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Pandemic Preparedness Capabilities

EnBiFlu, testing the efficiency of multifaceted environmental assessment of avian influenza threats and outbreaks


PI(s)/Head responsible for the resource:

Anna J. Székely

Host organisation(s):

Swedish University of Agricultural Sciences, SLU.

Resource description:

Avian influenza, commonly known as bird flu, poses a significant threat to both avian and human populations. The constant evolution of avian influenza viruses (IAVs) in natural reservoirs and their potential to jump the species barrier have made it essential to assess preparedness and response strategies. The EnBiFlu project focuses on evaluating the ability of the Swedish Environmental Epidemiology Center (SEEC) and its collaborators to address avian influenza threats and outbreaks.

This project comprises four distinct working packages (WPs), each addressing specific aspects of avian influenza research and response:

  • WP1 aims to establish standardized methods for detecting avian IAVs in environmental samples including improvement of concentration and viral nucleic acid extraction methods and validation of qPCR and hpPCR-based assays for IAV detection.
  • WP2 aims to assess the possibility to the detect avian IAVs in wild bird populations through sampling of lake water during the spring migration period.
  • WP3 aims to measure transmission of respiratory viruses in high-density poultry farms, which are a critical concern. WP3 will assess the risk of windborne virus spread between poultry units using model respiratory viruses used as aerosolised vaccines.
  • WP4 aims to evaluate the speed and efficiency of the SEEC PLP unit in detecting a potential human outbreak of avian IAV, or a novel IAV. This WP involves a real-time outbreak simulation, where wastewater monitoring protocols are put to the test in rapidly detecting, identifying and evaluating the novel IAV.

As quick and efficient detection and identification are pivotal in responding to potential outbreaks and pandemics, the results of the collaborative work involved in EnvBiFlu will definitely enhance our preparedness and response to the realistic possibility of an avian influenza related threat.

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.
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.

Available data, code, and protocols from the resource:

Dashboard- Wastewater: Influenza Quantification (SLU)

Contact information:

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