Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain

Abstract

Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8–36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.

Building-Scale Wastewater-Based Epidemiology for SARS-CoV-2 Surveillance at Nursing Homes in A Coruña, Spain

“…The maximum number of active clinical cases was reported on 13 January. This notable increase in both the SARS-CoV-2 viral load and the number of clinical cases reported corresponded to the emergence of the Alpha variant (B.1.1.7), detected for the first time in the wastewater of the metropolitan area on 16 December 2020 [19]. This emerging VOC totally replaced the previous variant installed in the area in January 2021 due to its greater transmissibility capacity [43,44] and its greater persistence capacity in the human respiratory tract, which leads to a higher viral load in the host.…”

“…Previous studies had already demonstrated the relationship between the viral load in wastewater and the clinical cases [41,42]. Simultaneously, our team performed a twoyear WBE study for the detection of SARS-CoV-2 in wastewater samples at the Bens WWTP in A Coruña (Spain) [19], where statistical modeling was performed to determine the real number of people infected by SARS-CoV-2 from the viral load data obtained in wastewater analysis [19]. These previous works have served as an early warning system throughout the COVID-19 pandemic in A Coruña, evidencing the potential of wastewater surveillance to alert about future outbreaks.…”

“…The 100 mL wastewater samples were kept at 4 • C throughout the process and concentrated by ultrafiltration in a final volume of 500 µL following the protocol previously described by Trigo-Tasende et al [19]. Finally, 500 µL of RNAlater reagent (Thermo Fisher Scientific, Vilnius, Lithuania) was added to preserve the samples at −80 • C for further analysis.…”

Unconventional data, unprecedented insights: leveraging non-traditional data during a pandemic

“…In Italy, these included participatory surveillance platforms ( 33 ), social media data ( 34 ), and wastewater-based epidemiology ( 35 ), among others. Similarly, non-traditional data was employed in Spain through mobility ( 36 ), wastewater ( 37 ), and participatory methods ( 38 ). Within each country in-depth, semi-structured interviews were conducted with key informants who utilized non-traditional data sources during the COVID-19 pandemic.…”

Tackling covid-19 variants

“…Declining testing rates have made case surveillance challenging, but wastewater surveillance can help understand the circulation of SARS-CoV-2 in the population 14. Many countries used wastewater surveillance to support their public health response during the covid-19 pandemic, including the US, the Netherlands, Spain, Hong Kong, Bangladesh, and Uruguay 15161718192021. Despite the clear need for these wastewater programmes, some challenges remain.…”