Environmental Surveillance & Disease Ecology

Environmental surveillance has emerged as a smart surveillance tool to detect, quantify and track pathogens of interest. It serves as an early warning system to take appropriate measures and build infrastructure to contain or circumvent public health crises. Monitoring public health by sample collection at individual patient level can be extremely costly. Environmental samples, such as wastewater samples, are composite samples that represent the contribution from many individuals in the community and are thus unbiased and cost efficient for routine surveillance of infectious diseases. Globally, wastewater-based epidemiology (WBE) has been used for over 40 years to track measles, cholera, polio and HIV outbreaks. More recently, with the ongoing pandemic, WBE has emerged as a cost -effective and efficient tool to predict rise in COVID-19 infections.

Environmental surveillance helps identify disease hotspots and needs to be combined with ecological drivers of diseases in both space and time. We strive to underpin this by studying the field of disease ecology which encompasses the ecological study of host-parasite interactions within the context of their environment and evolution. Many arboviruses, such as those that cause Chikungunya and Dengue, have zoonotic origins and their interactions with mosquito vectors have evolved in parallel with urbanisation of their key mosquito hosts (Aedes species), and this understanding is fundamental to the One Health approach. Vector-pathogen interactions are critical to the transmission and epidemiology of vector-borne diseases. Our work focusses on the mechanisms and scale of pathogen interactions at individual, population, and community levels. We take an interdisciplinary approach drawing on genetics, molecular ecology, epidemiology, and modelling to understand how biological, social, and physical aspects of our environment can influence disease transmission, intensity, and distribution.

Vertical Lead: Farah Ishtiaq

Investigators: Farah Ishtiaq, Mansi Malik, Sanjay Lamba, Shivranjani Moharir,


TIGS, is leading a longitudinal study (ongoing since August 2021) across 28 Bengaluru sewershed sites capturing wastewater data from more than 11 million people. The wastewater infrastructure of Bengaluru offers an effective resource to access and estimate the spread of the SARS-CoV-2 across the city. The Bangalore One Health Consortium (under the Bengaluru Science and Technology Cluster) initiated the city-wide WBE of SARS-CoV-2 and is now expanding it to other pathogens in Bangalore and nearby areas. The SARS-COV-2 viral trend in wastewater is shared on a regular basis with the municipal authorities (BBMP and BWSSB) which is helpful in making policy and taking decisions as early as by ~one-week of the emerging infection trend.

Investigators: Farah Ishtiaq, Sanjay Lamba

National Centre for Biological Sciences (NCBS), Bengaluru, Bangalore Water Supply and Sewerage Board (BWSSB), Bruhat Bengaluru Mahanagara Palike (BBMP) and Biome Environmental Trust, Bengaluru

Over the last year, routine WBE- based surveillance of SARS-CoV-2 in Hyderabad has been setup at 20 sampling locations, including open drains, across the city. Sampling protocols including collection, processing, and analysis have been standardized. SARS-CoV-2 RNA load at all the sampling locations is routinely monitored to map the trend of viral infectivity in different parts of the city and the viral RNA is sequenced for identifying emerging variants.

We have developed an interactive WBE data analysis dashboard to report on city-wide SARS-CoV-2 trends in real time (http://data.ccmb.res.in/wastewater/). This website and interactive dashboard is envisaged as a template for developing a broader platform for environmental surveillance data sharing, real time analytics and public outreach in the future.

We have also been developing systems for identifying the pathogen diversity and antimicrobial resistance genes in wastewater. Samples are collected less frequently, approximately once a month, from some of the locations established for SARS-CoV-2 sampling. The protocols have been optimized and the sequencing data are currently being analysed.

Investigators: Shivranjani C Moharir

CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad

Communicable diseases need continuous surveillance activities to track, predict and control emerging, re-emerging, and novel infections that are potential threats to human health and wellbeing. Dengue and chikungunya are the two common vector borne diseases in India transmitted by the Aedes spp. mosquitoes Aedes aegypti and Aedes albopictus, respectively. The epidemiology of chikungunya and dengue infections is thus likely to be temporally and spatially linked. Similarly, bacterial infections such as scrub typhus (caused by Orientia tsutsugamushi) and Leptospirosis (caused by Leptospira) account for 35 – 50% and 52% cases, respectively, of acute undifferentiated febrile illness. Currently, there are no molecular markers that can be used in clinical settings for a speedy diagnosis.

The objectives of the project are

1. To estimate the seroprevalence of Malaria, Dengue, Chikungunya, Leptospirosis, Scrub typhus and Hepatitis using a combination of screening methods – ELISA in BBMP nodal laboratory and advanced molecular diagnostics at TIGS.

2. To perform sequencing of samples for serotyping and strain identification of Malaria, Dengue, Chikungunya, Leptospirosis, Scrub typhus and Hepatitis to help in determining the prevalent strains/sero types in Bengaluru city.

Investigators: Mansi Malik, Farah Ishtiaq

Bruhat Bengaluru Mahanagara Palike (BBMP)