Longitudinal Surface Water Viral Surveillance Following the 2024 Extreme Flood: One-Year Monitoring in Porto Alegre, Brazil

Extreme flood events can overwhelm sanitation infrastructure and drive the widespread dispersal of viral pathogens into aquatic environments. In May 2024, Porto Alegre (southern Brazil) experienced an unprecedented flood that caused record-breaking overflow of the Guaíba hydrological system and prolonged urban inundation. Here we report a one-year longitudinal environmental viral surveillance study, comprising seven campaigns between May 2024 and April 2025. Surface waters were analyzed by RT-qPCR for SARS-CoV-2, norovirus genogroups I and II, hepatitis A virus (HAV) and hepatitis E virus (HEV). All five targets were detected simultaneously during the flood peak, reflecting widespread contamination possibly driven by sewage overflow and multi-site infrastructure failure. Thereafter, the number of targets detected per campaign was lower and fluctuating (two to four), tracing a transition from an initial multi-pathogen contamination pulse observed during the flood peak to persistent detection of viral genomic material in surface waters. SARS-CoV-2 was detected in every campaign, in a minority of sites in all campaigns except the last (C7, 14/22, 63.6%), where both detection frequency and viral load increased significantly ( p < 0.001 for both; median Ct 29.7 versus 36.8). HEV was detected only at the flood peak; norovirus GII was detected intermittently up to C6, without a significant temporal pattern ( p = 0.13); and norovirus GI was absent between C2 and C5, reappearing in C6 and C7. HAV detection increased significantly over the monitoring period (Cochran–Armitage p < 0.0005), temporally coincident with an officially declared hepatitis A outbreak. These findings demonstrate the value of longitudinal, multi-target environmental surveillance for capturing both the acute virological impact of extreme flooding and the persistent contamination dynamics that follow, pointing to chronic vulnerabilities in urban wastewater infrastructure that outlast the emergency.