Wastewater Surveillance Detects Silent COVID-19 Variant Waves in Western India

A year-long wastewater-based epidemiology (WBE) study in Pune by Fluid Analytics, CSIR-National Chemical Laboratory (NCL) and Partners demonstrates the critical role of sewage surveillance in tracking SARS-CoV-2 variants during periods of reduced clinical testing. Analyzing 1,128 wastewater samples collected between May 2022 and May 2023 from sewage treatment plants across the city, researchers employed a combination of Illumina and nanopore sequencing to enable high-resolution viral detection and lineage characterization.

The study uncovered multiple “silent waves” — periods of elevated viral load in wastewater despite minimal reported clinical cases — indicating cryptic community transmission. These waves coincided with the dominance of Omicron BA.2 during mid-2022 and the emergence of the recombinant XBB clade toward the end of 2022.

Notably, wastewater sequencing detected XBB lineages between 130 and 253 days before their first clinical identification, demonstrating a substantial early-warning advantage. Similarly, the BA.2.86.X lineage was identified in wastewater more than 100 days prior to its detection through clinical surveillance in Pune. The analysis also revealed BF.7.X and BQ.X variant fragments that had not yet been reported clinically, highlighting wastewater’s ability to capture a broader and more diverse spectrum of circulating variants.

By revealing silent transmission waves, detecting emerging variants months in advance, and overcoming limitations of declining clinical testing, the study reinforces wastewater surveillance as a powerful, population-scale public-health intelligence tool. The findings underscore WBE’s value in enabling earlier interventions and more informed decision-making for future outbreak preparedness in urban centers across India.