Wastewater-Based Epidemiology Monitoring for Endemics Like COVID-19 in India Through a Bi-Phase Detection Approach

Wastewater-based epidemiology (WBE) is increasingly recognized as a valuable tool for monitoring disease cycles, including pandemics like COVID-19. Unlike pandemics, epidemics exhibit distinct dynamics, spread patterns, multiple origin points, and varying levels of population immunity. This study evaluates the applicability of WBE for epidemic monitoring and emergency preparedness by analyzing SARS-CoV-2 presence in Jaipur’s wastewater over one year post-second pandemic wave, covering a minor surge (third) and a mild resurgence (fourth) of COVID-19. A total of 1050 samples from different city localities were analyzed using a combination of two concentration methods (the direct method and the Polyethylene Glycol (PEG) method) and two detection kits (qualitative and quantitative). WBE effectively detected both minor and major epidemic outbreak cycles of SARS-CoV-2. A total of 62.91% samples out of all untreated samples tested, were found to be positive with viral genome; however, the positivity rate of any particular day did not exceed 25% even during the peaks. Notably, short-distance transportation under ambient conditions had no significant impact (p > 0.05) on detection, and the combination of the direct method with quantitative kits provided the highest sensitivity. Based on these findings, a cost-effective bi-phase surveillance model is proposed for year-round epidemic monitoring. This model suggests routine use of the faster, cheaper direct method, switching to the PEG concentration method during rising viral loads for enhanced resolution. Such an approach ensures sustainable, resource-efficient surveillance, particularly benefiting low- and middle-income countries facing financial constraints.