Wastewater based epidemiology as a silent sentinel of the trend of SARS-CoV-2 circulation in the community in central Argentina

Abstract

Monitoring wastewater for the traces of viruses allows effective surveillance of entire communities, including symptomatic and asymptomatic infected individuals, providing information on whether a specific pathogen is circulating in a population. In the context of the COVID-19 pandemic, 261 wastewater samples from six communities of the province of Córdoba, Argentina were analyzed. From mid-May 2020 to the end of August 2021, raw sewage samples were collected from the central network pipe that enters into the Wastewater Treatment Plants (WWTP) in Córdoba city and five communities in the Punilla Valley. SARS-CoV-2 was concentrated by using the polyethylene glycol-6000 precipitation method. Viral genomes were extracted from concentrated samples, and N- and E-SARS-CoV-2 genes were detected by using real time RT-PCR. Wastewater samples that resulted positive for SARS-CoV-2 genome detection were subjected to viral variants of concern (VOCs) identification by real time RT-PCR. Overall, just by using the identification of the N gene or E gene, the rates of viral genome detection were 43.4% (86/198) and 51.5% (102/198) respectively, and by using both methodologies (positivity criterion: detection of N and / or E gene), the detection rate was 71.2% (141/198). Thereby, the optimal strategy to study the SARS-CoV-2 genome in wastewater would be the use of the combined detection of both genes. Detection of SARS-CoV-2 variants in wastewater reflected their circulation in the community, showing no VOCs detection in the first COVID-19 wave and their co-circulation with Gamma, Alpha and Delta VOCs during 2021. Therefore, SARS-CoV-2 Wastewater Based Epidemiology (WBE) described the introduction, permanence and/or the co-circulation of viral variants in the community. In geographical areas with a stable population, SARS-CoV-2 WBE could be used as an early warning sign of new COVID-19 cases, whereas in localities with a low number of inhabitants and high tourist influx, WBE may only be useful to reflect the circulation of the virus in the community. Overall, the monitoring of SARS-CoV-2 in wastewater can become a silent sentinel of the trend of viral circulation in the community, providing supplementary information for clinical surveillance to support public health measures.

Keywords: COVID-19; Pandemic; SARS-COV-2 variants in wastewater; SARS-CoV-2; Wastewater-based epidemiology.

Graphical abstract

Fig. 1

Geographical representation of the area under study: Argentina and the province of Córdoba, Argentina. The sampling points are indicated in colors. Córdoba City in red and Punilla Valley (Villa Giardino, Huerta Grande, La Falda, Valle Hermoso and Villa Carlos Paz) in yellow.

Fig. 2

Real-time RT-PCR variant detection strategy for the detection of relevant VOC/VOI mutations/deletions present in the spike protein (mutation/deletions identification: N501Y, E484K, delH69V70, K417T, delL242_244L, L452R and P681R).

Fig. 3

Detection of SARS-CoV-2 and VOCs in wastewater from Córdoba city. The curve with dotted line shows the number of cases of reported COVID 19 accumulated in 17 days in Córdoba city (Ministry of Health of Cordoba Province).Bullets and : detection of the SARS-CoV-2 genome by identifying the N and E genes respectively. Pointed Wheels: Identification of SARS-CoV-2 and VOCs by Typing: No VOCs; Alpha, Gamma and Delta.Vertical line: represents the first SARS-CoV-2 genome detection in wastewater on each period.

Fig. 4

Number of daily cases of COVID-19, detection of SARS-CoV-2 in wastewater from Carlos Paz city and circulation dynamics of VOCs. A. Number of COVID-19 cases accumulated at 17 days of integration in Carlos Paz city. Bullets and : detection of the SARS-CoV-2 genome by identifying the N and E genes respectively. Pointed Wheels: Identification of SARS-CoV-2 and VOCs by Typing: No VOCs; Alpha and Gamma.

Fig. 5

Number of daily cases of COVID-19, detection of SARS-CoV-2 in wastewater from La Falda, Villa Giardino and Huerta Grande, and circulation dynamics of VOCs. Number of COVID-19 cases accumulated at 17 days of integration from La Falda, Villa Giardino and Huerta Grande. Bullet and : detection of the SARS-CoV-2 genome by identifying the N and E gene respectively. Pointed Wheels: Identification of SARS-CoV-2 and VOCs by Typing: No VOCs; Alpha, Gamma and Delta.

Fig. 6

Number of daily cases of COVID-19, detection of SARS-CoV-2 in wastewater from Valle Hermoso city and circulation dynamics of VOCs. A. Number of daily COVID-19 cases reported. B. Number of COVID-19 cases accumulated at 17 days of integration from Valle Hermoso. Bullet and : detection of the SARS-CoV-2 genome by identifying the N and E gene respectively. Pointed Wheels: Identification of SARS-CoV-2 and VOCs by Typing: No VOCs; Alpha, Gamma and Delta.