Genomic surveillance of wastewater can be an early Covid warning system: study

Studies using clinical data on Covid are limiting in nature owing to the paucity of information available on virus variants and their abundance in the community. But in such cases, genomic-surveillance studies of wastewater have proven to be successful in predicting Covid infection trends and detecting viral loads in Brazil and many other South American countries.

The functionality and cost-effectiveness of this technique to monitor the spread of infections in highly populated areas with migrating populations and limited access to public health surveillance systems makes it suitable for countries like India, according to the study.

Previously, similar techniques have been used in nationwide surveys conducted to detect the presence of the polio virus.

The study was conducted in Bengaluru, a city with a population of 11 million inhabitants. Wastewater samples were collected every week from 28 sewer sites between January 2022 and June 2022. Positive samples were analysed using RT-PCR.

The scientists compared the viral load of the coronavirus in both wastewater samples and clinical samples obtained from Covid patients and found them to be positively correlated with each other. This confirmed the genomic surveillance of wastewater to be a complementary tool to gain insights on coronavirus populations in a community.

“Genomic sequencing is the backbone of wastewater surveillance and needs to be done in real time to understand the variants that cause the emerging viral load patterns in wastewater,” said Dr Farah Ishtiaq of the TIGS, who led the study.

Wastewater was also found to have more virus variants than in clinical samples. The emergence of new variants in wastewater is indicative of a significant number of individuals in the community having been already infected by new viral strains. Many new variants were observed at different intervals. However, these variant types and their time of detection were consistent across all sampling sites in the city.

“Wastewater surveillance should be used as a complementary surveillance approach to identify disease hotspots” said Dr Uma Ramakrishnan, an NCBS professor involved in the study’s design and execution.

The outcomes of the sensitivity analysis suggest that the number of individuals infected with the coronavirus in Bengaluru was four times higher than the number obtained via clinical tests. This crucial information was shared with officials of the Bruhat Bengaluru Mahanagara Palike and the Bangalore Water Supply and Sewerage Board to help them take informed decisions while making plans to curtail the virus spread. On the basis of these findings, Covid testing was increased in some locations in Bengaluru. The scientists believe the insights gained from this study will significantly improve public health surveillance, both for the Covid pandemic and for other future infections.

“Surveillance and infrastructure are being scaled beyond SARS-CoV-2 to other pathogens (e.g. dengue, malaria). This will also help understand major pathways and drivers of antimicrobial resistance in the environment,” said Dr Rakesh Mishra, director of the TIGS.

The study titled “SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater — a longitudinal study in Bengaluru, India” was published in The Lancet Regional Health–Southeast Asia on January 18.

The study was supported by funding from a Rockefeller Foundation grant to Bengaluru’s National Centre for Biological Sciences — which is part of Mumbai’s Tata Institute of Fundamental Research, and an Indian Council of Medical Research grant to the TIGS and Tata Trusts.