Coordinating a rapid response to epidemic outbreaks, Response to current COVID-19 pandemic

Biomax provides the knowledge platform for the PREPARE (Platform for European Preparedness Against (Re-)emerging Epidemics) network, a framework for harmonized large-scale clinical research studies on infectious diseases (ID). The project aims to facilitate timely responses to severe infectious disease outbreaks with real-time evidence from clinical research that will inform public health actions, advance medical knowledge and save more lives.

Biomax provides the BioXM™ Knowledge Management Environment for the PREPARE network to integrate and analyze comprehensive knowledge for any “System under Study” (SuS). The BioXM platform allows fast deployment of large-scale, patient-oriented pathogenesis research studies to respond quickly to outbreaks using a systems medicine approach. It can be used to provide insight into personalized clinical management strategies for patients with acute infections and give real-time evidence to inform wide-ranging public health responses.

In the light of the current global SARS-CoV-2 spread the EC FP7 PREPARE project has switched into outbreak mode level 3 to start clinical research. Biomax contributes to the pathobiological research by generating a comparative human Coronavirus (h-CoV) disease maps.

The h-CoV disease map is produced in a stepwise process starting with automatic literature mining based on available ontologies moving to optimization of ontologies for the h-CoV use case, to manual curation and qualification of results. An extension to in-depth immune system interaction to support vaccine research beyond PREPARE is under consideration.

See how disease maps help PREPARE researchers visualize experimental data in the BioXM knowledge base.

As the worldwide trends of globalization, tourism and climate change continue, infectious diseases have become one of the greatest threats to human health. Recent global epidemics (like the 2009 H1N1 influenza pandemic) have shown that implementing clinical research in response to an emerging infectious disease of global public health importance is extremely challenging.

Before PREPARE there was no European framework to ensure that clinical research is built into epidemic responses. Clinical studies often missed the initial waves of an epidemic and in many cases failed to enroll significant numbers of patients across the clinical spectrum of the disease, thus missing opportunities to improve patient outcomes and coordinated responses.

PREPARE aims to transform Europe’s research response to future epidemics or pandemics by establishing a common European clinical research infrastructure that will be a one-stop shop for public health agencies, policymakers, regulators and funders of research into pathogens with pandemic potential.

To do this, PREPARE is implementing inter-epidemic “peacetime” research programs covering large-scale observational, interventional and adaptive clinical studies, patient-oriented studies into the pathogenesis of infectious diseases, and development of novel near-patient diagnostics. These studies are supported by pre-emptive solutions to ethical, administrative, regulatory, logistical and clinical bottlenecks that hinder rapid responses. In coordination with large European societies (like ERS, ESICM, WONCA Europe, ESCMID and ESWI), PREPARE is educating and training members of the clinical network, external opinion leaders, funders and policymakers, to strengthen the collective capacity and streamline future responses.

These efforts will train the PREPARE consortium to execute a rapid, coordinated deployment of Europe’s elite clinical investigators within 48 hours of a severe infectious disease outbreak.

Biomax provides the BioXM™ Knowledge Management Environment as a flexible multidisciplinary platform for the PREPARE network. With it, PREPARE can use a systems medicine approach to mount a rapid deployment of harmonized, large-scale patient-oriented pathogenesis research studies in response to emerging outbreaks. The BioXM platform integrates comprehensive clinical, biological and functional genome data analysis and pathophysiological insights to inform personalized clinical management of infections as well as collective response strategies.

Initially, PREPARE has used the BioXM system to integrate existing structured sources, literature mining, public databases and ontologies into contextualized graph networks and disease maps to structure prior knowledge on acute respiratory infections (ARI), the project’s pilot System under Study. Molecular, cellular and physiological information has been structured, formalized and integrated with patient-specific clinical and experimental data to enable integrated multi-type data analysis. In this way, the BioXM platform can be used to quickly prepare knowledge bases related to any other SuS (like gastrointestinal or CNS infections) in response to novel emerging outbreaks.

Initial development and validation of the platform is performed using existing patient cohorts. In the event of a new emerging ID outbreak, resources and efforts will be redirected to use the research tools, approach and framework of this platform to rapidly gain pathophysiological insights and inform real clinical management strategies as quickly as possible.

The PREPARE network covers 300 hospital sites and 600 primary care sites in 27 countries and includes some of the leading European academic research groups on infectious diseases. See the PREPARE website for a complete list of partners.

PREPARE is funded by the European Commission’s FP7 Programme under grant number 602525.