Sewage surveillance spots new covid-19 variants as effectively as PCRs

Monitoring waste-water samples for coronavirus remnants enabled researchers in Austria to identify when omicron became the dominant variant and track the virus’s transmission in communities

By Jason Arunn Murugesu

A person takes samples from sewage water near a retirement home in Marseille, France, to detect coronavirus traces in December 2020

Arnold Jerocki/Getty Image

Sewage analysis may effectively identify­­ the arrival of a new covid-19 variant in a community, as well as the extent and duration of the virus’s spread.

Waste-water surveillance has been used worldwide throughout the pandemic, analysing sewage samples for virus remnants shed by infected people in their faeces.

But no study had looked at how reliable the method was at identifying a new variant or determining the speed and distance the virus spreads.

To learn more, Andreas Bergthaler at the Medical University of Vienna and his colleagues sampled waste water covering 59 per cent of the Austrian population, about 9 million people, from December 2020 to February 2022. The results of the ongoing study have been informing Austrian policy-makers since mid-2021.

The team compared the waste-water surveillance data with the results of polymerase chain reaction (PCR) covid-19 tests. When it came to identifying new variants and tracking the virus’s spread, the results from the two methods generally matched.

Like the PCR data, the sewage samples showed that the more-transmissible omicron variant became dominant throughout Austria within a few weeks, while the delta variant’s rise to dominance was more gradual, says Bergthaler.

Waste-water surveillance may have several advantages compared with contact tracing, which involves testing people for covid-19 after they were in close proximity to someone who was probably infectious.

Referring to waste-water surveillance, Bergthaler says: “This method is not subject to sampling bias, does not require an advanced healthcare system and may be considered more economical compared to individual tests.”

But waste-water surveillance doesn’t find infected individuals quickly, he says.

“I consider waste water a complementary surveillance system to classical care-based epidemiology, if available,” he says.

Bergthaler says the method could be particularly useful in lower-income countries that may lack the means to conduct extensive contact tracing.

“I expect waste water-based epidemiology to turn into a central surveillance tool for the global fight against infectious diseases,” he says.

But Francis Hassard at Cranfield University in the UK says waste-water surveillance may only be effective in countries with well-connected waste-water networks. “Less data is available in resource-constrained settings without established waste-water systems, such as the Global South,” he says.

“The potential demonstrated in this study is perhaps one of the first studies that goes beyond correlating epidemiological records with waste water by showing the feasibility of using waste water as a tool for calculating the spatiotemporal dynamics of new [coronavirus] variants,” says Andrew Singer at the UK Centre for Ecology & Hydrology and the head of the UK’s covid-19 waste-water surveillance programme.

Journal reference: Nature Biotechnology, DOI: 10.1038/s41587-022-01387-y