Skip to main content
Data Highlights Editorials
All dashboards COVID Symptom Study Sweden (Partner) COVID-19 publication overview CRUSH Covid Uppsala (Partner) Multi-disease serology Post COVID-19 condition Register-based vaccination (RECOVAC) SARS-CoV-2 tests at National Pandemic Centre SARS-CoV-2 variant competition SARS-CoV-2 whole genome sequencing (Region Uppsala) Serology tests for SARS-CoV-2 at SciLifeLab Vaccine administration: COVID-19 Wastewater: Enteric Virus Quantification (GU) Wastewater: Influenza Quantification (SLU) Wastewater: RSV Quantification (SLU) Wastewater: SARS-CoV-2 Quantification
Share data Available datasets Data dashboards Data sources & repositories Sample collection database Research data management
Funding opportunities Ongoing research projects Register-based research Swedish COVID-19 Publications
Emerging Pathogens SciLifeLab PLP PLP Capabilities
All topics Antibiotic resistance COVID-19 Enteric viruses Infectious diseases Influenza Mpox Respiratory Syncytial Virus (RSV)

Pandemic Preparedness Capabilities

SEEC: Swedish Environmental Epidemiology Center


Funding given for project project entitled:

Establishment of the Swedish Environmental Epidemiology Center (SEEC)

PI(s)/Head responsible for the resource:

Anna J. Székely

Host organisation(s):

  • Swedish University of Agricultural Sciences, SLU (Wastewater, Water, Surface, Air & Viability testing). Maja Malmberg, Anna J. Székely, Klas Udekwu.
  • KTH Royal Institute of Technology (Wastewater & Sludge): Zeynep Çetecioğlu Gürol.
  • Karolinska Institute (Air & Viability testing): Antonio Gigliotti Rothfuchs.
  • Uppsala University (Statistical modelling): Stefan Engblom.

Resource description:

SEEC is a national capacity-building center that bridges the current gap between epidemiology and environmental assessment. It provides for rapid and effective response to detected pathogens as well as population level epidemiology. SEEC also stands for the standardization of molecular and experimental methods for continuous assessment of known and emerging pathogens of concern in Sweden.

Our aim is to provide:

  • Continued and extended wastewater-based monitoring of the ongoing Covid-19 pandemic.
  • Pathogen profiling of the built environment and expanded sampling capacity.
  • Help for infection transmission risk assessment in public places.
  • An accessible repository of environmental samples of public health relevance.
  • Capacity for environmental epidemiology research and development.
Research findings:

Over the past two years, SEEC has continued to grow and expanded its reach, capabilities, and impact. Here are some highlights of our most important achievements:

WBE: Core Infrastructure, Surveillance, Method Development & Cutting Edge Research

  • Nationwide Monitoring: SEEC continued weekly wastewater sampling and biobanking, now covering 43% of the Swedish population with over 2,000 samples collected over almost five years.
  • COVID-19 and Beyond: We continued SARS-CoV-2 monitoring and expanded surveillance to include influenza A/B, RSV, and norovirus GI/GII, all presented weekly with open data on the Pathogen Portal. In addition, most recently we confirmed the suitability of wastewater analysis for rotavirus surveillance, and are currently evaluating the potential detection of Mycoplasma.
  • Method Development & Improvements: We evaluated various data normalization approaches and introduced new quality standards to enhance the reliability of our quantitative results—ultimately improving their predictive power and epidemiological relevance.
  • Rapid Variant Tracking: Developed and established fast pipelines using NGS that have helped us detect novel variants of concern before they appeared in the clinical samples (Espinosa-Gongora et al., 2023). In collaboration with AplexBIO, we also benchmarked hyperplex PCR, as a fast and sensitive alternative of NGS (Soares et al., 2025).
  • Antibiotic Resistanc: We are leading a Sweden–South Africa collaboration to assess ETEC bacteria in rural and urban wastewater, and assissted researchers to evaluate AMR geographic spread among Swedish populations.
  • Chemical Markers & Exposome: Explored artificial sweetener consumption during the pandemic (Haalck et al., 2024), and benchmarked Pepper Mild Motile Virus (PMMoV), a food derived plant virus as a population size marker in wastewater against chemical metabolic markers such tobacco, kaffein and various pharmaceutical derivatives. Working with the European Human Exposome Assessment Platform (HEAP), we evaluated the use of wastewater to explore the extent of exposure of different populations to pathogens and chemicals.
  • Flu typing by hp-PCR and qPCR was evaluated and is expected to be included in our routine monitoring from Autumn 2025 offering valuable complement to the current limited clinical flu typing. Beyond Wastewater: Emerging and Endemic Pathogens in Air, Surface and Natural Waterbodies
  • Avian influenz: We developed a method for detection of influenza viruses from natural waters and launched an ongoing surveillance campaign of migratory birds at a nature reserve (Hjällstavik). • Human Fecal Indicators (HuFI) for Safer Waters: We evaluated the use of PMMoV and other molecular HuFIs to track human fecal pollution for surveillance of natural bathing waters.
  • Air Surveillanc: In collaboration with BSL3 PLP (REPLP1-001), we conducted air sampling surveys in nursing homes to study the spread of respiratory viruses in indoor environments.
  • Putting Preparedness to the Tes: We participated in a simulated zoonotic outbreak (PLPTEST, successfully detecting the target in both environmental and vector samples. Collaboration Across Europe and Beyond, and Funding for the Future
  • EU-WISH (EU-Wastewater Integrated Surveillance for Public Health) is a Joint Action under the EU4Health programme supporting the European Union’s capacity to prevent, prepare for and respond to serious health threats. SEEC is not only part of this but also leads the influenza working group..
  • HySE: Beside various new research grants, we also got funding from the Swedish Research Council (VR) to develop cost-effective public health surveillance tools for developing countries.

KTH Nod: The KTH team monitored SARS-CoV-2 in Stockholm (April 2020 - May 2023) and Malmö (August 2021 - May 2023). Our data correlated significantly with clinically diagnosed COVID- 19 cases, aiding in case esHmaHon when widespread tesHng ceased. We explored various methodologies, including two sampling protocols, two RNA concentraHon/extracHon methods, two RT-qPCR methods (TaqMan vs. SYBRgreen), different primers (N1, N2 and N3) and three calculaHon/normalizaHon approaches. From January 2021, we began monitoring SARS-CoV-2 variants of concern (VOCs) using next-generaHon sequencing, hyperplex padlock PCR (hpPCR), and RT-qPCR. Between January and May 2023, at the request of the Public Health Agency of Sweden (Folkhälsomyndigheten), we extended our monitoring to include Arlanda Airport and aircraW from China, as well as the surrounding airport region, to detect potenHal new SARS-CoV-2 variants. The Freyja pipeline analysis was employed to assess VOCs at these sampling points. Our findings were submiged to Nature CommunicaHon. We opHmized RT-qPCR assays for Monkeypox, Adenovirus-F41, and influenza, with long-term surveillance of adenovirus F in Stockholm’s wastewater. Since May 2023, we shiWed focus to analyzing anHmicrobial resistance (AMR) genes in water sources from Sweden, Bolivia, India, Thailand, and Cambodia, collaboraHng with the University of Manchester. Our joint research was published in Environmental PolluHon. Nine scienHfic publicaHons stemming from the project are published in open-access journals and one is under review.

Impact on prepardness for future pandemics:

All surveillance results produced by SEEC are openly accessible through the Pathogen Portal (quantitative data), or in sequence repositories (ENA), ensuring transparency and broad usability for both the professions and public. These data are not only useful from a research perspective but also allows for evidence-based public health interventions. SEEC strengthens Sweden’s ability to detect emerging pathogens, significantly boosting preparedness for future pandemics. Furthermore, the continuous development and evaluation of new methods help future-proof environmental epidemiology, making it a key for a resilient public health system.

KTH Node**: Our findings improve the understanding of monitoring pathogens like SARS-CoV-2, monkeypox, influenza, adenovirus, and microbial pollutants such as anHmicrobial resistance genes in wastewater. This knowledge is crucial for early detecHon and tracking, aiding in controlling infecHous disease spread. Through popular science events, radio, television, newspapers, social media and sharing our data weekly, we raised public awareness about wastewater surveillance, highlighHng its role in detecHng and managing outbreaks.

How this resource can be used for Pandemic Preparedness research:

SEEC provides weekly data on Wastewater-based Epidemiology: SEEC actively monitors wastewater levels of the virus responsible for Covid-19 disease, SARS-CoV-2, in various municipalities of Sweden, covering more than 25% of the population. This data is continuously updated and freely accessible on the Swedish Pathogens Portal.

SEEC offers analysis of diverse environmental samples (e.g., water including wastewater, surface samples, air samples), for presence of pathogens, using both targeted approaches such as qPCR or amplicon sequencing as well as unbiased metagenomics approaches.

Built Environment Epidemiology: SEEC is involved in the worldwide analysis and profiling of built environment surfaces and air, with intermittent sampling of air in clinics, schools, subways, and indoor malls. Through an extensive network, datasets, sampling methods and analysis pipelines are readily available for comparative studies of environmental signals.

SEEC also offers support in experimental design, sampling, logistics, storage and other monitoring relevant processes.

Who is able to access the resource (and under what conditions):

Data (relative virus quantity) is weekly uploaded by Zeynep Cetecioglu Gurol (KTH) and Anna Székely (SLU). Uploaded data can be openly accessed by the general public. Capacities of the resource are available to researchers upon request.

Available data, code, and protocols from the resource:

Dashboard- Wastewater: Influenza Quantification (SLU), Wastewater: RSV Quantification (SLU), Wastewater: SARS-CoV-2 Quantification

Contact information:

Anna J. Székely
Researcher
Email: anna.szekely@slu.se