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.
Team
Farah Ishtiaq, Mansi Malik
Sanjay Lamba, Shivranjani Moharir
- Wastewater-based Epidemiology in Bengaluru city: Beyond SARS-CoV-2
- Wastewater-based Epidemiology in Hyderabad and Public Health Surveillance using Molecular Biology, Genomics and Data Analytics
- Modelling the Longitudinal Data Obtained from Wastewater-Based Surveillance of SARS-CoV-2 in Hyderabad City
- 𝑹 − Software Package: Early Warning System for Infectious Diseases
- Air Surveillance Study to Identify Pathogens in Different Environmental Niches
- Surveillance of Pathogens from Clinical Samples
- Molecular Identification and Surveillance of Pathogens from Vectors and Clinical Samples from Cauvery Delta Districts of Tamil Nadu
In India, tracking of the COVID-19 pandemic relies heavily on testing symptomatic individuals for the presence of SARS-CoV-2 RNA and counting the positive tests over time. Many SARS-CoV-2 infected persons are asymptomatic or oligosymptomatic (few symptoms) and are generally not tested by RT-qPCR, leading to underestimation of COVID-19 cases. Furthermore, infected and even asymptomatic individuals start to shed the virus via faecal route 4-7 days in advance of symptoms and clinical testing, which means the increase in viral load in sewage water ahead of reported cases works as an early warning system. Wastewater-based epidemiology (WBE) thus complements the routine diagnostic surveillance by capturing near real-time virus circulation at a community level.
• Using 3 years data, identification of bellwether sewershed sites which led to scaling down of sites from 26 to 11 STPs
• Sewage mapping for public health action: To identify hotspots at the ward level
• Using SARS-CoV-2 as case study to apply to other pathogens: expansion of surveillance to Mpox, dengue, influenza (human and avian), Human Papilloma Virus, Hepatitis E etc.
• Robust protocols created, detailing the sample collection, sample processing, differences if any during sample collection from different sites, pathogen detection protocols and analysis
• Integration of environmental surveillance in the public health care system for wastewater surveillance
Investigator: Farah Ishtiaq
Collaborators:
National Centre for Biological Sciences (NCBS), Bengaluru
Bangalore Water Supply and Sewerage Board (BWSSB), Bengaluru
Bruhat Bengaluru Mahanagara Palike (BBMP), Bengaluru
Biome Environmental Trust, Bengaluru
Routine monitoring of public health can help in the early detection of emerging or upcoming infectious disease waves in the community and can help in preventing future pandemics. Wastewater is the warehouse of thousands of parasitic, non-parasitic, infectious, non-infectious, and saprophytic microorganisms. These microorganisms find their way in the wastewater mainly through human or animal excreta or through soil. We work on open drains, which are most commonly found in India. The qualitative and quantitative analysis of the microbiome of sewage water in a particular geographical location can be a read out of the general health of the people inhabiting that area.
We analyse environmental samples using molecular biology and genomics approaches for surveillance of pathogenic microbial diversity, including SARS-CoV-2, in wastewater. Since SARS-CoV-2 is shed by infected individuals in their faeces irrespective of their symptomatic status, wastewater-based epidemiology serves as a tool to monitor even dormant and unreported COVID-19 infections.
Investigator: Shivranjani C Moharir
Collaborator:
CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad
The longitudinal data generated from wastewater-based surveillance of SARS-CoV-2 is being used for disease modelling. Using statistical modelling and different machine learning approaches, we developed an early warning system and demonstrated how wastewater monitoring could be used for community-level detection and tracking of the SARS-CoV-2 virus, thereby informing public health policy decisions. In conclusion, monitoring temporal variation in viral loads in wastewater combined with other analyses can detect a virus outbreak at least one week in advance.
Investigator: Shivranjani C Moharir, Sanjay Lamba
Collaborator:
CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad
Using clinically tested SARS-CoV2-positive cases and viral load in wastewater from Sewage Treatment Plants (STPs) and Open Drains (ODs), we developed an early warning system (EWS) for SARS-CoV-2. This system detected virus outbreaks 7-14 days before clinical cases were reported, providing crucial advance notice for public health interventions. Also, we are developing a user-friendly R-software package designed as an early warning system for infectious diseases. This tool is invaluable for enhancing real-time monitoring and ensuring timely responses to potential outbreaks. It can be adapted for various infectious diseases by incorporating disease-specific parameters. The package leverages factors such as historical data on positive cases, viral load findings, and infection rates to forecast potential outbreaks in advance. This initiative is crucial for the effective implementation of public health measures, thereby minimizing the adverse impact of outbreaks.
Key features of the R-software package:
· Packages have been tested and validated for SARS-CoV2 detection using clinically tested SARS-CoV2 positive cases and viral load in wastewater from Sewage Treatment Plants and Open Drains.
· Package can be used for other infectious diseases (chickenpox, dengue, etc.), adjusting parameters relevant to the target disease.
Investigator: Sanjay Lamba
Air surveillance of pathogens is a critical aspect of public health and epidemiological monitoring. It involves the systematic monitoring of the air to detect the presence of microorganisms, such as viruses, bacteria, and fungi. This surveillance is essential to understanding infectious disease transmission patterns and implementing timely preventive measures.
This project involves collecting and analyzing air samples from diverse environmental settings, including hospitals, zoos, densely populated areas, and sparsely populated regions.
Currently we are working
- To standardise procedures for air sample collection, processing and analysis
- To conduct metagenomic analysis of air samples collected from diverse environmental conditions
- To develop methods for detection of specific pathogens in air
Investigator: Shivranjani C Moharir
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 aim is to detect and analyze the seroprevalence of pathogens causing vector-borne diseases (such as Dengue, Malaria, Chikungunya Leptospirosis, Scrub typhus, Hepatitis) using molecular screening methods and to correlate the findings and disease etiologies with patient metadata obtained from various labs. The objectives of the project are
- 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.
- 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.
We have filed provisional and final patents for inhouse-developed q RT-PCR based assays for early and accurate diagnosis of vector–borne diseases.
Investigator: Mansi Malik, Farah Ishtiaq
Collaborators:
Bruhat Bengaluru Mahanagara Palike (BBMP), Bengaluru
Anand Neuberg Laboratories, Bengaluru
Bangalore Baptist hospital, Bengaluru
All India Institute of Medical Sciences, Bhopal
Aster CMI Hospital, Bengaluru
ICAR – National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru
We aim to estimate the prevalence of pathogens responsible for infectious vector-borne diseases (Scrub typhus and serotypes, Dengue, Dengue serotypes, Chikungunya, Malaria, and Leptospirosis) from both entomologically identified vectors and clinical samples using molecular screening methods. To correlate the findings of vector surveillance with clinical surveillance to estimate disease burden and hotspots across delta districts of Tamil Nadu, we have initiated the following:
- Molecular surveillance of Aedes sp , mosquito vectors across Cauvery Delta districts of Tamil Nadu to detect the prevalence of Dengue, Dengue serotypes, and Chikungunya.
- Molecular surveillance of mites collected from rodent ear pinna, blood, and other tissues, to detect the prevalence of Leptospirosis, Scrub typhus and serotypes of Scrub typhus from Cauvery Delta districts of Tamil Nadu.
Investigator: Mansi Malik
Collaborator:
Central University of Tamil Nadu, Thiruvarur