The surveillance started in mid-September 2020 for the whole country.

Samples are collected every week at each selected wastewater treatment plant (WWTP) using 24-hour volume proportional or time proportional auto-samplers. Samples are stored at 4°C and analyzed within 24 hours. The samples from Wallonia were analyzed by E-BIOM until December 2023, after which the Foodborne Pathogens Unit of Sciensano took over the analyses. Samples from the Brussels-Capital Region and the provinces of West-Vlanderen, Oost-Vlanderen and Vlaams-Brabant are analyzed by the Foodborne pathogens unit of Sciensano while samples from the provinces of Antwerpen and Limburg are analyzed by the Microbiology, Parasitology and Hygiene Laboratory of the University of Antwerp. The three laboratories use a harmonized protocol. After concentration and RNA extraction, the samples were analyzed by RT-qPCR until June 2023 and later on by RT-dPCR. Three target sequences located in two regions of SARS-Cov-2 genome are analyzed. The gene fragments are the N1 and N2 sequences targeting the N gene encoding for the nucleoprotein, and the E gene encoding for the viral envelope protein. Since June 2023 only N2 and E sequences are analyzed. Until June 2023, analyses were performed in duplicates for the three genes (in triplicates until mid-September 2022 in Wallonia, then in duplicates) but since June 2023, each analysis is conducted only once.

The quality of the results is checked and validated at the laboratory level. If the quality is insufficient, additional analyzes are performed. Once received by the data manager, the laboratory results undergo a second validation before being integrated in the database.

The 24 hours-representative flow rates of each WWTP are collected using flowmeters and are provided by the wastewater agencies (Hydria and Aquiris for the WWTPs of Brussels, Société Publique de Gestion de l'Eau (SPGE) for the WWTPs of Wallonia and Aquafin for the WWTPs of Flanders). Domestic inhabitant equivalents (IE) are used to estimate the population coverage of each WWTP. IE are based on several data sources (population data, building type data, connection to the network and WWTPs geographical coverage data). IE are provided by SPGE in Wallonia and by the Vlaamse Milieumaatschappij (VMM) in Flanders. In Brussels the population is estimated based on the data provided by Statbel. The data provided by the wastewater agencies and VMM are validated by the data manager before being integrated in the database.