Preparedness and capacity building for emerging epidemics

EMPERIE - European Management Platform for Emerging and Re-emerging Infectious Disease Entities

Summary:

The EMPERIE project will establish a network of centres of excellence combining the expertise, techniques and resources necessary for effectively countering (re)- emerging infectious diseases. The consortium will establish common processes, procedures and communication channels in the network linked to relevant stakeholder organisations, notably the World Health Organization (WHO), and local 'grassroots' sites to contribute to a structural and systematic prediction, identification, modelling and surveillance of (re)-emerging infectious disease health threats and pathogens.

Problem:

The expertise and resources necessary for adequate prediction, modelling and surveillance of infectious pathogens today are scattered. In the current situation, when a group of patients presents with a particular disease, and some infectious agent is thought to be the cause, scientists lack a functioning networked infrastructure to respond in a quick and powerful manner. This is the root problem this large-scale Collaborative Project aims to tackle.

Aim:

To effectively counter the potential public health threat caused by new and emerging infectious diseases in Europe, the EMPERIE partners will establish a powerful network capable of structural and systematic prediction, identification, modelling and surveillance of infectious diseases health threats and pathogens.

Expected results:

Specimen collection

The overall objective is to collect sufficient specimens and samples for further processing and analysis or banking. The collections will serve to make an initial inventory of 'pathogen diversity' in humans in several parts of the world and in key risk reservoir species in Europe. Moreover, the collections will be used for the initial identification of unknown pathogens in humans and animals. Sampling will be designed in a way that facilitates the identification of:

• new viruses from animals, especially those in key reservoir species that have previously been shown to represent an imminent health threat to humans;
• viruses already present in humans, but unrecognised - about 30% of all respiratory, enteric, and central nervous system infections appear clinically like viral processes, but no aetiology has been identified.

Isolation and identification

An integrated set of laboratory methods will be provided, which in the manner of a virtual technology platform facilitate the identification of novel viruses. It will also characterise crucial traits of identified novel agents.

Metagenomic sequencing and analysis

The aim is to identify a baseline of DNA and RNA sequences present in various physiological compartments of the chosen populations. This will be done using high-throughput sequencing techniques on pooled samples from different populations. Using samples with known infectious agents, the partners will develop methods to detect novel agents against this defined background. The consortium will generate baseline databases, and the bioinformatic tools to query them using test samples. In addition, novel algorithms for assessing the zoonotic potential of novel viruses by quantifying homologies with viruses in other species will be developed, plus downstream analyses of the molecular basis of species specificity.

Pathogen containment: diagnostics and intervention options

The information from virus identification studies will be used in order to facilitate early intervention by diagnostics, vaccines and antiviral agents. The transfer of critical material and information from fundamental studies into diagnostic and clinical application is currently a bottleneck in virology research. Test formats to be developed include real-time RT-PCR, recombinant ELISA, and standardised immunofluorescence assays.

Whenever a new pathogenic virus is recognised, timely development of vaccines is desirable. Validated animal models are a necessary prerequisite for entering into vaccine research. Animal models will be tested for their congruence with human immune response, and after validation, these animal models will be established in centralised facilities that are available for evaluating candidate vaccines as produced in this project.

Antiviral drugs have proven useful options for immediate and mid-term intervention into virus outbreaks. The consortium will use full virus cell-culture systems for screening antiviral drug candidate libraries, and will provide replicon systems that can be forwarded to the pharmaceutical industry for high-throughput screening of antiviral drug candidate libraries. A company is participating in this project to facilitate transfer to industry.

Synthesis, prediction and preparedness

New analytical tools will be built for rapid epidemiological characterisation of an emerging epidemic and optimisation of control options. The focus is on making maximum use of limited and noisy/uncertain data using sophisticated statistical and mathematical tools, plus more fundamental work on the evolutionary drivers for zoonotic transfer and adaptation to new host species.

There are six objectives:

1. modelling pathogen emergence and establishment, and predicting risk factors for zoonotic transfer;
2. real-time analysis of outbreaks of poorly characterised emerging pathogens;
3. optimising syndromic surveillance for detection of case clusters of emerging infections;
4. developing generic modelling toolkits for modelling emerging pathogens;
5. using novel diagnostics to optimise public health interventions for containment of emerging pathogens;
6. optimising intervention strategies to minimise adaptation of emerging pathogens.

Potential applications:

• diagnostic real-time PCR and ELISA or IFA assay with validation data;
• full virus antiviral assay;
• reverse genetics system;
• replicon system;
• recombinant vaccine;
• exemplar modelling and analysis computer programs.

Coordinator:

Partners: