Multi-Virus Surveillance Across Diverse Freshwater Systems in Tehran, Iran

Environmental surveillance of viral contaminants in water systems is an essential tool for assessing exposure risk and supporting early-warning frameworks for emerging infectious diseases. In this study, a comprehensive one-year surveillance of SARS-CoV-2 and six enteric viruses was conducted across diverse freshwater systems in Tehran, Iran - including rivers, wells, and traditional qanat (underground aqueduct) infrastructures. Water quality parameters (turbidity, pH, Total Dissolved Solids, nitrate) and fecal bacterial indicators (total coliforms, fecal coliforms, and E. coli) were also measured to contextualize viral contamination within a broader environmental risk framework. Between September 2020 and August 2021, a total of 118 water samples were collected and analyzed using quantitative molecular detection methods. Overall, 61 of 118 samples (51.7%) tested positive for at least one virus. Surface water (rivers) showed substantially higher contamination rates (80.3%; 53/66 samples) compared to groundwater (15.4%; 8/52 samples). Among groundwater sources, qanat systems were markedly more vulnerable than conventional wells, with 25.0% (6/24) of qanat samples testing positive versus only 7.1% (2/28) of well samples. This elevated contamination in qanats was dominated by rotavirus (5/6 positive qanat samples, detection rate 20.8%) and was associated with higher fecal bacterial loads (total coliform geometric mean: 245 MPN/100 mL in qanats vs. 28 MPN/100 mL in wells), consistent with the susceptibility of shallow horizontal collection channels to fecal infiltration. SARS-CoV-2 RNA was detected in 34.8% of river samples and 3.9% of groundwater samples, with concentrations reaching 1.28 × 10⁴ genome copies per liter (GC/L) in surface waters, demonstrating sustained fecal contamination across all seasons. The most prevalent viruses in river water were norovirus GII (45.5%), adenovirus (43.9%), rotavirus (42.4%), and norovirus GI (40.9%), with mean concentrations ranging from 1.26 × 10² to 3.76 × 10³ GC/L. Hepatitis A and E viruses were not detected in any sample. Seasonal variation in viral detection was observed for enteric viruses, while SARS-CoV-2 and adenovirus showed year-round persistence. Strong correlations between fecal indicators and viral contamination (Spearman r = 0.61-0.63) support the use of bacterial monitoring as a cost-effective screening proxy. The results highlight the particular vulnerability of qanat systems and underscore the value of integrated environmental surveillance for water safety management in arid, water-stressed urban environments.