Covid in wastewater early warning system upgraded to detect Omicron variant

Philippe Sébérac, director of technological and scientific expertise at Veolia, explains how the firm and its project partners have updated their early warning system for identifying and quantifying Covid-19 in wastewater to cope with new variants, and discusses a broader rollout.

In the latter stages of 2021, waste management and energy firm Veolia announced that its Vigie Covid-19 project to detect and quantify the presence of SARS-CoV-2 in wastewater had been upgraded to track signs of the Omicron variant.

Launched in September 2020, and acting as an early warning system of monitoring the pandemic’s progression, Vigie Covid-19 had previously tracked the Alpha, Beta and Gamma variants before cracking Delta in summer 2021.

Used to complement clinical data, testing the presence of Sars-Cov-2 in wastewater has the potential to become an important indicator and help manage the pandemic, according to Veolia.

Harnessing polymerase chain reaction (PCR) screening techniques like those used in coronavirus lab testing, the project identifies the presence of known mutations originating from existing variants and evaluates their concentration. Sequencing then identifies mutations, as well as each variant’s proportions.

Created in tandem with the Institute of Molecular and Cellular Pharmacology (IPMC) – a joint research unit between the National Center for Scientific Research (CNRS) and Université Côte d’Azur – biological analysis start-up IAGE and the Marseille Naval Fire Battalion (BMPM), Vigie Covid-19 is already in use at a dozen sites across several European countries and could yet be rolled out further.

Having updated the system to track the Omicron variant in December, Philippe Sébérac, Veolia’s technological and scientific expertise director, believes that the solution is ready to be made more widely available.

“A large-scale roll-out would make it possible, by tightening up the territorial network, to cross-reference data with those of local health authorities,” he explained.

“Our method can thus constitute an excellent complement to clinical trials in the fight against the spread of the pandemic by providing readable information and dynamics consistent with the incidence rates reported by health authorities in Europe”.

How does the system work?

Speaking to Utility Week Innovate, Sébérac explains that the Veolia-led collaboration sees wastewater samples collected and sent to startup IAGE for PCR screening, before being passed to the CNRS-IPMC for sequencing.

“In the context of the variant soup found in wastewater for several months, wastewater sample sequencing is used at the R&D level to regularly check for marker consistency,” he says.

“Sequencing provides a reliable confirmation of the identity of the variants. The Omicron variant, like any other variant of concern, is searched by PCR screening.”

Though the virus in wastewater is very unlikely to be active nor alive, any traces found offer sufficient warning of its potential presence at a larger scale.

(Veolia Group: February 2021)

Keeping pace with new variants

At the time of writing, five strains of Covid-19 are listed as global “variants of concern” by the World Health Organisation (WHO). Alpha, Beta, Gamma and Delta – the dominant strain in the UK, Europe and the United States – as well as Omicron, which has been detected in more than 100 countries since emerging in November 2021 and has accelerated infection rates due to its increased transmissibility.

On top of these, the WHO lists two “variants of interest”. Lamda, first detected in Peru in December 2020, and Mu, first detected in Colombia in January 2021, as well as monitoring three further strains of the virus first recorded in January, May and September 2021 and having relegated a further 17 strains deemed no longer of concern after failing to circulate to any worrying extent.

Though the number of new variants is ever-changing, according to Sébérac the contributors to Vigie Covid-19 are part of a “scientific ecosystem” that enables them to develop protocols for quantifying new variants very quickly.

“Only two weeks are needed to launch a monitoring campaign for a new variant and the results can be used as soon as the new variant arises in the region,” he explains. “Only a few changes are made to detect the Omicron variant as the operation and deployment of the solution remains the same for each variant.”

Broader innovation

Additionally, Sébérac forecasts that these processes and technology used to detect Covid-19 variants in wastewater could lay the foundations for further innovation in wastewater treatment.

“The Covid-19 pandemic confirmed the importance of wastewater monitoring in providing authorities with a cost-effective, fast and reliable source of information on the health of populations connected to wastewater systems,” he tells Utility Week innovate.

“Based on the lessons learned for sampling and analytical strategy from SARS-CoV-2, wastewater-based epidemiology could be used as a support to clinical data to detect other biological and chemical markers of health and environmental interest such as waterborne pathogens, antimicrobial resistance (AMR) markers and antimicrobial substances (AR).”

News of Veolia’s latest pandemic innovation comes months after Veolia’s chief operating officer — treatment, Donald Macphail, revealed that the firm’s energy recovery facilities (ERFs) are helping to cut the healthcare sector’s post-Covid carbon footprint.

According to figures reported by Utility Week Innovate in September, Veolia’s ten ERF plants take around 2.3 million tonnes of non-recyclable waste and convert it into electricity for over 400,000 homes.

These facilities are said to generate around 1.4TWh of electricity through non-recyclables per year and have helped tackle pandemic medical waste — such as used test kits and PPE — by treating a 15 per cent increase in orange bagged clinical and infectious materials.

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