Periodic Reporting for period 1 - PREPARE-TID (Pipeline for Rapid Diagnostics of Emergency Transboundary Infectious Diseases)
Período documentado: 2024-01-01 hasta 2025-06-30
The increasing threat of transboundary infectious diseases, accelerated by climate change, global travel, and environmental shifts, poses a significant challenge to global health security. Many outbreaks originate at the human-animal-environment interface, yet diagnostic and surveillance systems often operate in silos. The PREPARE-TID project addresses this critical gap by establishing a fully integrated, field-deployable pipeline for the rapid detection, surveillance, and response to emerging pathogens. Grounded in a One Health framework, which recognizes the deep interconnection between human, animal, and environmental health, the project's overall objective is to create a suite of innovative, cost-effective, and easy-to-use tools that can be rapidly deployed to point-of-need settings, especially in resource-limited areas. The project’s pathway to impact involves developing novel diagnostic technologies, integrating them into portable hardware platforms, and linking them with a digital surveillance system. By empowering local experts with these tools, PREPARE-TID aims to drastically reduce the time from sample collection to actionable intelligence, enabling faster containment of outbreaks at their source and strengthening global pandemic preparedness.
The PREPARE-TID consortium has successfully developed a comprehensive, end-to-end diagnostic pipeline. Work began with creating novel nucleic acid extraction chemistries and a unique portable, battery-operated extraction instrument designed to process challenging samples like wastewater, blood, and arthropod vectors directly in the field. For pathogen detection, two distinct hardware platforms were developed. The first is the One Health Pod, a versatile, low-cost (€2−5 per sample), point-of-care qPCR platform. It uses pre-loaded cartridges that allow minimally trained personnel to screen for up to 22 different respiratory agents, mosquito- or tick-borne pathogens, and critical antimicrobial resistance (AMR) markers in under an hour. The second is the self-contained Mobile Suitcase Laboratory, a rugged, all-in-one unit for on-site nanopore sequencing, which has been deployed across seven countries. To make field-based genomic analysis accessible, the project developed Lazypipe NP, a user-friendly, offline bioinformatics pipeline that allows non-specialists to perform complex data analysis in real-time. All diagnostic data is integrated into an innovative One Health digital surveillance platform, which combines a mobile app for field data collection with a web dashboard for real-time monitoring and outbreak visualization. The true power of this integrated pipeline was proven in real-world crises. In Sierra Leone, the Mobile Suitcase Laboratory was deployed to respond to an mpox outbreak, reducing diagnostic turnaround time from days to hours. Following Cyclone Chido in Mayotte, a mobile water-testing laboratory was used to rapidly assess water safety, enabling authorities to target interventions effectively.
The PREPARE-TID project delivers a paradigm shift in infectious disease surveillance by creating a truly integrated "sample-to-action" pipeline that is greater than the sum of its parts. Unlike conventional laboratory-based approaches, this entire workflow is designed for decentralised, field-based operation in resource-limited settings. A key innovation is the combination of speed, affordability, and accessibility. The One Health Pod platform makes multiplex qPCR testing, a gold-standard technology, available for as little as €2 per sample without the need for cold-chain storage of reagents. The Mobile Suitcase Laboratory, coupled with the offline Lazypipe software, democratizes genomic sequencing, removing the dependency on high-end computing infrastructure and stable internet connectivity—a common barrier in outbreak zones. The project moves beyond simply identifying a pathogen; its integrated digital surveillance platform provides immediate epidemiological context by mapping potential transmission routes between humans, animals, and the environment. This holistic One Health approach provides actionable intelligence that is often missing from traditional surveillance. The validated success of the project's emergency deployments in Sierra Leone and Mayotte demonstrates a capability that goes beyond the state of the art, proving that this advanced, integrated system is not just a theoretical concept but a field-tested reality for strengthening global health security.