Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance

The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance to support health authorities. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from the Province of Salta (Argentina), two of them receiving the discharges of the wastewater plants (WWTP) of the city of Salta, were monitored from July to December 2020 during the first wave of COVID-19. Fifteen water samples from each point (75 samples in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantitatively detected by RT-qPCR. In addition, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize the SARS-CoV-2 concentration, which was ultimately compared to the active reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality, and FIB were within acceptable limits for recreational activities. Although Mojotoro River receives the discharge of the northern WWTP of the city, it did not affect the water quality. Instead, the Arenales River presented the poorest water quality and the river at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to the significant increase of fecal contamination. SARS-CoV-2 was only found in about half of the samples and in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in the Arenales River. None of the two human tracers was detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and the normalized (using the two tracers) viral concentrations strongly correlated with the curve of active reported COVID-19 cases; thus, the Arenales River at AR-2 reflected the epidemiological situation of the city. This is, to the best of our knowledge, the first study that showed the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.