Leveraging wastewater surveillance in India as a public health threat response

One of the fundamental lessons from the Covid-19 pandemic for the global community has been that the traditional public health response must evolve and have a multifaceted approach considering the changing nature of our environment. As climate change impacts human health through the rise in the incidence rate of zoonotic diseases, pandemic preparedness and disaster management are critical aspects of public health safety. Disease surveillance tools will play an integral role in effective pandemic preparedness. Timely detection and monitoring of infectious diseases are critical to control their spread, helping minimize morbidity and mortality. It is, therefore, necessary to focus on tracking the emergence and distribution of such diseases while developing tools to help better equip our healthcare systems to tackle future outbreaks.

Wastewater surveillance (WWS) is one type of environmental surveillance tool that has been empirically utilized to track pathogens transmitted by waterborne or fecal-oral routes. It is most easily implemented at a wastewater treatment plant, providing a representative sample for all individuals connected to a sewer network. WWS plays a vital role in monitoring the polio virus post its eradication in 2011, through select wastewater treatment plants and unregulated catchment areas where sewage is drained. As the surveillance mechanisms that existed focused on the detection of polio, it could not be effectively repurposed. Therefore, when the pandemic struck, urgency demanded a rapid expansion of pathogen surveillance efforts to detect the Covid-19 virus in sewage systems even before clinical cases were reported. This critical lead time allowed authorities to take targeted measures to prevent further escalation and spread.

As a result, scientists and practitioners worldwide, are increasingly turning to wastewater-based epidemiology as a potential tool for anticipating, assessing, and managing public health threats. Towards this, the Alliance for Pathogen Surveillance Innovations (APSI)-India, supported by the Rockefeller Foundation, is working on further developing wastewater-based epidemiology as a potential tool for anticipating and managing public health threats.

The focus on WWS has steadily grown across the government of India, where during the pandemic, the ministry of health and family welfare (MoHFW) further underscored the significance of wastewater surveillance, deploying it for expanded pathogen monitoring and disease burden estimation. The wastewater surveillance initiatives spearheaded by APSI are in alignment with the government’s National Health Policy, which emphasizes the need for bolstering disease surveillance through continuous monitoring beyond clinical settings, while also advocating for an intersectoral approach. Furthermore, APSI’s endeavours play a pivotal role in advancing the objectives outlined in NITI Aayog’s Vision 2035 for Public Health Surveillance in India, which aims to establish a predictive, responsive, and integrated system for disease detection.

Established during 2021, APSI is a multi-city consortium comprising of research and academic institutions in Hyderabad, Pune, Delhi/NCR and Bengaluru. APSI’s primary focus is to support the government’s efforts to bolster SARS-CoV-2 genomic surveillance in India, viral genome sequencing, and wastewater-based detection, and to complement the mammoth task of government initiatives like INSACOG (Indian SARS-CoV-2 Genomics Consortium). The consortium has now expanded wastewater surveillance beyond SARS-CoV-2, employing a metagenomics-based approach for comprehensively identifying various pathogens such as influenza viruses and bacteria contributing to anti-microbial resistance. APSI has sequenced over 40,000 clinical samples detecting SARS CoV-2 variants since August 2021 of which 75 per cent of the clinical sequences had been submitted to the Global Initiative on Sharing All Influenza Data (GISAID), INSACOG and various other databases, promoting global and national data sharing.

APSI has built a country-wide network that collates, collects and processes results that allow for systemic analysis and interpretation and envisions an environmental surveillance-based early warning system integrated into the state’s public health protocols. Using bioinformatic and genomic tools, APSI researchers have developed standardised protocols to detect SARS CoV-2 silent waves by detecting variants such as JN.1 in wastewater when clinical testing had reduced significantly. APSI is also focused on developing low-cost indigenous pathogen detection kits which could be utilized by public health authorities to detect various pathogens of public health concern in wastewater. This will enhance the overall health sector’s capabilities and help enhance testing infrastructure, ensuring a cost-effective and efficient approach to disease surveillance.

APSI has developed standard operating procedures (SoPs) and workflows to streamline wastewater sampling, sample processing, genome sequencing and data analysis that will serve as a guide to monitoring pathogens of interest in the future. By seamlessly integrating these standardized procedures into the existing framework, APSI’s demonstrated model can enhance the state’s preparedness for emerging health threats and other diseases through its dissemination to local governments. Leveraging these SoPs at the local level would help drive accountability towards overseeing and operationalising pandemic preparedness and response policy for any outbreak that may arise. The integration of APSI’s work on WWS into the policy framework of the country will significantly add to the disease surveillance reportiore.

Wastewater surveillance in India happens in silos, and a nation-wide effort to cohesively develop a system under one umbrella still needs to be undertaken. Multiple interacting factors have heightened the need for integrating environmental surveillance and building robust wastewater surveillance systems into public health response at the local, sub-national, national, and global levels such as the rise in the frequency of zoonotic diseases highlight the criticality of adopting well-functioning wastewater surveillance systems to combat public health threats. This would require a collective effort from stakeholders across the ecosystem to help achieve this vision of integrating wastewater surveillance into existing surveillance programmes in India with a focus on detecting and predicting disease outbreaks.

Dr. Aruna Panda is the programme director at The Rockefeller Foundation-Alliance for Pathogen Surveillance Innovations-India Consortium, CSIR-Center for Cellular and Molecular Biology, Hyderabad (APSI); and Priyanki Shah is the senior project manager at Pune Knowledge Cluster (APSI)