Updated: 10 February 2022
International borders are reopening. Active COVID-19 cases in the Australian community were moving towards half a million in early-2022. So, is wastewater testing still useful?
Actually, with the emergence of new variants, surveillance of our wastewater is more important than ever.
Early detection
It's a tough job predicting when case numbers will peak. Research from around the world shows most wastewater surveillance systems provide an early heads-up. These systems enable detection before the peak is observed through clinical testing in the community.
Our Land and Water Science Director, Dr Paul Bertsch, says this data provides additional information to assist health professionals.
And when it comes to better understanding the rise of variants, our studies of aircraft wastewater play an important role.
Omicron variant and Australia
Our researchers were the first in the world to detect the Omicron variant in aircraft wastewater. This was from a flight arriving to Darwin from Johannesburg, South Africa, on 25 November 2021.
This achievement was a team effort involving a collaboration with Qantas, The University of Queensland, Queensland Health, gene sequencing technology company MGI, as well as international collaborators from USA and Canada.
Northern Territory Health later confirmed there was one passenger onboard the flight who was infected with the Omicron variant. This was confirmed by a nasal swab.
Our team detected and confirmed this single Omicron infection via aircraft wastewater. This bolsters the important role aircraft wastewater can play as an independent and non-intrusive surveillance point for infectious diseases, particularly coronavirus.
This latest study was published recently in Science of the Total Environment journal. It follows our work testing wastewater samples from repatriation flights from COVID-19 hotspots last year.
We spoke with the lead author, our researcher Dr Warish Ahmed, about the importance of wastewater testing.
With so much COVID-19 in the community, is wastewater testing still useful?
From a scientific perspective, wastewater testing is more useful than ever. Around the world, 24 studies found the peak of COVID-19 signals for multiple waves and variants in wastewater precedes peaks in clinical testing numbers by 10 or more days.
A comprehensive wastewater monitoring program in Sweden has demonstrated the observed peak in SARS-CoV-2 in wastewater precedes hospitalisations by 19-21 days.
When levels of testing in a community are low, wastewater can provide a clearer picture of the spread of COVID-19.
Why is testing for COVID-19 variants important?
About 50 per cent of the global population is still not vaccinated against COVID-19. New variants are likely to emerge.
As borders open internationally, Australia needs an early alert to potential new variants coming into the country.
Why is the ability to detect COVID-19 variants in plane wastewater important?
The surveillance of wastewater from passenger aircraft can afford an efficient means of monitoring variants. Especially in the context of emerging variants.
Early in the pandemic, SARS-CoV-2 RNA was successfully detected in wastewater from passenger aircraft following international flights.
More recently, aircraft wastewater surveillance demonstrated 83.7 per cent accuracy in detecting SARS-CoV-2 infections among passengers of international flights. All of these passengers tested negative for COVID-19 prior to boarding.
Why test the wastewater directly off the plane?
This method enables us to collect samples at the point of entry into Australia.
Results come back within four to 24 hours. With faster analysis methods, results could come back within one or two hours. We currently testing these fast methods for deployment at airports.
This will indicate which planes were positive for SARS-CoV-2 genetic fragments at the same time as passengers are entering quarantine or not.
If they do not need to quarantine, a simple text message can be sent to them by alerting aircraft wastewater was positive and ask them to get tested if symptoms appear. The method is also non-intrusive. It doesn’t require samples to be provided by individuals.
Most passengers who use the lavatory can be screened using a single aggregated wastewater sample. There is also very little ‘flush water’ in a plane lavatory. Therefore, the signal is less diluted than in a large quarantine facility.
How can this help us control infection from overseas travellers?
Infected people shed SARS-CoV-2 two to five days before they show symptoms. Therefore, wastewater analysis gives an early heads-up that someone on the arriving flight potentially has COVID-19.
This information may be useful to public health agencies in prioritising clinical testing. It also provides an extra layer of data if there is a possible lag in viral detection in deep nasal and throat swab samples.
In the future, there may not be any requirements for passengers to quarantine. However, aircraft wastewater detection data can be shared with passengers. They can be advised to look for symptoms and if symptoms appear then can get tested and isolate.
This will help reduce transmission of diseases in the community.
How does the aircraft wastewater testing work and how do you find variants?
The SARS-CoV-2 virus is diluted in aircraft wastewater. Once the wastewater sample is collected, it is then concentrated to a small volume.
The virus’ RNA, carrying the genetic information, is then extracted from a portion of the concentrated sample. The wastewater samples are analysed for specific genetic fragments of SARS-CoV-2 using RT-qPCR analysis.
This process is akin to a molecular copy machine, which makes many (millions to billions) copies of molecular gene fragments. A variant can be detected using RT-qPCR specific for the detection of the variants or using genomic sequencing approaches which can identify defining mutations.
What if a COVID-19 infected person does not use the aeroplane lavatory?
The successful application of aircraft wastewater surveillance largely depends on the toilet usage of passengers. It’s likely to be applicable for long-haul flights (longer than seven hours).
Nasal secretions of SARS-CoV-2 RNA via sputum and cough may also enter the wastewater tank. This is via the lavatory sink (this may apply for certain aircraft models, but not all).
We need to conduct more research on the toileting behaviour of passengers.
How is CSIRO advancing the wastewater surveillance of aircraft?
We are developing rapid and sensitive methods that could potentially be used in an airport to detect SARS-CoV-2 within one or two hours.
We're also developing methods that can be used to detect other pathogens of interest. These could include respiratory viruses, antimicrobial resistant genes (ARGs), or other clinically relevant biological signatures in aircraft wastewater.
This will continue to provide an early warning of the entry of dangerous pathogens into Australia.