Pandemic and post-pandemic dynamics of respiratory viruses in a Spanish middle-size city using a long-term wastewater surveillance

The prevalence of SARS-CoV-2, Influenza virus (Inf) types A and B, and Respiratory Syncytial Virus (RSV) lineage A and B was monitored over a 3-year period (November 2021–2024) using urban sewage samples collected from twelve different locations in Burgos, Spain ( n = 600). Specific RT-qPCRs with aluminum-based adsorption-precipitation viral concentration and nucleic acid extraction were performed. Recovery rates averaged 28.73% ± 1.40%, allowing for accurate viral quantification. Results demonstrated the presence of SARS-CoV-2 across all sampling sites and throughout the entire study period, with a mean concentration of 6.07 ± 0.04 log genomic copies per liter per 100,000 inhabitants. Moreover, a significant correlation was observed between SARS-CoV-2 concentration levels and reported clinical cases, with the predictive capability improving when a seven-day lead time was applied. In contrast, the remaining respiratory viruses exhibited intermittent prevalence, at lower concentrations when detected. Seasonal differences were observed for Infs and RSVs from the pandemic to the post-pandemic period, along with unexpected outbreaks of all three virus groups. This study highlights WBE as an effective tool for monitoring respiratory viruses, including specific subtypes, and provides insights into the prevalence and seasonal variations of SARS-CoV-2 from the pandemic to the post-pandemic period, as well as its potential impact on other respiratory viruses.