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. 2022 Nov 20:848:157707.
doi: 10.1016/j.scitotenv.2022.157707. Epub 2022 Jul 29.

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

Affiliations

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

María Noel Maidana-Kulesza et al. Sci Total Environ. .

Abstract

The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance. 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 Salta (Argentina), two of them receiving discharges from wastewater plants (WWTP), were monitored from July to December 2020. Fifteen water samples from each point (75 in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantified by RT-qPCR. Also, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize SARS-CoV-2 concentration, which was compared to 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; FIBs were within acceptable limits for recreational activities. Mojotoro River's water quality was not affected by the northern WWTP of the city. Instead, Arenales River presented the poorest water quality; at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to significant increase of fecal contamination. SARS-CoV-2 was found in about half of samples in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in Arenales River. No human tracers were 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 normalized viral concentrations strongly correlated with reported COVID-19 cases; thus, Arenales River at AR-2 reflected the epidemiological situation of the city. This is the first study showing 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.

Keywords: Epidemiological surveillance; Human tracers; Normalization; Rivers impacted by wastewater; SARS-CoV-2; Water quality.

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Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Unlabelled Image
Graphical abstract
Fig. 1
Fig. 1
Geographical representation of the sampling sites (a) in Salta city and vicinities at the Province of Salta, northwest of Argentina (b). Three rivers were monitored: Arenales River before (AR-1) and after (AR-2) the discharge of the southern wastewater treatment plant (WWTP-S); Mojotoro River before (MR-1) and after (MR-2) the discharge of the northern wastewater treatment plant (WWTP-N), and La Caldera River (CR). An old wastewater stabilization pond (WWSP), out of use, located between CR and MR-1is also indicated. Shaded pink area corresponds to the coverage of WWTP-N, while shaded orange area corresponds to the coverage of WWTP-S. Illustrative photographs of the sampling points are shown: AR-1 (c), AR-2 (d), MR-1 (e), MR-2 (f), and CR (g).
Fig. 2
Fig. 2
Violin plots representing indicator bacteria determined in 15 monitoring events in five different sampling points (75 samples in total): AR-1 and AR-2 in the Arenales River (before and after the discharges of the southern wastewater treatment plant, respectively), CR in La Caldera River, and MR-1 and MR-2 in the Mojotoro River (before and after the discharges of the northern wastewater treatment plant, respectively). The concentrations of total (TC) and thermotolerant coliforms (TTC) are expressed as the Most Probable Number per 100 mL, while those of E. coli (EC) and Enterococcus sp. (EN) are in Colony Forming Units (CFU) per 100 mL. Violin shapes show the data kernel probability with the boxplots embedded. Boxplots show the interquartile range (IQR) in boxes divided by median values (horizontal lines) with whiskers depicting ±1.5 IQR and outliers as points. The segmented horizontal lines represent the limit values accepted by legislation for recreational water (USEPA, 2012). Bonferroni Post Hoc test from Kruskal Wallis was performed. Medians with different letters for each variable are significantly different (p < 0.05).
Fig. 3
Fig. 3
Evolution of SARS-CoV-2 (CCoV, red solid line), human polyomavirus (CHPyV, green solid line), and RNase P (CRNase P, blue solid line) concentrations, determined in five sampling points: AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River, from July to December 2020 (15 sampling events). Dashed lines represent the limit of detection (LOD) for SARS-CoV-2 (red), HPyV (green) and RNase P (blue). Non detects were arbitrarily represented as LOD/2. Values plotted are the average of duplicates and error bars correspond to the standard deviation (some bars are too small to be seen). Concentrations are expressed in gene copies per liter (gc/L).
Fig. 4
Fig. 4
Cluster analysis performed with nine variables (temperature, pH, conductivity, turbidity, and concentrations of total and thermotolerant coliforms, E. coli, enterococci and SARS-CoV-2) measured in a total of 75 water samples collected in five sampling points: AR-1 and AR-2 in the Arenales River, MR-1 and MR-2 in the Mojotoro River, and CR in La Caldera River, from July to December 2020 (15 sampling events).
Fig. 5
Fig. 5
Plots of the first two axes (with eigenvalues higher than 1, explaining 97.7 % of the accumulated variance) obtained with a linear discriminant analysis conducted with nine variables: temperature, pH, conductivity, turbidity, and concentrations of total coliforms, thermotolerant coliforms, E. coli, enterococci, and SARS-CoV-2. A total of 75 water samples were collected in five sampling points: AR-1 (red circles) and AR-2 (blue circles) in the Arenales River, MR-1 (gray circles) and MR-2 (pink circles) in the Mojotoro River, and CR (green circles) in La Caldera River, from July to December 2020 (15 sampling events).
Fig. 6
Fig. 6
Evolution of SARS-CoV-2 concentration (CCoV) in the Arenales River at two sampling points: AR-1 and AR-2 before and after the southern wastewater treatment plant, respectively, and of the number of COVID-19 active cases accumulated for 14 days before sampling. LOD: limit of detection for SARS-CoV-2 in surface water. Non-detects were arbitrarily represented as LOD/2.
Fig. 7
Fig. 7
Concentration of SARS-CoV-2 experimentally determined (CCoV) at AR-2 in Arenales River and the normalized concentration using three different alternatives: (a) alternative 1 (CN1CoV), using the concentration of human polyomavirus (HPyV), according to Eq. (1), (b) alternative 2 (CN2CoV), using the concentration of RNase P, according to Eq. (2), and (c) alternative 3 (CN3CoV), using the concentration of HPyV and RNase P, according to Eq. (3).
Fig. 8
Fig. 8
Evolution of the normalized concentration of SARS-CoV-2 (gc/L) (CN3CoV, according to Eq. (3)) in the Arenales River at AR-2 and the two-weeks accumulated reported COVID-19 cases, from the 12 July to 27 December 2020 during the first wave of COVID-19 in the city of Salta, Argentina.

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