Identification and characterization of viruses causing Acute Respiratory Infections in environmental matrices

Environmental surveillance and monitoring complement traditional syndromic systems by enabling the detection of both symptomatic and asymptomatic viral infections. Integrating environmental and clinical data provides insights into the circulation of respiratory viruses, including SARS-CoV-2, Human Adenovirus (HAdV), Respiratory Syncytial Virus (RSV) and Influenza Virus (IV). Analytical challenges related to matrix variability, viral dilution, and inhibitory substances highlight the need for standardized methods. This research project aimed to standardize the respiratory viral detection in wastewater and air and to apply it for a monitoring on three vulnerable closed settings: an elementary school, a prison, and nursing home. Lab-scale experiments identified the most efficient wastewater concentration method, followed by evaluation of sampling strategies for each matrix. Selected methods were applied from November 2023 to February 2025 and compared with clinical nasopharyngeal swabs from symptomatic individuals. In the end, Droplet digital PCR assays for RSV and IV were optimized to improve sensitivity and quantification reliability. Ultrafiltration was most effective for wastewater, as were grab sampling and solid air collection. HAdV and SARS-CoV-2 were detected across all settings, whereas RSV and IV were absent. Clinical data confirmed SARS-CoV-2 as the only circulating virus. Overall, the standardized approaches improve detection of respiratory viruses in environmental samples and, integrating clinical data, support public health surveillance in vulnerable communities.