How Prayagraj is leveraging wastewater surveillance to prevent another pandemic

This note by Agrawal and Siva outlines efforts taken by the Prayagraj district in Uttar Pradesh to collect samples from sewage treatment plants and test them for the SARS-CoV-2 pathogen. They found a correlation between surveillance results and test results two weeks later, suggesting that wastewater surveillance can be used for early detection of the disease. They also highlight the potential to use wastewater surveillance to understand antimicrobial resistance, and to monitor diseases during large events.

Wastewater surveillance was a valuable tool to monitor and manage the spread of the virus during the Covid-19 pandemic (Medema et al. 2020). In fact sewage samples from more than 4,600 sites across 72 countries are still being monitored for SARS-CoV-2 RNA, the genetic material causing coronavirus. The SRM Institute of Technology in Tamil Nadu even created a set of standard operating procedures (SOPs) for wastewater surveillance in April 2021, which were later adopted by NITI Aayog. However, the efforts lost momentum as the second wave of the pandemic took over.

In simple terms, wastewater surveillance involves monitoring wastewater to gain insights into the presence and concentration of disease-causing pathogens in communities. Wastewater samples can be collected from sewage treatment plants or open drains. The primary criterion for conducting this type of surveillance of the targeted pathogen is that it must withstand stomach acidity and be excreted in faeces. Besides SARS-CoV-2 and poliovirus – the original driver for wastewater surveillance – several other pathogens meet these criteria. These include viruses such as adenoviruses, hepatitis A and E viruses, and rotaviruses. Additionally, bacteria and parasites like E. coli, Salmonella, Shigella, Ascaris, and Giardia can also be detected using wastewater sample analysis.

For public health authorities, wastewater surveillance carries promise for the early detection of disease outbreaks. During the Covid-19 pandemic, many individuals remained asymptomatic for several days after contracting the virus. Therefore, governments had limited ability to be one step ahead of the disease– a gap that can be effectively filled by wastewater surveillance. In addition, local authorities can monitor trends and hotspots in disease concentration if sewage samples are collected from different drains around a city or from various sewage treatment plants (STPs). Although costlier and more complex, genomic sequencing of sewage samples can further help identify new and emerging variants of concern.

Wastewater as an early warning system

With these insights in mind, the Prayagraj district administration in Uttar Pradesh collaborated with the Council of Scientific and Industrial Research’s Centre for Cellular and Molecular Biology (CCMB), a premier research institute in Hyderabad working at the frontier of modern biology, for a one-of-its-kind initiative in December 2022. As per the agreement, CCMB conducted wastewater surveillance to detect SARS-CoV-2 pathogen and antimicrobial resistance in sewage samples. The city currently has six sewage treatment plants (STPs) with a collective treatment capacity of around 270 million litres per day, processing nearly 60% of the city's sewage.

Each month, samples from all six STPs are meticulously collected during periods of higher sewage flow (typically between 7 am and 11 am) following an SOP established by CCMB scientists. These samples are then delivered to Hyderabad, securely packaged in a 1% sodium hypochlorite solution to preserve their integrity. They typically reach their destination in seven to ten days. The cost of doing this is quite low and is borne by the concessionaire running the STPs. At CCMB, RT-PCR, a molecular technique¹, is applied for the quantitative detection of SARS-CoV-2 in the wastewater samples.

Since our intervention has been running successfully for over eight months, we are now able to correlate results from wastewater surveillance with the daily Covid-19 caseloads gathered from laboratory test results. Although Covid-19 is less of a concern now, we still find a striking correlation between surveillance results and test results two weeks later. These findings mirror those obtained in other cities and countries – including in CCMB’s prior work in wastewater surveillance in Hyderabad, Kolkata, Delhi and Chennai, to name a few – suggest that wastewater surveillance can provide a 15-day advance warning for Covid-19. We have circulated our findings within the public health community in the district as well as with the state surveillance authorities in the Lucknow, the capital of Uttar Pradesh.

We also attempted to detect other pathogens in Prayagraj’s wastewater through genomic sequencing of the sewage samples. Although these results are still preliminary, we find a high concentration of certain pathogens across STPs over months. These include microbes like Pseudomonas aeruginosa, a germ that causes infections such as pneumonia in humans. Over time, one can use a more focused approach to trace pathogens that are most likely to cause disease outbreaks in a particular geography.

Going beyond Covid-19

In addition to tracking SARS-CoV-2 and certain other germs, our work in Prayagraj also focuses on tackling antimicrobial resistance (AMR), caused when pathogens evolve to evade antimicrobial drugs such as antibiotics, antivirals, antifungals and antiparasitics. It is an escalating problem that requires a comprehensive approach, encompassing both quantitative and qualitative analyses of its environmental impact as well as controlling the spread of antimicrobial resistant pathogens.

Wastewater surveillance for AMR can also prove to be an informative tool in pursuance of the Indian government’s ‘One Health’ mission, in two ways. First, wastewater surveillance, particularly through genomics-based STP monitoring, aids in understanding the AMR profile within the community. Our work currently focuses on tracking the presence of antibiotic-resistant bacteria (ARBs) and the contribution of wastewater components, such as antibiotic residues from industries and mobile genetic elements, in fostering the emergence of ARBs on-site.

Secondly, wastewater plays a crucial role in the development and dissemination of AMR, as it serves as a habitat for ARBs and antimicrobial resistance genes (ARGs). Sewage-based surveillance is widely employed to comprehend the occurrence and distribution of antimicrobial resistance in communities. Such studies can help us develop an early warning system for emerging diseases and antimicrobial resistance.

In our preliminary biological analysis conducted on the samples collected from Prayagraj, we find a high concentration of ARGs across all six STPs. Although outlet samples generally have a lower number of these genes per million reads, it appears that the wastewater treatment process is unable to eliminate them completely. The insights obtained from these studies are significant for source tracking, risk assessment, and AMR management in urban environments. Additionally, sewage surveillance can be utilised to monitor drug and antimicrobial consumption patterns, providing further valuable data for effectively tackling AMR.

The way ahead for wastewater surveillance

This unique collaboration between CCMB scientists and public administrators in Prayagraj has been running smoothly since last year. It serves as a good example of a productive engagement that can be emulated in other cities as well. We are also exploring ways to incorporate wastewater surveillance as one of the tools for disease monitoring during the Kumbh Mela in 2025, during which Prayagraj is expecting to host over 400 million pilgrims from around the world.

Despite its benefits, sewage surveillance is not a silver bullet. Going forward, we must continuously assess the cost-effectiveness of this approach and compare its efficacy with alternative methods being deployed by state governments (for instance, the Government of Uttar Pradesh has developed a system which integrates test data on communicable diseases from all laboratory test reports in the state). The time lag between sample collection and the availability of results needs to come down as well. Furthermore, being able to identify specific localities of concern will be important to aid in containment efforts and boost this method’s popularity among officials tasked with reducing disease spread.

Once these issues are resolved, the next steps involve integrating the results from wastewater surveillance into public health authorities’ decision-making processes. This will necessitate the development of digital systems capable of analysing the data and assisting officials in comprehending the findings. For one, it will be essential to account for population and demographic differences across various catchment areas to make analyses and comparisons more meaningful. To facilitate this integration, some local governments are already developing and using dynamic dashboards which map results from wastewater surveillance and other data sources.

There are other equally exciting use cases of wastewater surveillance. Some countries are using it to track illicit drug use in their population. A research paper by Australian and Norwegian researchers (Choi et al. 2019), featured in The Economist, discusses wastewater-based epidemiology’s potential in estimating socio-demographic characteristics and consumption patterns within catchment areas. Policymakers can use such novel data sources to assess nutritional deficiencies and lifestyle diseases, and design appropriate interventions to address them. Ultimately, wastewater surveillance’s true success lies in transitioning from laboratory and research seminars to review meetings and discussions among administrators and public health officials – this is what we have attempted to do in Prayagraj.

The views expressed in this article are personal.

Note:

At CCMB, in a biosafety level II cabinet, approximately 50 ml of each sample undergoes RNA extraction using standard protocols. Subsequently, reverse transcription polymerase chain reaction (RT-PCR) is the technique used to reverse transcription of RNA into DNA and then specific DNA targets are amplified using polymerase chain reaction (PCR).