SARS-CoV-2 quantification

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) is a positive-sense single-stranded RNA virus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the COVID-19 pandemic. SARS-CoV-2 was first identified in the city of Wuhan, Hubei, China, and the World Health Organization (WHO) declared a public health emergency of international concern from January 30, 2020, to May 5, 2023. For more information about symptoms, risks and vaccination against SARS-CoV-2, visit the corresponding site of the Swedish Public Health Agency.

Beside respiratory droplets and aerosols, SARS-CoV-2 viral particles, like many other human coronaviruses, are also excreted in the stools of infected individuals. This enables the possibility for SARS-CoV-2 virus to be detected in wastewater and population-level infection trends of COVID-19 to be followed by wastewater-based epidemiology (WBE).

The data presented on this page is generated in the SLU (Swedish University of Agricultural Sciences) laboratories of SEEC (Swedish Environmental Epidemiology Center). The data and visualisation on this page are usually updated weekly, typically on Mondays. Please refer to the Methods for details on measurements and calculations. All related dashboards can be found on the Wastewater Surveillance page, and sampling sites and project details are available in the Wastewater Monitoring Background.

Important Note:
The scores provided in the dataset and depicted in the plot below are preliminary, so corrections and changes may occur. Data and information about the group on this dashboard are updated frequently, so please check back regularly to stay up to date.
Please note that although the same methods are used for all cities shown on this tab, differences in the wastewater collection systems and populations of different cities might bias direct comparisons between cities.

Visualisations

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Code used to produce plot: Script to produce plot.

Commentary from the research group

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Commentary:

Reports from the research group

The group provide reports to summarise their latest findings. The latest report is available here (only available in Swedish).

Dataset

Contact: anna.szekely@slu.se and javier.vargas@slu.se

Download the data: Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file.. Data are available from week 38 of 2020; updated weekly.

How to cite the dataset:

Székely, A. J., Malmberg, M., Vargas, J., Mohamed, N., Dafalla, I., Petrini, F., Davies, L. (2023). Dataset of SARS-CoV-2, influenza A and influenza B virus content in wastewater samples from wastewater treatment plants in Sweden. https://doi.org/10.17044/scilifelab.14256317.

Methods

Wastewater is collected from several different treatment plants around the country. For more information about the treatment plants, visit the page about the background of wastewater surveillance. For most cities represented on this page, raw, untreated wastewater samples that are representative of a single day are collected by flow compensated samplers at the wastewater treatment plants (WWTP). Uppsala is the exception, with all measurements since week 16 of 2021 instead representing 1 week. In Uppsala, samples are collected daily, and then combined flow-proportionally into one composite weekly sample for the purpose of analyses.

The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method (Ahmed et al., 2020). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega).

Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes 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). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of 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). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: Isaksson et al. (2022).

The data in the graphs and datafile is presented in three different formats:

PMMoV normalised SARS-CoV2 content represents the ratio of the copy numbers of SARS-CoV2 and PMMoV measured by the SARS-CoV2 assay and PMMoV-assays, respectively, multiplied by 1000. As the SARS-CoV2 assay provides proxies for SARS-CoV2 virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of SARS-CoV2 infections in the population of the wastewater catchment area.
SARS-CoV2 genome copies concentration presents the SARS-CoV2 copy number concentration measured in the wastewater. These data is influenced by the setup of the different wastewater collection nsystems and is therefore not suitable for comparison betwwen sites. The virus concentrations in the wastewater are also influenced by the weather events that impact wastewater flow (e.g., heavy rain or snow melt).
SARS-CoV2 genome copies/day/inhabitant represents the daily virus amount estimated in the wastewater normalized for the number of inhabitants connected to the system. These data allows for comparison of different sites but some delays in the presentation of these data may occur compared to the other.

How to cite the method:

Isaksson, F., Lundy, L., Hedström, A., Székely, A. J., Mohamed, N. (2022). Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. Environments, 9, 39. https://doi.org/10.3390/environments9030039.

SARS-CoV-2 variant analysis from wastewater (data available in the European Nucleotide Archive (ENA) under project number PRJEB60156): The group at SLU analysed samples from Uppsala, Örebro, Umeå, and Kalmar (2021-2022).

Archived data from SLU

Quantification of SARS-CoV-2 by other groups

Other groups also quantified SARS-CoV-2 in wastewater in Sweden. The groups used different methods to quantify SARS-CoV-2 and, in some cases, measured different areas of Sweden. All of the data from the groups below is historic:

Gothenburg university (GU): Quantification of the level of SARS-CoV-2 in wastewater from Gothenburg by the Norder group at GU.
SEEC-KTH node: Quantification of the levels of SARS-CoV-2 in wastewater from Stockholm and Malmö by the SEEC-KTH node (no longer updated after June 2023, historic data is available).