Katarina Öjefors Stark

The network of the national COVID-19 Data Portals was developed and linked to the COVID-19 Data Portal (https://www.covid19dataportal.org/)inresponsetothe need for rapid data sharing and analysis during the 2020–2022 SARS-CoV-2 pandemic. Built on open-source code developed by the Swedish COVID-19 Data Portal (now the Swedish Pathogens Portal, www.pathogens.se) the network included 12 national portals addressing demand for local open data sharing and access, across data types and resources. It provides a robust case study of national initiatives for FAIR (Findable, Accessible, Interoperable and Reusable) resources and a foundation for future pandemic preparedness across pathogens globally. In this paper we outline the structure of the origins of the network of National COVID-19 Datal Portals, the technical aspects and code originating from the Swedish Portal and provide an overview of the services and tools offered by each Portal. The paper showcases the process and operation of four Portals: Sweden, Poland, Spain, Norway and The Netherlands. In this study, we observe that pandemic response greatly benefits from an established infrastructure that can be quickly mobilised, developed and extended. Collaborations and preparation built on solid foundations over several years, supported by investment in the form of national and international research grants, is key for sustainability, continuation and readiness to deploy such efforts.

Genomic technologies such as PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring—including the detection of vaccine escape variants and new strains. Applying NGS to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based approaches. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities. We further highlight that the infrastructure, funding and government-policy context in which surveillance operates acts as an enabling condition for these activities, and that technical standardisation alone is unlikely to deliver durable, comparable surveillance in its absence.

Genomic technologies such as PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring—including the detection of vaccine escape variants and new strains. Applying NGS to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based approaches. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities.

Genomic technologies like PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring—including the detection of vaccine escape variants and new strains. NGS applied to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based ones. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities.

The network of the national COVID-19 Data Portals was developed and linked to the COVID-19 Data Portal ( https://www.covid19dataportal.org/) in response to the need for rapid data sharing and analysis during the 2020-2022 SARS-CoV-2 pandemic. Built on open-source code developed by the Swedish COVID-19 Data Portal (now the Swedish Pathogens Portal, www.pathogens.se) the network included 12 national portals addressing demand for local open data sharing and access, across data types and resources. It provides a robust case study of national initiatives for FAIR (Findable, Accessible, Interoperable and Reusable) resources and a foundation for future pandemic preparedness across pathogens globally. In this paper we outline the structure of the origins of the network of National COVID-19 Datal Portals, the technical aspects and code originating from the Swedish Portal and provide an overview of the services and tools offered by each Portal. The paper showcases the process and operation of four Portals: Sweden, Poland, Spain, Norway and The Netherlands. It considers useful lessons and approaches for future pandemic preparedness which enable researchers to easily identify and obtain the key data from resources on a national and international level.