Wastewater genomic surveillance identifies the emergence of the SARS-CoV-2 JN.1 lineage in urban settings of Gujarat

Introduction Wastewater based epidemiology (WBE) has become a crucial epidemiological tool to supplement clinical surveillance to monitor the spread of SARS-CoV-2 and variant dynamics on the population level. As viral shedding occurs early and independently of healthcare seeking behavior, WBE provides advanced signals of infection trends and variant emergence. Materials and methods This longitudinal, multicenter, quantitative and genomic surveillance study of SARS CoV2 was done using wastewater samples from Ahmedabad, Gandhinagar and Vadodara between January 2023 to July 2024. Digital PCR (dPCR) was used to determine the amount of viral load in 2,130 wastewater samples followed by whole genome sequencing (WGS) of high-titer samples. Results The concentration of wastewater viral genome has strong statistical correlation with reported cases of clinical COVID-19 (Pearson correlation coefficient r = 0.898; p < 0.001), which serves as a robust predictor. Wastewater showed strongest predictive value at 1-week lag in Gandhinagar and Vadodara, while Ahmedabad showed statistical significance for 2 weeks lag. Notably, abundance-based dominance analysis showed that wastewater monitoring also predicted alterations in dominant variants. In Ahmedabad, JN.1 was detected one week earlier than in clinical samples, while KP.x had a lead time of three weeks in Ahmedabad. Temporal mapping at the mutation level also supported the initial occurrence and maintenance of mutations that define lineages in wastewater even before clinical identification, suggesting that there was a gradual formation of new variants on the population level. Discussion This study demonstrates that comprehensive quantitative and genomic wastewater monitoring aids to detect presence of SARS-CoV-2 in community early with proactive understanding of the changes in the most common variants within the community. These results highlight the importance of wastewater monitoring as a sensitive, scalable, and proactive tool of population health in terms of early warning and preparedness of pandemics.