Dataset of SARS-CoV-2, RSV, influenza A and influenza B virus content in wastewater samples from wastewater treatment plants in Sweden

This is a metadata record for a continuously updated dataset of respiratory virus RNA in wastewater in Sweden.The dataset is part of a research study led by associate professor Anna J. Székely (SLU, Swedish University of Agricultural Sciences) and her research group in collaboration with multiple wastewater treatment plants across Sweden, including Uppsala Vatten. The research group is part of the Environmental Virus Profiling Research Area of the SciLifeLab National Pandemic Preparedness framework.The data is generated by routine measurements of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus (RSV) in wastewater samples from Sweden. Monitoring started in Uppsala in August 2020, while additional sites joined the program over time, resulting in a national surveillance system. For all sites, raw, untreated wastewater samples representative of a single day (24 hours) are collected using flow-proportional composite samplers. Measurements generally represent 24-hour composite samples. In Uppsala, since week 16 of 2021, samples are collected daily and combined flow-proportionally into a weekly composite sample.The samples are processed according to standardized protocols. Viral genomic material is concentrated and extracted using a direct capture method (Maxwell RSC Enviro TNA kit, Promega), followed by absolute quantification using One-Step RT-qPCR.Absolute quantification of SARS-CoV-2 genome copy numbers is performed using One-Step RT-qPCR. Until week 31 of 2023, quantification was performed using the SARS-CoV-2-specific N1 assay from the Centers for Disease Control and Prevention (CDC). From week 32 of 2023, quantification is performed using the Flu SC2 Multiplex Assay (CDC).Absolute quantification of influenza A and influenza B virus genome copy numbers is performed using One-Step RT-qPCR with the same Flu SC2 Multiplex Assay (CDC) as SARS-CoV-2.Absolute quantification of RSV genome copy numbers is performed using One-Step RT-qPCR with the assay described by Hughes et al. (2022).To correct for variations in population size and wastewater flow, pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay described by Zhang et al. (2006). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content (Symonds et al., 2019).The dataset is presented in multiple formats depending on the pathogen and analysis purpose. PMMoV-normalized virus content represents the ratio of virus copy numbers to PMMoV copy numbers, providing a proxy for infection prevalence in the contributing population. For RSV, three data formats are provided:PMMoV-normalized RSV content, expressed as the ratio between RSV and PMMoV copy numbers multiplied by 1000, representing a proxy for infection prevalenceRSV genome copy concentration in wastewater, reflecting measured concentrations influenced by sampling systems and environmental factors such as precipitation and snowmeltRSV genome copies per day per inhabitant, representing daily virus load normalized to the connected population, enabling comparisons across sites (with possible delays in reporting compared to other metrics)Equivalent normalization and reporting approaches are applied to SARS-CoV-2 and influenza viruses where relevant.The dataset is available as part of the dashboard “Virus surveillance in wastewater from SLU-SEEC”. It can be accessed and downloaded under the heading “Dataset.” Please note that the dataset is continuously updated and preliminary. Ongoing method evaluations and quality control procedures may result in minor adjustments to reported values.An older version of the data was made available via 3 separate dashboards on pathogens.se: "wastewater: influenza quantification (SLU)", "wastewater: RSV quantification (SLU)", "wastewater: SARS-CoV-2 quantification". This has now been combined on to the singular “Virus surveillance in wastewater from SLU-SEEC" dashboard on pathogens.se.<br><br>