A researcher collecting wastewater sample from the Doddabelee Sewage Treatment Plant in Bengaluru, India. Credit: Manoj Kumar

The COVID-19 pandemic illustrated the value of wastewater-based epidemiology (WBE) — also known as wastewater or environmental surveillance — as an effective population-wide monitoring technique. Such mapping captured viral shedding by people with or without symptoms of the coronavirus disease.

Countries have used WBE for more than 40 years for retrospective indication of poliovirus, norovirus, influenza, hepatitis and measles outbreaks. In India, environmental surveillance played a crucial role in poliovirus eradication in 2012. It continues to confirm the absence of poliovirus and provides active surveillance of acute flaccid paralysis (AFP) cases.

A single case of AFP indicates substantial underlying polio transmission in a population.

Systematic environmental sampling has been estimated to detect one case of wild poliovirus among 10,000 inhabitants1.

In the latest use of WBE to detect the polio virus, the US Centers for Disease Control and Prevention plans to test wastewater over a wider spread of counties and communities after the first US polio case in almost a decade was discovered in Rockland County, New York in June 2022.

In India, a handful of cities such as Hyderabad, Pune, Surat and Bengaluru used WBE to track SARS-CoV-2, recognising it as an economical and effective surveillance tool.

Bengaluru’s environmental surveillance platform sampled 1,140 million litres of wastewater daily, covering almost 11 million people2. It monitored a hybrid network of 46 open drain sites between March 2021 and March 2022, and 28 sewage treatment plants (STPs) since August 2021, representing nearly 92% population of the city. The researchers obtained raw data on viral load of SARS-CoV-2 RNA copies from STP samples using RTqPCR. This data was normalized to average daily flow of sewage and population size of catchment area, which essentially represent viral load copies per person per day. Normalised viral data from the STPs was used to estimate the number of infected individuals in a given catchment area (or sewershed site). There are some limitations of using open drain network, as it can only help detect the viral presence on a weekly or biweekly basis. Therefore, long-term data from the same location can be used to generate a 7-day rolling average where a positive slope suggests that viral load is increasing, and negative slope indicates a declining trend.

WBE allowed comparison of viral load in various parts of the city, correlating it with number of COVID-19 cases helped identify infection hotspots. The early warning system showed how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8–14 days earlier in wastewater than in clinical data. The real-time genomic surveillance from wastewater representing pooled samples from community is key to understanding the variants that cause the emerging viral load patterns in wastewater.

In places, with or without sewage networks, where WBE can be applied with or without sewage network, it is key to remember the following:

(i) When and where to sample: Once or twice a week, sampling is required for accuracy in trend analysis. For identification of hotspots, it is important to have granular information of catchment areas and sanitation mapping for site selection. This can be scaled up with rise in infection.

(ii) Complementary tool: Wastewater surveillance should be used as a complementary surveillance approach to identify disease hotspots.

(iii) Building capacity: The cost of conducting WBE involves onsite sample collection and bringing it back to the lab for analysis, which makes it expensive and impractical for increasing sampling frequency from remote sites. A smart surveillance tool needs localised capacity building of sewershed staff with protocols for easy onsite processing, which can help maintain sample quality in low-resource settings.

(iv) Communication: Regular communication among WBE practitioners, epidemiologists, public health authorities is essential to inform policy. Wastewater sequencing reveals emerging variants which might not have been recorded in clinical data.

(v) Scaling up for other pathogens: Current surveillance and infrastructure are being scaled beyond SARS-CoV-2, to other pathogens (e.g. dengue, influenza, scrub typhus). This will also help understand major pathways and drivers of antimicrobial resistance in the environment.

The author is with the Tata Institute for Genetics and Society, Bengaluru, India.