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

Abstract

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.

Presence and persistence of SARS-CoV-2 in aquatic environments: A mini-review

“…Studies on aquatic environments reported a wide range of SARS-CoV-2 concentration [ 13 ] ( Figure 1 ). In wastewater, the viral load of reported studies varied between 1.9 × 10 1 and 7.0 × 10 6 copies/L [ 4 , 9 , 6 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ], in secondary treated wastewater between 1.6 × 10 2 and 2.51 × 10 5 copies/L [ 6 , 24 , 25 ], in tertiary treated effluent between 2.0 × 10 1 –1.0 × 10 5 copies/L [ 20 , 21 , 24 , 26 , 27 ], in sludge between 1.3 × 10 3 and 4.6 × 10 8 copies/L [ 28 , 29 ], in river water between 2.0 × 10 2 and 3.19 × 10 6 copies/L [ 16 , 22 , 25 , 30 , 31 , 32 ], and in groundwater between 2.6 × 10 3 and 3.8 × 10 4 copies/L [ 8 ]. As expected, primary sludge has in general higher viral loads than wastewater, because it contains a broad diversity of human viruses, including commonly circulating coronavirus strains.…”

Wastewater, waste, and water-based epidemiology (WWW-BE): A novel hypothesis and decision-support tool to unravel COVID-19 in low-income settings?

“…Advanced wastewater treatment systems, including a combination of secondary and then tertiary treatment based on disinfection using chemicals or ultraviolet irradiation commonly used in developed countries have a higher potential to remove SARS-CoV-2 and its proxies (Randazzo et al, 2020;Rimoldi et al, 2020) than conventional systems dominant in LICs such as those based on aerobic digestion (Guerrero-Latorre et al, 2020;Kolarević et al, 2021;Mahlknecht et al, 2021;Maidana-Kulesza et al, 2021;Westhaus et al, 2021). For example, in Murcia, Spain, all tertiary and secondary effluents from wastewater treatment plants combining advanced treatment processes in the form of disinfection and ultra-violet irradiation tested negative for SARS-CoV-2 RNA (Randazzo et al, 2020).…”

“…(1) SARS-CoV-2 RNA detection in groundwater and surface water systems in low-income settings A few recent studies drawn from LICs and other low-income settings in east Europe, and Latin America provide direct evidence on SARS-CoV-2 RNA presence in raw/untreated surface water and groundwater impacted by sewage (Guerrero-Latorre et al, 2020;Maidana-Kulesza et al, 2021;Mahlknecht et al, 2021;Kolarevic et al, 2021). For example, during the COVID-19 peak in Quito, Ecuador, SARS-CoV-2 RNA was observed in surface water samples from three different sites of a river receiving untreated sewage (Guerrero-Latorre et al, 2020).…”

“…Recent studies have detected SARS-CoV-2 RNA in environmental settings relevant to surveillance of COVID-19 in LICs including: (i) onsite sanitation and toilet systems (Amoah et al, 2021;Del Brutto et al, 2021;Liu et al, 2021;Meng et al, 2020;Peccia et al, 2020aPeccia et al, , 2020bZhang et al, 2020a), and (ii) raw/untreated surface water and groundwater systems receiving raw/untreated or partially treated sewage (Guerrero-Latorre et al, 2020;Kolarević et al, 2021;Rimoldi et al, 2020;Mahlknecht et al, 2021;Maidana-Kulesza et al, 2021). Such raw/untreated surface water and groundwater systems serve as drinking water sources in low-income settings, where such water is often consumed without treatment.…”

Application of human RNase P normalization for the realistic estimation of SARS-CoV-2 viral load in wastewater: A perspective from Qatar wastewater surveillance

“…An accurate normalization factor can be obtained by averaging a series of selected housekeeping genes using the geometric mean approach ( Vandesompele et al, 2002 ). A study conducted by Maidana-Kulesza et al (2021) utilized RNase P to standardize SARS-CoV-2 levels and compared to COVID-19 cases. Although there has not been a consensus method, normalizing using reference genes could result in better accuracy.…”