amount of genetic matter or other proteins in there, and the tiny tiny bits therein potentially belonging to someone’s faeces of which a tiny tiny, even tinier amount might be the fingerprint of a particular virus, even if there is a great number of infected persons who have defecated in this water at roughly the same point in time via the same sewage pipe. Those detectable proteins are likely not evenly diluted but rather local to a portion of the water, which is constantly turned over in huge quantities and therefore not a stable testing medium. It is not like the parts that lab technicians are searching for can be easily extracted or filtered out, like metal with a strong magnet is extracted from rubbish on a conveyor belt. Not at all the same, and any attempt to claim otherwise is BS.
    In order to find a certain fraction of a protein which could stem from a known virus in mega- or gigalitres of waste water, you would either have to run every little droplet through the PCR detection method, which is not feasible, or you would have to know the exact drop that contains it before you test, which is also not possible.
    I am not a conspiracy theorist, but I truly believe that usually big money dictates what humans say or do, or falsely claim. There’s obviously huge business potential brought about by this pandemic, and among the greatest beneficiaries are pharmaceutical concerns and the scientists whose work gets funded by them, as well as investors, and obviously people who claim they can simply find the virus in waste water also want a piece of this pie. It is literally like trying to find a specific drop in the ocean, but think how easily the results could be faked.

    1. I agree, having worked in Local Gov, the sewerage wastewater treatment plant primary claifyers contain around 2 million litres of untreated sewerage. I find it hard to believe how the labs in these plants can detect such miniscule fragments, however if it so, I would like to know how.

  2. Yes, re those of us who are fully vaccinated – does either the Astra Zeneca or Pfizer vaccines process through the body and into faeces and, can their resulting spike protein be differentiated from actual alpha or delta variants of the sars-cov-2 or covid-19 virus?

  3. At worst 1 in 100, at best 1 in 1M seems quite a large spread. If the data in the initial wave was accurate, why the huge uncertainty of its effectiveness? I’m interested in how many rna fragments are created from one infected person and then how many rna fragments are needed per litre of waste water to provide an accurate positive result? The other question I have is how you separate one infection from another? How are the case numbers determined?

  4. Would vaccinations give a misleading reading in the sewage?.

    1. Hi David,

      Someone who has been vaccinated and has not had COVID-19 will not show a positive signal in wastewater testing.

      Team CSIRO

  5. Given covid is in animals and their wast can get into sewage waste can you tell the difference

    1. Hi David, thanks for your question. The reports of animals contracting COVID-19 while few, several have been confirmed. So it is possible but highly improbable since most animal excrement is not discharged into wastewater systems.

      Team CSIRO

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