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The Alliance for Pathogen Surveillance Innovations (APSI-India) was set up in July 2021 to strengthen India’s public health surveillance capabilities using advanced pathogen monitoring tools. We are a pan-India consortium generously supported by The Rockefeller Foundation (RF), New York, bringing together four highly populated cities in the country - Bengaluru, Delhi-NCR, Hyderabad and Pune.

The journey so far

The first phase of our work focussed on supplementing SARS-CoV-2 surveillance by INSACOG via clinical Covid testing and sequencing samples from patients across the country. APSI’s efforts have led to the incorporation of a large number of viral genomes from India into the global repository GISAID. Over 75% of sequences submitted from the consortium cities bear the tag of the RF program.

In addition to clinical surveillance, we also set up a robust system of detection of SARS-CoV-2 and identification of its variants in wastewater, including sewage treatment plants (STPs), open drains and water bodies. We developed standardized methodologies and SOPs for wastewater surveillance (WWS) allowing for data reproducibility across the consortium.

About Wastewater surveillance

WWS is an important tool to analyze the health status of a community, specifically by tracking disease associated agents. Many disease-causing pathogens find their way into wastewater through the feces excreted by patients. Sewage, which is the centralized collection point, can serve as an unbiased sampling site to capture the footprints of these pathogens – as exemplified by the detection of SARS-CoV-2 from wastewater in this pandemic. SARS-CoV-2 is shed in the stools of COVID-19 patients regardless of whether the patient suffers from gastrointestinal disturbance or not. Symptomatic as well as asymptomatic COVID-19 affected individuals shed the virus and traces of the viral genome can be detected for several days even after the patient tests negative in conventional nasopharyngeal tests. This provides an advantage in terms of accurate and early (upto two weeks in advance of clinical symptoms) detection of actual viral burden in a community or city, even if patients do not appear for clinical testing or in hospitals.

The flowchart below outlines the WWS process followed by APSI

methodology for pathogen DNA extraction

Adapted from Manupati et al., 2021, Sci Total Environ

Over the last two years, the APSI team has developed a model for WWS which has been crucial for monitoring the extent and spread of COVID-19 infections in cities such as Bengaluru and Pune at a much lower cost than mass testing.

Our teams collect wastewater samples from multiple locations identified across the city at a frequency of about once a week to gather insights into the pathogen load in these areas. Tracking the wastewater data alongside reported clinical cases will help provide granular geographic and temporal patterns of infection spread.


Pune Collection sites

Monitoring the trend of SARS-CoV-2 viral load in STPs in Bengaluru city

bengaluru collection sites
SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater – a longitudinal study in Bengaluru, India. 2023. The Lancet.

These data are shared on a weekly basis with the Bengaluru municipal corporation, the Bruhat Bengaluru Mahanagara Palike (BBMP) and shared on social media to provide warning of disease spread to relevant authorities.


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Monitoring the trend of SARS-CoV-2 viral load in open drains in Hyderabad city

Pune Collection sites


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Pune Collection sites

Monitoring the trend of SARS-CoV-2 viral load in open drains in Pune city

Current Endeavours

Moving beyond SARS-CoV-2 detection, APSI is currently leveraging its experience to develop advanced surveillance platforms for monitoring other diseases such as Dengue, by incorporating wastewater-based prevalence detection, genome sequencing, bioinformatics, data analytics, and information dissemination to public and government stakeholders. APSI is also focused on the crisis of antimicrobial resistance (AMR) via tracking the emergence of pathogens resistant to antibiotics and other drugs. The consortium has scientific and clinical collaborative networks with academic institutions, laboratories, municipal administrations as well as hospitals to enable efficient integration of data from environmental surveillance with clinical correlates across the 4 core cities.

These collaborations serve as nodes for expanding disease surveillance networks to other satellite centres (such as Vijaywada, Shillong and Sonipat). We are now building locally tailored networks at other locations across India, taking crucial steps to strengthen the country's public health surveillance network and mitigate future pandemic risks.

Future Roadmap

APSI envisions an environmental surveillance based early warning system as a part of the State’s public health protocols. The roadmap along which the team is currently working across the APSI cities begins with identifying disease-causing agents that can be detected in wastewater, both open drains as well as sewage treatment plants (STPs). It will be critical to be able to connect pathogen load or genomes identified via WWS with the clinical caseloads and correlates such as severity, hospitalization etc.

For WWS to be adopted into the routine monitoring systems of public health programs, another critical element is the development of reliable and cost effective kits, specifically for environmental surveillance. The APSI team would be involved in handholding the technology as well as product development stages with industry and clinical partners for POC and validation. Finally, WWS needs to be seen from the lens of long-term surveillance where local administrations implement data-driven surveillance which in turn helps in understanding pathogen evolution and behaviour over time and the impact of anthropomorphic measures for implementation at the policy level. The infographic on the left visualizes the routine monitoring processes that need to be in place for such a proactive system to be in place. In the future, these powerful tools will be invaluable for localized disease management and prevention of epidemics and pandemics.

Infographic Design: Superheroes against Superbugs and Rupsy Khurana

Meet our Team

With APSI-India at the forefront of pathogen surveillance innovations, we are marching towards a healthier and safer future for all. Connect with our cluster team or contact the APSI Program Director to join us in preventing the outbreak of infectious diseases. Together, we can make a significant difference in safeguarding public health!

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For queries and feedback, please reach out to us at apsi@csirccmb.org