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Pr i n t e d o n w h i t e c h l o r i n e -f r e e p a p e r

Chapter 1 - Preparedness and capacity building for Emerging PREFACE by Manuel Hallen, Acting Director for Health Directorate-General for Research

nfectious diseases are a moving target. The vCJD in the mid 1990s triggered a substantial how in fields as diverse as molecular , evolution of hosts and microbes as well as research effort on transmissible spongiform entomology, and health systems Ithe influence of other environmental factors encephalopathies (TSEs) starting from FP4 un- analysis are required in order to have a lasting such as climate, changes in travel patterns and til today in both the food safety as well as the impact on the health of populations in Europe other social determinants, the use of antibiot- human health programmes. Recognising the in- and worldwide. The project portfolio presented ics/antivirals etc., all lead to changes in the creasing importance of these diseases, the lat- in this publication underlines this fact: it includes distribution, the epidemiology and the clinical est Framework Programme, FP7 (2007-2013), projects not only from the Food Quality and picture of existing infectious diseases and to adds a new dimension of support by creating Safety and the human Health programmes of the development of new infectious diseases. a specific area within the Collaborative Re- FP6, but also from the programme on Scien- Emerging and re-emerging infectious search HEALTH theme dedicated exclusively to tific Support for Policies, and the International diseases (EID) are just the most visible “tip the field of “potentially new and re-emerging Collaboration, Environment and Infrastructures of the iceberg” of these changes that affect epidemics”. This new focal point will allow us to programmes. Importantly, we crossed again all infectious diseases. In its most recent World strategically plan funding priorities and to sys- (as we did in the above mentioned Health Report 2007, the World Health Organi- tematically build a European research capacity research publication) the borders between re- zation (WHO) stresses that infectious diseases in this field. search, policy support and implementation by are not only spreading faster, but also appear to including a number of projects funded through be emerging more quickly than ever before, at Going forward, however, is not possible without the Programme of Community Action in the field a rate of more than one new per year. looking back and taking stock. The present pub- of Public Health. I am very grateful to our col- There are now nearly 40 diseases that were un- lication aims to do exactly that: to give an over- leagues within the Research Directorate General known a generation ago.1 The names of some view of the existing portfolio of EU-supported as well as to our colleagues from the Directorate of these newly emerging diseases, such as projects in the area of EID. As explained in more General for Health and Consumer Protection and AIDS, variant Creutzfeld-Jacobs disease (vCJD - detail in the Introduction, there is no uniform the Public Health Executive Agency for gener- the human version of “mad cow disease”) and classification of this group of illnesses, and our ously sharing information on their projects with SARS as well as those of re-emerging diseases selection of some of the most relevant patho- us and advising us in the selection of projects such as and influenza, emphasise gen-specific projects as well as a larger group of included in this publication. the relevance and extent of this threat. more generic approaches to different aspects of EID is certainly not perfect. It needs to be seen As I hope reading about the different projects About 25% of all annual deaths worldwide are in the context of the structure of our work pro- will convince you, research on EID is crucial still due to infectious diseases and since many gramme, which for example has a separate and for Europe and the world in order to confront of these diseases disproportionately afflict the very important section for research on antimicro- these threats with innovative , drugs, younger population, they are responsible for bial drug resistance, as well as in the context of surveillance schemes and diagnostic tests, as more than 50% of years-of-life lost.2 More previous publications: the very significant invest- well as containment and mitigation methods. specific data on emerging infectious diseases ment into EU-funded influenza research justified Fortunately, new scientific and technological depend on the exact definition of this group a separate publication.3 Influenza projects are developments also make this one of the most and are difficult to consolidate. Importantly, therefore not included here even though they exciting interdisciplinary research areas with a however, the impact of EID goes far beyond just are an essential part of the EID portfolio. The direct impact on the health of millions of people. those numbers: the or pandemic po- present synopsis provides firm evidence of the I look forward to hearing about the successful tential of many of these diseases is what deter- Commission’s ongoing commitment to support outcome of the projects presented here, as well mines the magnitude of their threat. Therefore, research on EID (with an EC contribution total- as to the further strengthening and integration research on surveillance, early recognition and ling over €100 million for the 34 projects listed of the European Research Area through FP7 early intervention are essential in “preparing herein). It is my hope that it will also be a useful funding in this area. for the unknown”. source of information for the scientific community as well as for the interested general public. Research on EID has been included in the Eu- ropean Commission’s Framework Programmes With the majority of EID being of zoonotic (i.e. (FP) for Research since their very inception: animal) origin, research in this field is by its very HIV projects for example were funded as early definition interdisciplinary. But in addition to as 1985 in the first FP, and the emergence of veterinary and human health expertise, know- Manuel Hallen

1 World Health Organisation. World Health Report 2007 (World Health Organisation, Geneva 2007) 2 World Health Organisation. World Health Statistics 2008 (World Health Organisation, Geneva, 2008). 3 http://ec.europa.eu/research/health/poverty-diseases/doc/influenza-research_en.pdf Chapter 1 - Preparedness and capacity building for Emerging Epidemics 5 INTRODUCTION

nfectious Diseases, once considered to be an It also includes the first two projects funded exclusively relevant in low-income countries issue of the past, remain firmly on the agenda in FP7 and six projects funded through the – and under EID we address emerging viral Iof major causes of mortality and years of Programme of Community Action in the field diseases – which to some extent coincide life lost. Emerging and re-emerging infectious of Public Health (see list under “Funding with diseases presenting a potential threat diseases (EID) are of particular concern Programmes” on page 88). to Europe. Hence, research on diseases because they usually hit unprepared populations. such as leishmaniasis or Chaga’s disease is Appropriate diagnostic tests, vaccines, drugs, There is no uniform classification of EID. A not included in this catalogue, while dengue and containment and mitigation measures are frequently used definition states that EID are research projects for example are. frequently not available and there is danger of “ that have newly appeared in a n Influenza is arguably the single most an epidemic or a pandemic outbreak. Research population or have existed previously but are important EID, and constitutes the so on EID is the only way to confront these issues, rapidly increasing in incidence or geographic far largest single disease portfolio in the to enhance preparedness, to react quickly in range”2. But questions like (i) for how long are “Potentially new or Re-Emerging Epidemics” the case of a new epidemic and – to the extent diseases considered “emerging” once they are activity. The Commission has invested more to which that is possible – to “ for the established (is HIV/AIDS still considered and than € 100 million since 2001 into (co-) unknown” through novel surveillance tools, the EID?), (ii) whether antimicrobial drug resistance funding of 49 research projects on a wide development of generic methods and learning is considered an EID, if the pathogen and the variety of aspects of influenza. Because from past experience. clinical picture are otherwise similar to an existing of this extraordinary effort, a separate disease, or (iii) the interpretation of “rapidly publication exclusively dedicated to influenza As outlined in the Preface, the Commission has increasing in incidence or geographic range” (to research projects has been issued3, for a long time invested significant amounts into what extent and where is an EID?) complemented by a press release on the research on EID through previous Research lead to varying lists of pathogens or diseases in first round of FP7 influenza projects4. These Framework Programmes. What is new in different institutions or programmes. projects are therefore not included in this FP7, however, is the creation of a dedicated catalogue. “slot” for EID in the legal basis of this part With a view to the new FP7 activity of “Potentially n As stated in the Preface, we fully recognise of the Framework Programme. The Specific new and re-emerging Epidemics” we considered the importance of a close collaboration Programme Cooperation1 states with regard the following inclusion and exclusion criteria when between human and animal health to its HEALTH theme “Potentially new and selecting projects from a variety of different researchers and consider the pursuit of the re-emerging epidemics: the focus will be on programmes (see Preface) for this publication: “One Health” concept essential in order to confronting emerging pathogens with pandemic n HIV/AIDS, , tuberculosis and tackle the scientific and medical challenges potential including zoonoses (e.g. SARS and antimicrobial drug resistance are all covered of EID. Therefore we include a number of highly pathogenic influenza). Where appropriate, by other sections in the Infectious Diseases projects on zoonotic diseases, even if they provisions will be made for rapidly initiating part of the HEALTH theme. We therefore are primarily concerned with the animal collaborative research aimed at expediting did not include projects on these diseases health aspects. However, again in view of development of new diagnostics, drugs and (which are gathered in other publications). the newly defined FP7 area in the human vaccines for efficient prevention, treatment, and n Similarly, the FP7 HEALTH theme introduces HEALTH theme, projects on emerging animal control of infectious disease emergencies.” a new focus on “Neglected Infectious diseases that are not transmissible to Diseases” – which is more difficult to humans are not found in this synopsis. As a basis for the identification of research differentiate from EID. Our working n For practical purposes we limited our search to capacities, gaps and future funding priorities, definition is to subsume under Neglected the Cooperation and Capacities programmes the present publication therefore attempts Infectious Diseases protozoan, bacterial (and their FP6 predecessors) and did not to assemble the most relevant emerging and helminth infections – which largely include the comparatively (financially) small infectious diseases projects funded in FP6. coincide with diseases that are primarily or fellowship programmes of the People (Marie

1 Council Decision Specific Programme “Cooperation”, Official Journal of the European Union L400/124, 30.12.2006 2 Morse, S.S. Factors in the emergence of infectious diseases. Emerg. Infect. Dis. 1:7-15 (1995) 3 http://ec.europa.eu/research/health/poverty-diseases/doc/influenza-research_en.pdf 4 http://europa.eu/rapid/pressReleasesAction.do?reference=MEMO/06/381&format=HTML&aged=1&language=EN&guiLanguage=en%20-%2030k%20-%201%20 mai%202006%20-

6 Curie Actions) programme. zoonoses are grouped together in a chapter on ENP4Lab, EUTRICOD). Others yet address the n Finally, research projects on the specific food- and waterborne EID and zoonoses. search for new viral drug targets (VIZIER), novel aspect of potential deliberate release of diagnostic screening methods for the detection pathogens (bioterrorism) are not included This however, still leaves us with a substantial of pathogens in blood products (RaSP) or the in our selection. number of 10 admittedly rather heterogeneous assessment of tools for the response to EID projects, which, however, in our opinion each (REACT). We decided to group these projects The decision on how to group the different provide an important contribution to the overall under the heading of “preparedness and projects into chapters for a reader-friendly project portfolio of EID. Some of them cover a capacity building for Emerging Epidemics”. structure proved to be difficult and is certainly large number of core EID research questions, such open to discussion and should be considered as EMPERIE, the first non-influenza FP7 project We hope that the projects included in this as only one of many possible options. The funded under the new activity of “Potentially new brochure document the Commission’s significant number of projects on Dengue and and re-emerging epidemics”. Others concern commitment to support the research needed to other Haemorrhagic fevers, on SARS and on specifically -borne diseases (EDEN), work confront the threat of EID. On the other side this Transmissible spongiform encephalopathies on modelling and economic evaluation of the overview should allow us to identify – together (TSE) lent themselves to disease-specific impact of several infectious diseases (POLYMOD), with the scientific community and public health chapters. Two projects on enteric , one or constitute networks for imported viral stakeholders – gaps to fill and opportunities project on microbial pathogens in drinking water diseases, highly infectious diseases, or high bio- for future funding priorities, which we can and two projects on vector-borne and other safety-level (P4) laboratories (ENIVD, EuroNHID, systematically address over the course of FP7.

Cornelius SCHMALTZ

This publication is the work of many people. First and foremost it is of course the coordinators and scientific teams behind the presented projects, who have – through the concise, well written and interesting description of their work and their results – contributed the content of this brochure. Anna Lonnroth and Alain Vanvossel (Deputy Head and Head of Unit of the Infectious Disease Unit) gave the initial impetus and – together with my direct colleagues Tuija Jansson and Rachida Ghalouci – have provided critical support and advice in every phase of the preparation of the publication. Isabel Minguez-Tudela was an essential counterpart in the unit responsible for animal health and gave valuable advice on the selection of projects from this closely related area. A number of other colleagues in the Research Directorate General (Laurence Moreau, Albrecht Jahn, Jean-Luc Sanne, Jean-Charles Cavitte, Tuomo Karjalainen, Jeremy Bray, Judit Krommer, Sasa Jenko, Maria Douka, Adriana Tumeo, Dirk Pottier and Miroslawa Pezik) have been extremely helpful in identifying and contributing information on projects under their responsibility within the scope of “Emerging Epidemics”. In a well established cooperation, colleagues from the Directorate General for Health and Consumer Protection and from the Public Health Executive Agency have generously shared their project portfolio in this area. My thanks for this go to Michel Pletschette (Head of Unit at the Public Health Executive Agency), Cinthia Menel-Lemos, Marie Christine Avargues, Albrecht Werner, Frank Karcher and Irene Athanassoudis.

7 TABLE OF CONTENTS

Chapter 1 Chapter 2 Preparedness and Capacity Building Dengue and Other For Emerging Epidemics Haemorrhagic Fevers

EMPERIE DENCO European Management Platform for Emerging and Re-emerging Infectious Towards successful dengue prevention and control 34-35 Disease Entities 12-13 DENFRAME EDEN Innovative diagnostic tools and therapeutic approaches for dengue Emerging Diseases in a Changing European Environment 14-15 disease 36-37

VIZIER VHF Diagnostics Comparative Structural Genomics on Viral involved in Replication Development of rapid field diagnostics for identification, control and 16-17 management of haemorrhagic fever outbreaks 38-39

POLYMOD VHF/VARIOLA-PCR Improving Public Health Policy in Europe through Modelling and Economic Development and commercial production of standardised PCR-assays Evaluation of Interventions for the Control of Infectious Diseases 18-19 for detection of haemorrhagic fever viruses and variola and their implementation in the diagnostic service of EU P4 laboratories 40-41 EuroNHID European Network for Highly Infectious Diseases 20-21

ENIVD Chapter 3 Improving the diagnostic and monitoring of encephalitis viruses in Europe SARS with the support of the European Network for Diagnostics of Imported Viral Diseases 22-23 SEPSDA Sino-European Project on SARS Diagnostics and Antivirals 44-45 EUTRICOD European Training and Research Centre for Imported and Highly DISSECT Contagious Diseases 24-25 Development of intervention strategies against SARS in a European- Chinese taskforce 46-47 ENP4Lab European Network of P4 Laboratories 26-27 SARS-DTV Complementary research action to support SARS-related diagnostic REACT tests, therapeutic interventions and development 48-49 Response to Emerging infectious disease: Assessment and Development of core capacities and tools 28-29 SARSVAC Immunoprevention and immunotherapy of SARS 50-51 RaSP Rapid SPR for parallel detection of pathogens in blood 30-31 SARSTRANS Control policy optimisation for SARS and other emerging infections: characterising transmission dynamics and estimating key epidemiological parameters 52-53

8 Chapter 1 - Preparedness and capacity building for Emerging Epidemics EPISARS Chapter 5 Prevention of future SARS epidemics through the control of animal and Zoonoses, Food- and Waterborne human infection 54-55 Emerging Epidemics

SARSControl Med-Vet-Net Effective and acceptable strategies for the control of SARS and new Network for the prevention and control of zoonoses 78-79 emerging infections in China and Europe 56-57 ARBO-ZOONET International Network for Capacity Building for the Control of Emerging Chapter 4 Viral Vector Borne Zoonotic Diseases 80-81 Transmissible Spongiform HEALTHY-WATER Encephalopathies Assessment of human health impacts from emerging microbial pathogens in drinking water by molecular and epidemiological studies 82-83 (N)EUROCJD European Creutzfeldt-Jakob Disease surveillance 60-61 EVENT Providing tools to prevent emergence of enteric viruses 84-85 Prionscreen Development of a blood screening assay for diagnosis of prion diseases DIVINE-Net in humans 62-63 Prevention of emerging (food-borne) enteric viral infections: diagnoses, viability testing, networking and epidemiology 86-87 TSEUR An integrated immunological and cellular strategy for sensitive TSE diagnosis and strain discrimination 64-65 FUNDING PROGRAMMES 88-89 AntePrion Development of a preclinical blood test for prion diseases 66-67 PROJECT INDEX 90 NeuroPrion Prevention, control and management of prion diseases 68-69 COORDINATORS INDEX 91 IMMUNOPRION Immunological and structural studies of prion diversity 70-71 PROJECT ACRONYMS 91 StrainBarrier Understanding prion strains and species barriers and devising novel diagnostic approaches 72-73

GoatBSE Goat BSE: proposal for improvement of goat TSE discriminative diagnosis and susceptibility based assessment of BSE infectivity in goat milk and meat 74-75

Chapter 1 - Preparedness and capacity building for Emerging Epidemics 9

CHAPTER 1 PREPAREDNESS AND CAPACITY BUILDING FOR EMERGING EPIDEMICS

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

Summary: and in key risk reservoir species in Europe. early intervention by diagnostics, vaccines The EMPERIE project will establish a Moreover, the collections will be used for the and antiviral agents. The transfer of critical network of centres of excellence combining initial identification of unknown pathogens in material and information from fundamental the expertise, techniques and resources humans and animals. Sampling will be designed studies into diagnostic and clinical application necessary for effectively countering (re)- in a way that facilitates the identification of: is currently a bottleneck in research. emerging infectious diseases. The consortium • new viruses from animals, especially Test formats to be developed include real-time will establish common processes, procedures those in key reservoir species that have RT-PCR, recombinant ELISA, and standardised and communication channels in the network previously been shown to represent an immunofluorescence assays. linked to relevant stakeholder organisations, imminent health threat to humans; notably the World Health Organization (WHO), • viruses already present in humans, Whenever a new pathogenic virus is and local ‘grassroots’ sites to contribute but unrecognised — about 30% of all recognised, timely development of vaccines to a structural and systematic prediction, respiratory, enteric, and central nervous is desirable. Validated animal models are a identification, modelling and surveillance system infections appear clinically like necessary prerequisite for entering into vaccine of (re)-emerging infectious disease health viral processes, but no aetiology has been research. Animal models will be tested for their threats and pathogens. identified. congruence with human immune response, and after validation, these animal models will Problem: Isolation and identification be established in centralised facilities that are The expertise and resources necessary for An integrated set of laboratory methods will available for evaluating candidate vaccines as adequate prediction, modelling and surveillance be provided, which in the manner of a virtual produced in this project. of infectious pathogens today are scattered. technology platform facilitate the identification In the current situation, when a group of of novel viruses. It will also characterise crucial Antiviral drugs have proven useful options for patients presents with a particular disease, traits of identified novel agents. immediate and mid-term intervention into virus and some infectious agent is thought to be the outbreaks. The consortium will use full virus cause, lack a functioning networked Metagenomic sequencing and analysis cell-culture systems for screening antiviral infrastructure to respond in a quick and powerful The aim is to identify a baseline of DNA and drug candidate libraries, and will provide manner. This is the root problem this large-scale RNA sequences present in various physiological systems that can be forwarded to the Collaborative Project aims to tackle. compartments of the chosen populations. This pharmaceutical industry for high-throughput will be done using high-throughput sequencing screening of antiviral drug candidate libraries. Aim: techniques on pooled samples from different A company is participating in this project to To effectively counter the potential public populations. Using samples with known infectious facilitate transfer to industry. health threat caused by new and emerging agents, the partners will develop methods infectious diseases in Europe, the EMPERIE to detect novel agents against this defined Synthesis, prediction and preparedness partners will establish a powerful network background. The consortium will generate New analytical tools will be built for rapid capable of structural and systematic baseline databases, and the bioinformatic tools epidemiological characterisation of an emerging prediction, identification, modelling and to query them using test samples. In addition, epidemic and optimisation of control options. surveillance of infectious diseases health novel algorithms for assessing the zoonotic The focus is on making maximum use of limited threats and pathogens. potential of novel viruses by quantifying and noisy/uncertain data using sophisticated homologies with viruses in other species will be statistical and mathematical tools, plus more Expected results: developed, plus downstream analyses of the fundamental work on the evolutionary drivers Specimen collection molecular basis of species specificity. for zoonotic transfer and adaptation to new The overall objective is to collect sufficient host species. specimens and samples for further processing Pathogen containment: diagnostics and and analysis or banking. The collections will intervention options serve to make an initial inventory of ‘pathogen The information from virus identification diversity’ in humans in several parts of the world studies will be used in order to facilitate

12 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: EMPERIE Contract/Grant Agreement No: 223 498 Project type: CP-IP EC contribution: €11 909 560 Starting date: To be determined Duration: 60 months

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 Dr James Simon infections; CEO Viroventures CoroNovative BV 4. developing generic modelling toolkits for Rotterdam, Netherlands modelling emerging pathogens; [email protected] 5. using novel diagnostics to optimise public Dr Paul Rota health interventions for containment of Centers for Disease Control and Prevention emerging pathogens; Measles, Mumps, Rubella and Herpesvirus Laboratory Branch 6. optimising intervention strategies Atlanta, US to minimise adaptation of emerging [email protected] pathogens. Prof. M.D. De Jong Academic Medical Center, University of Potential applications: Amsterdam Coordinator Department of Medical Microbiology • diagnostic real-time PCR and ELISA or IFA Prof. Albert D.M.E. Osterhaus Amsterdam, Netherlands assay with validation data; Erasmus MC [email protected] Department of Virology • full virus antiviral assay; ‘s-Gravendijkwal 230 Prof. Neil Ferguson • reverse genetics system; Faculty Building MRC Centre of Outbreak Analysis and • replicon system; P.O. Box 2040 Modelling Imperial College of Science, 3000 CA Rotterdam, Netherlands Technology and Medicine • recombinant vaccine; [email protected] Imperial College Faculty of Medicine • exemplar modelling and analysis computer London, UK [email protected] programs. Prof. Institute of Virology Prof. Derek Smith Key words: Rheinische Friedrich-Wilhelms-Universität University of Cambridge Bonn Department of Zoology emerging infectious diseases, virus, zoonoses, Bonn, Germany Cambridge, UK outbreak, pathogen, containment [email protected] [email protected]

Prof. Sylvie van der Werf Dr Julian Parkhill Unité de Génétique Moléculaire des VR Wellcome Trust Sanger Institute Institute Pasteur Pathogen Sequencing Unit , France Cambridge, UK [email protected] [email protected]

Prof. J.S.M. Peiris Prof. University of Oxford University Clinical Research Unit Department of Microbiology Hospital for Tropical Diseases Pok Fu Lam, Hong Kong , Vietnam [email protected] [email protected]

Dr Masato Tashiro Prof. L. Enjuanes Head of Virology Consejo Superior de Investigaciones Department of Virology Cientificas National Institute of Infectious Diseases Department of Molecular and Cell Biology Toyama 1-23-1, Shinjuku, Tokyo 162 Cantoblanco 8640 Tokyo, Japan Madrid, Spain [email protected] [email protected]

Chapter 1 - Preparedness and capacity building for Emerging Epidemics 13 Emerging Diseases in a Changing European Environment

Summary: Aim: meeting is organised during each annual EDEN gathers 49 public and private research The goal of EDEN is to identify, evaluate and meeting with the selection of a PhD award and institutes from 24 countries with the combined catalogue European ecosystems, environmental a PhD representative. A website was set up experience and skills to reach the project’s com- and socioeconomic conditions linked to global and maintained for these PhD students (http:// mon goals. The ecological and geographical change — including both abiotic (e.g. climatic) ergodd.zoo.ox.ac.uk/edenphd), with a great diversity of the project area covers all relevant and biotic factors — which can influence the deal of practical information, job offers, etc. At European ecosystems: from the polar circle in spatial and temporal distribution and dynamics present, more than 60 students are involved in the north to the Mediterranean basin and its link of pathogenic agents. A coordinated European this network, thus preparing a strong community with West Africa in the south, and from Portugal approach has been adopted to provide predictive of European, Middle East and African scientists in the west to the Danube delta in the east. emergence and spread models including in the domain of emerging vector-borne global and regional preventive, early warning, diseases related to environmental changes. EDEN is organised into a series of ‘vertical’ surveillance, and monitoring tools and scenarios. sub-projects, led and managed by internation- Such tools will have a major impact on improved To cement the EDEN scientific community, open ally recognised experts, and linked together by EU policy development and decision-making, workshops were organised on laboratory a series of integrative ‘horizontal’ activities that both for national and international agencies like diagnosis, geographical information systems, include biodiversity monitoring, environmental the European Centre for Disease Prevention and processing and analysis of remotely sensed data, change detection, disease modelling, remote Control (ECDC) (Stockholm, Sweden). statistical and mathematical modelling. The next

sensing and image interpretation, information workshop, on the R0 concept, will be organised in and communication. Results: Paris in October 2008. The collaborative approach allowed the The leader of each group (sub-project or inte- coordinated collection of field and public A strategy document and several concept grative team) is directly responsible for central health data in a wide range of ecosystems. notes were written to summarise and promote management and sits on the steering commit- Methodological developments were made to original concepts, methods and tools that have tee. Relevant management decisions are taken model these data with environmental variables been developed within the frame of the project: at each level with maximal use of e-communica- remotely sensed at various resolution scales, or risk maps, strategies and scenarios to monitor tion, on the principle of no reply constituting an characterising biodiversity. After the identification and manage vector-borne emerging diseases, agreement. of the main risk factors involved in vector etc. Follow-up projects have been designed dynamics and/or disease emergence and and awarded in competitive calls (the Seventh Problem: dissemination, major conceptual, biological and Framework Programme (FP7), ECDC, the In recent years, several vector-borne, parasitic mathematical advances were made to step from European Space Agency (ESA)). or zoonotic diseases have (re-)emerged and statistical to biological models, and from specific spread in Europe and elsewhere with major to generic models.. Potential applications: health, ecological, socio-economic and political The project will assist in the creation of: consequences. At present, little is known about Up to April 2008, around 100 papers reporting • risk maps of the European ecosystems for a the causes of such changes and the relative these findings were published or submitted to wide range of vector-borne diseases; contributions to them of human-induced land- journals. Many more papers are expected before • disease surveillance/monitoring and early- scape changes, changing activity patterns, the the end of the project because some field studies warning systems to help public health breakdown of traditional control methods and are not completed yet and important results on agencies and decision makers in targeting global and local changes in climate. Europe must modelling and integration will soon be available. surveillance and control of emerging anticipate, prevent and control new emergences vector-borne diseases in Europe and the to avoid major societal and economical crises. Moreover, the first wave of PhD theses is Mediterranean basin. EDEN offers a unique opportunity to prepare for being defended. An important result of the uncertainties about the future of the European project is the establishment of a network of Key words: environment by exploring the impact of environ- PhD students and post-docs sharing common Emerging disease, rodent-borne diseases, ma- mental and other changes on human health. methods and tools, and interacting. A PhD laria, leishmaniasis, tick-borne encephalitis, West-

14 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: EDEN Contract/Grant Agreement No: GOCE-CT-2003-010284 Project type: Integrated Project EC contribution: €11 500 000 Starting date: November 1, 2004 Duration: 60 months

Nile fever, Rift Valley fever, rodents, mosquitoes, sandflies, ticks, ecosystem, remote sensing, mathematical modelling, biology, ecology, risk map, public health, early-warning system, Europe, biome, climate change, environmental change Jean-Pierre Dedet Maciej Kondrusik Université Montpellier I Medical University of Bialystok Jean-François Cosson Laboratoire de Parasitologie Department of Infectious Diseases and Centre de Biologie et Montpellier, France Coordinator Bruno Mathieu Neuroinfections de Gestion des Populations (CBGP) [email protected] Renaud Lancelot EID Méditerranée Białystok, Poland Montferrier-sur-Lez, France CIRAD – Département Systèmes Montpellier, France [email protected] [email protected] Ouafaa Fassi-Fihri Biologiques [email protected] Institut Agronomique et Campus international de Baillarguet - Monka Zahler-Rinder Ake Lundkvist Vétérinaire Hassan II TA A-DIR / B Zdenek Hubalek University of Munich Swedish Institute for Rabat, Morocco 34398 Montpellier Cedex 5, France Academy of Science Munich, Germany Infectious Disease Control [email protected] [email protected] Institute of Vertebrate Biology [email protected] Swedish Defence Research Agency Center Brno, Czech Republic for Microbiological Preparedness Amadou Diaïte Hans Heesterbeek [email protected] Maria Kazimirova Solna Municipality, Sweden Institut Sénégalais de Recherches Agricoles Faculty of Veterinary Medicine Slovak Academy of Sciences [email protected] Laboratoire National de Utrecht, Netherlands Marina Gramiccia Institute of Zoology l’Elevage et de Recherches [email protected] Istituto Superiore di Sanita (ISS) Bratislava, Slovakia Herwig Leirs , Senegal Reparto di Malattie trasmesse [email protected] University of Antwerp [email protected] Eric Lambin da vettori e sanita Internazionale Antwerp, Belgium Université Catholique de Louvain Dipartimento di malattie infettive, Veera Vasilenko [email protected] Gabriela Nicolescu Louvain, Belgium Parassitarie e Immunomediate National Health Development Institute National Institute of Research-Development [email protected] , Italy Tallinn, Estonia Antti Vaheri for Microbiology and [email protected] [email protected] Haartman Institute, University of Helsinki ‘Cantacuzino’ David Rogers, Sarah Randolph Helsinki, Finland , Romania University of Oxford Didier Fontenille, Tatjana Avsic-Zupanc [email protected] [email protected] Department of Zoology Jean-François Guegan University of Ljubljana Oxford, UK Centre IRD de Montpellier, UR 016 (DF) / Institute for Microbiology and Immunology Malcolm Bennett Janos Botond Kiss [email protected]; UMR 2724 IRD-CNRS (JFG) Ljubljana, Slovenia University of Liverpool, Senate House Danube Delta National Institute for [email protected] Montpellier, France [email protected] Liverpool, UK Research [email protected] [email protected] Tulcea County, Romania Willy Wint [email protected] Ana Luisa Garcia-Perez [email protected] Environmental Research Group Oxford Instituto Vasco de Investigaciones y Paul Ready Department of Zoology Nurdan Ozer Desarrollo Agrario Museum Ramon Soriguer Oxford, UK Hacettepe University Derio (Biscay), Spain London, UK Estacion Biologica de Donana [email protected] Biology Department, Ecology Section [email protected] [email protected] Seville, Spain Ankara, Turkey [email protected] Alessandra Dellatorre [email protected] Emoke Ferenczi Yusuf Ozbel University of Roma ‘La Sapienza’ ‘Béla Johan’ National Center for Ege University Medical School Zoubir Harrat Rome, Italy Virgilio Do Rosario Epidemiology Department of Institut Pasteur d’Algérie [email protected] Instituto de Higiene e Medicina Tropical Department of Virology İzmir, Turkey Hamma Anassers, Algeria Lisbon, Portugal Budapest, Hungary [email protected] [email protected]; Rosella Lelli [email protected] [email protected] [email protected] Istituto Zooprofilattico Sperimentale Clive Davies ‘G. Caporale’ Rajae El Aouad Antra Bormane London School of Hygiene Laszlo Egyed Teramo, Italy National Institute of Health Public Health Agency & Tropical Medicine MTA Allatorvos-Tudomanyi [email protected] Rabat, Morocco Riga, Latvia London, UK Kutato Intézete (VMRI) [email protected] [email protected] [email protected] Budapest, Hungary Paul Reiter [email protected] Institut Pasteur Maria Dolores Bargues Milda Zygutiene Robert Farkas Insectes et Maladies Infectieuses Universidad de Valencia Centre for Communicable Diseases, Szent Istvan University Amadou Sall Paris, France Dep. Parasitologia, Fac. Farmacia Prevention and Control Budapest, Hungary Institut Pasteur de Dakar [email protected] Valencia, Spain Vilnius, Lithuania [email protected] Dakar, Senegal [email protected] [email protected] [email protected] Antonio Tenorio Montserrat Gallego Centro Nationale de Microbiologia Annapaola Rizzoli Heikki Henttonen Universitat de Barcelona Guy Hendrickx Instituto de Salud Carlos III Centro di Ecologia Alpina Finnish Forest Research Institute Unitat de parasitologia Euro-Aegis Madrid, Spain Trento, Italy Vantaa, Finland Barcelona, Spain Zoersel, Belgium [email protected] [email protected] [email protected] [email protected] [email protected]

http://www.eden-fp6project.net Chapter 1 - Preparedness and capacity building for Emerging Epidemics 15 Comparative Structural Genomics on Viral Enzymes involved in Replication

Summary: genetics and structure. Yet, it is a strange paradox scientific sections: (1) bioinformatics, for The VIZIER project aims to impact the antiviral that genomic and structural characterisation annotation, target selection and data drug-design field through the identification of of RNA viruses was not accepted as a priority integration; (2) virus production and genome potential new drug targets against RNA viruses until very recently. The VIZIER project proposes sequencing; (3) HTP protein production; (4) and their use in a comprehensive structural to fill the existing gap between the necessary HTP crystallisation and structural determination; characterisation of a diverse set of viruses. The scientific characterisation of emerging viruses and (5) target validation to assess the function common strategies used for the development and preclinical drug evaluation. of enzymes and design strategies for virus of antiviral drugs are mainly based on the inhibition. VIZIER rounds off the plan with knowledge accumulated through studies of Aim: training, implementation and dissemination. This virus genetics and structure. The VIZIER project To address society’s needs, scientists need organisation will allow the full characterisation, proposes to fill the existing gap between the to anticipate potential threats in order to be in record time, of a viral target that can necessary scientific characterisation of emerging ready should they arise. The participants of quickly be used to design drugs, either by the viruses and preclinical drug evaluation. the VIZIER project have created a team that pharmaceutical industry through the VIZIER brings together the leading authorities on RNA Industrial Platform, or by any R&D institution. Problem: viruses available in the EU or elsewhere, as well RNA viruses include more than 350 different as many leading European structural biologists. Expected results: major human pathogens and most of the This team includes three partners with P4 VIZIER will produce an unprecedented wealth aetiological agents of emerging diseases: facilities and leaders in the field of structural of data on the replicases of RNA viruses with viruses of gastroenteritis (more than 1 genomics. The development of protocols for a window into antiviral drug development. A million deaths annually), measles (more high-throughput (HTP) protein production representative set of RNA-based viruses that than 45 million cases and 600 000 deaths means that a concerted programme of structure belong to three major classes, profoundly annually), influenza (more than 100 million determination is now appropriate and feasible. different in their replicative strategies, cases annually), (approximately Because they are both the most likely to emerge will be characterised by a concerted and 300 million cases annually), enteroviruses and the most prone to genetic variability, RNA multidisciplinary effort unparalleled to date. At and encephalitis (several million cases of viruses constitute the main VIZIER targets. These the end of this programme, the percentage of meningitis annually), hepatitis C virus (more virus classes use profoundly different replicative sequenced of RNA virus species that than 170 million infected people in the world). mechanisms driven by poorly characterised infect vertebrates will virtually double from 30% replication machineries. Although virus-specific, to 55%. The Severe Acute Respiratory Syndrome the latter are the most conserved and essential (SARS) outbreak has dramatically demonstrated viral components and, thus, the most attractive As an example, the genomic characterisation of how high the economic cost of an epidemic targets for antiviral therapy. Flavivirus (ssRNA+) and Arenavirus (ssRNA-) caused by an emerging virus could be. This genera, which include a large number of human negative impact is actually widening every In the framework of this project, the core pathogens, will be systematically achieved. A day, as many governments are forced to make enzymes/proteins of the replication machinery dramatic advancement is expected in the number costly arrangements to cope with the threat carefully selected among 300 different RNA and diversity of 3-D structures of the replicative of bio-terrorism, which lists some deadly RNA viruses, including strains of medical interest, subunits, now in the one-digit range. VIZIER viruses in its arsenal. To meet these challenges, will be characterised. One unique feature of will aim at the identification of lead molecules science needs to look for new therapeutic and VIZIER, compared to other structural genomics inhibiting the replicative enzymes, but will not prophylactic substances active against RNA projects, is the integration of a major structural enter into the broad field of drug development. viruses, since those currently available are effort within a broad multidisciplinary study, Offers of cooperation will be made to the scarce and of poor potency. having virology upstream and target validation pharmaceutical and biotechnology industry for (candidate drug design) downstream. further drug development, on a contractual The common strategies used for the development basis, and through the VIZIER Industrial Platform, of antiviral drugs are mainly based on the As a result, the implementation plan of the which connects upfront scientific results with the knowledge accumulated through studies of virus VIZIER project is structured into five interacting pharmaceutical industry.

16 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: VIZIER Contract/Grant Agreement No: LSHG-CT-2004-511960 Project type: Integrated Project EC contribution: €12 905 986 Starting date: November 1, 2004 Duration: 48 months

Potential applications: With no equivalent integrated programme in the world, the VIZIER project will undoubtedly have a profound impact on the field of structural Prof. Miguel Coll genomics of emerging viruses. In particular, Collectively, such information is seen as Consejo Superior De Investigaciones it is expected that VIZIER will contribute very being of strong strategic value, not only Prof. Ernest Gould Cientificas (CSIC) significantly to the sequencing of new viruses for the health issues described, but also for Natural Environment Research Council Madrid, Spain CEH Oxford [email protected] (viral genomics), as well as to the deposition in the development of industrial enterprises. Oxford, UK the Protein Data bank of new crystal structures Although diverse DNA-based cellular and [email protected] Dr Gerard Bricogne Global Phasing of viral proteins. These viral proteins can then be viral parasites are also responsible for a Dr Helene Norder Cambridge, UK considered as targets for drug design. large fraction of different human infections, Swedish Institute for Infectious Disease [email protected] none of them is so poorly controlled by Control Virological Department Prof. Alwyn T. Jones The scientific impact on drug design is expected drugs as the RNA viruses are. Recent viral Solna Municipality, Sweden Uppsala University to be considerable through concepts and outbreaks (H5N1, SARS, Chikungunya) [email protected] Uppsala, Sweden [email protected] methods implemented up to the drug design confirm the difficulty of designing drugs Dr Boris Klempa step. Indeed, current drug discovery still often in a timely fashion and the need for Slovak Academy of Sciences Prof. Rolf Hilgenfeld relies on screening compounds in a blind scientific anticipation. Consequently, drug Institute of Zoology Institut Fur Biochemie Bratislava, Slovakia Universitat zu Lübeck manner. Thousands or millions of compounds development against RNA viruses — [email protected] Lübeck, Germany are screened on infected cells or purified the ultimate goal of the VIZIER project [email protected] Dr Hervé Bourhy enzymes, and ‘hits’ are selected. However, initial — is becoming a top priority for global Institut Pasteur Prof. Johan Neyts discovery of the inhibitor activity is followed healthcare programmes. Laboratoire De La Rage K U Leuven Research & Development Paris, France Leuven, Belgium by a lengthy and costly process of toxicology [email protected] [email protected] and other confirmatory studies. It is widely Keywords: RNA viruses, genomics, believed that structural biology is capable of structural genomics, antiviral drugs, Dr Jacques Rohayem Prof. Paolo La Colla Technische Universitat Dresden Universita Degli Studi Di Cagliari speeding up the whole process, and providing crystal structure, bioinformatics, protein Dresden, Germany Monserrato the anticipatory power for future emerging production, high-throughput, screening [email protected] Cagliari, Italy [email protected] viruses. HTP crystallography, coupled to a Etienne L’Hermite strong validation section such as that proposed Bioxtal Dr Andrei M. Leontovich in VIZIER, will undoubtedly reinforce this trend by Coordinator: Mundolsheim, France Moscow State University Dr Bruno Canard [email protected] A.N Belozersky Institute of Physical and leading the field. Indeed, the concept of finding Centre National de la Recherche Chemical Biology a drug together with its target and the putative Scientifique (CNRS) Prof. Dave Stuart Moscow, Russia Université de la Méditerranée The Chancellor, Masters and Scholars of [email protected] bottlenecks to further improvement is scientifically Structural Virology the University of Oxford challenging, innovative, and promising. ESIL Case 925 Oxford, UK Prof. Par Norlund 163, Av de Luminy [email protected] Karolinska Institutet 13288 Marseille, France Department of Biochemistry and VIZIER will develop new products, technologies [email protected] Dr Paul Tucker Biophysics and strategies. The products are RNA virus European Laboratory Stockholm, Sweden Dr Segolene Arnoux (EMBL) [email protected] genomic sequences, soluble viral protein Alma Consulting Group Heidelberg, Germany domains, their 3-D structures, assigned protein Lyon, France [email protected] Dr Stephan Günther [email protected] Bernhard Nocht Institute for Tropical functions, and inhibitors or ligands for selected [email protected] Prof. Martino Bolognesi Medicine protein targets (drug leads). All the above Consiglio Nationale Delle Ricerche Hamburg, Germany products will have a substantial impact on the Dr Alexander Gorbalenya Genoa, Italy [email protected] Leiden University Medical Center [email protected] researchers’ (currently limited) understanding of Molecular Virology Laboratory Dr Eric Leroy, Dr Jean Paul Gonzales the RNA viral replication machinery. They will also Department of Medical Microbiology Prof. Andrea Mattevi Institut de Recherche pour le Leiden, Netherlands University of Pavia Développement identify entirely new targets for the development [email protected] Pavia, Italy Paris, France of specific drugs, with a high level of detail. [email protected] [email protected] [email protected]

http://www.vizier-europe.org Chapter 1 - Preparedness and capacity building for Emerging Epidemics 17 Improving Public Health Policy in Europe through Modelling and Economic Evaluation of Interventions for the Control of Infectious Diseases

Summary: New techniques have been developed to policymakers with the aim of helping improve The aim of POLYMOD is to strengthen public analyse these data, and they are already public health decision-making. health decision-making in Europe through the proving invaluable in helping improve our development, standardisation and application understanding of transmission mechanisms Problem: of mathematical, risk assessment and economic and helping improve mathematical models. Mathematical models are increasingly used to models of infectious diseases. There are four Predicting the impact of control programmes estimate the impact of control programmes issues that are addressed by this project. The against infectious diseases requires the use of against infectious diseases. The accuracy of first is that mathematical models are only as sophisticated transmission dynamic models, as, model predictions depends on the quality of good as the assumptions and parameters on due to the infectious nature of the organism, the data used to parameterise them. Contact which they are built. interventions often have knock-on effects patterns between individuals are critical to beyond those that were directly targeted. the spread of many infectious diseases (e.g. Patterns of mixing are central determinants of as influenza, TB, smallpox, meningitis etc). the transmission of many infections. However, POLYMOD has adapted and developed such However, very little is known about the relevant little is known about contemporary mixing models, based on the contact pattern data, to contact patterns. Instead, analysts have patterns. POLYMOD has therefore surveyed, address a number of public health issues, such assumed certain contact patterns based on for the first time, epidemiologically relevant as the impact that vaccination against varicella very little (or no) data. Clearly, this affects the contact patterns from representative samples may have on the epidemiology of varicella reliability of predictions and the policy advice of eight difference European countries. These zoster virus-related disease. In addition, that follows from this. internationally important datasets have been novel techniques for assessing dose-response supplemented by other information sources, relationships and estimating incidence for use in POLYMOD aims to collect relevant contact including serological data from a number of risk assessments of gastrointestinal pathogens pattern data, improve mathematical models, different countries. have been developed. use these models in economic analysis, and then convey the results to policymakers. Figure 1. Age-specific contact matrices for different The results from models are being combined with European countries. White colour indicates high contact cost and outcome data in a series of economic Aim: rates, green intermediate contact rates and blue colour indicates low contact rates, relative to the country- analyses to assess the cost-effectiveness of To improve public health decision-making, specific contact intensity. Data were presented in different vaccination programmes in Europe. through improved mathematical models of the Mossong et al., PLoS Medicine, 2008. Finally, the results are being presented to spread of infectious diseases.

BE DE FI GB Results: Highlights of the results are presented here.

Figure 1 summarises the age-dependency in contact patterns observed in the eight different countries that performed a survey. It is clear that 0 10 30 50 70 0 10 30 50 70 0 10 30 50 70 0 10 30 50 70 contact patterns tend to be highly correlated AGE OF PARTICIPANT AGE OF PARTICIPANT AGE OF PARTICIPANT AGE OF PARTICIPANT with respect to age (people tend to contact IT LU NL PL others that are similar in age to themselves) and that this is particularly true for children and young adults. This has particularly important implications for vaccination programmes, which are often targeted at one age group, but may have an impact on other ages. Furthermore, it 0 10 30 50 70 0 10 30 50 70 0 10 30 50 70 0 10 30 50 70 is very important for understanding the spread AGE OF PARTICIPANT AGE OF PARTICIPANT AGE OF PARTICIPANT AGE OF PARTICIPANT of emerging pathogens, such as pandemic

18 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: POLYMOD Contract/Grant Agreement No: SP22-CT-2004-502084 Project type: Specific Targeted Research Project EC contribution: €1 613 500 Starting date: September 1, 2004 Duration: 48 months

influenza, and the potential impact of various control measures, including school closure. It is also very noticeable that contact patterns are similar in different European countries, suggesting that it may be able to extrapolate Potential applications: from these surveys to other countries. Full POLYMOD should lead to improved decision- details of the results are given in Mossong et making in the area of infectious disease al. ‘Social contacts and mixing patterns relevant control. The results generated are directly to the spread of infectious diseases’, PLoS applicable to a wide range of diseases, including Marc Aerts Med, 2008, Mar 25;5(3):e71. gastrointestinal diseases, vaccine-preventable Centre for Statistics diseases, and emerging infectious diseases, Hasselt University Utilising these contact patterns new models such as pandemic influenza. Diepenbeek, Belgium of VZV transmission have been developed Mirjam Kretzschmar and have been used to predict the impact of Key words: Department of Public Health Medicine School of Public Health vaccination. The results of these models are modelling infectious diseases; contact patterns; University of Bielefeld being fed into economic analyses, and are health economics; policy evaluation Bielefeld, Germany being presented to decision-makers. Joanna Siennicka Departments of Virology and Epidemiology Figure 2 gives an example of the cost- of National Institute of Hygiene Warsaw, Poland effectiveness of rotavirus vaccination in a number of different countries (Jit et al., Conor Patrick Farrington Open University unpublished). The results suggest that rotavirus Department of Statistics vaccination may not be cost-effective at current Milton Keynes, UK vaccine prices. Piero Manfredi Coordinator Università di Pisa Figure 2. The estimated cost-effectiveness of rotavirus John Edmunds Dipartimento di Statistica e Matematica vaccination in 5 different European countries (data from Health Protection Agency Applicata all’Economia London, UK Pisa, Italy Jit et al. unpublished). [email protected] Gianpaolo Scalia Tomba Pierre van Damme Universita degli studi di Roma Tor Vergata UA-UIA Centrum voor Dipartimento di Matematica Cost effectiveness ratio (base case) de Evaluatie van Vaccinaties Rome, Italy E 250000 Health Universitaire Instelling Antwerpen (UIA) provider Antwerp, Belgium Benoît Dervaux Centre de Recherches en Economie, E 200000 Petrus Franciscus Maria Teunis Sociologie et Gestion (CRESGE) Societal National Institute of Public , France Health and the Environment (RIVM) E Bilthoven, Netherlands Rose-Marie Carlsson 150000 Swedish Institute for Infectious Disease Auranen Kari Control (SMI) National Public Health Institute (KTL) Solna Municipality, Sweden E 100000 Helsinki, Finland Daniel Levy-Bruhl Joel Mossong Institut de Veille Sanitaire (National E 50000 WTP Laboratoire National de Santé Institute for Public Health Surveillance), treshold Luxembourg, Luxembourg (InVS) Saint-Maurice, France

Dominated Dominated availableNot Stefania Salmaso Francesco Candeloro Billari E The Communicable Disease Epidemiology Istituto di Metodi Quantitativi (IMQ) BE FI FR NL UK Unit (CDEU) at Istituto Superiore di Sanità Università Commerciale Luigi Bocconi Rome, Italy Milan, Italy

http://venice.cineca.org/polymod.html Chapter 1 - Preparedness and capacity building for Emerging Epidemics 19 European Network for Highly Infectious Diseases

Summary: passing from a theoretical to a practical, and Expected results: The EuroNHID project aims to develop practicable, approach to infection control and 1. Development of consensus checklists evidence-based checklists to assess hospital HCWs’ safety in the management of patients as a standard and shared tool for the capabilities on infection control and healthcare affected by HIDs, and from a quantitative to a appropriate assessment of infection control workers’ (HCWs’) safety in a network of centres qualitative evaluation of hospital capability in and HCWs’ safety policies. involved in the management of patients dealing with agents of HIDs. affected by highly infectious diseases (HIDs). 2. Performance of a complete, on-the-field Selected centres involved in or planning for Aim: survey that will provide greater knowledge management of HIDs will be identified in The mission of EuroNHID is to prepare on: participating countries and will be surveyed and support referral centres for providing a. capabilities for infection control in using the checklists. Collected data will be appropriate infection control measures and referral centres in Europe, revised to define affordable and sustainable strategies for HCWs’ safety during coordinated b. planned strategies of surge capacity, if improvements based on pre-existing and effective care to patients in case of existing, regarding both structures and conditions, national goals and priorities, which emergencies deriving from naturally emerging personnel, are consistent with EU Community policy. A or deliberately released agents of HIDs, as well c. skilled workforce in referral centres in final report, as an open-access source for the as in the care of sporadic or imported cases. Europe, safe management of HID, will be issued. d. policies of evaluation of knowledge and The specific objectives of the project will be attitude of HCWs working in referral Problem: reached through the following steps: centres, In recent years, attention has been increasingly e. policies for HCWs’ safety, such as focused on threats to health security, including 1. Development of specifically designed surveillance, policies of vaccination those that might be caused by emerging checklists in order to assess hospital and prophylaxis, post-exposure infections or by deliberate release of biological capabilities. The checklists will explore management; agents. Isolation capabilities, infection hospital resources, hospital infection control procedures, and skills of HCWs are control procedures, and HCWs safety 3. Evaluation of the results and their fundamental issues for HID containment. From policies. dissemination to project participants. recent public health threats, such as the SARS This approach will improve the common epidemic, we learned that it is important to 2. Collection of data, using the checklists, know-how and represent a support for assess the effectiveness of infection control through a survey. Only referral centres for participants to highlight problems that practices planned by national and local HIDs will be surveyed. emerged during the survey, to identify authorities, and to improve HCWs’ knowledge aspects that require strengthening, altering of, and compliance with, safer procedures and 3. Performance of a comparative review of or accelerating, and to identify solutions. policies. national capabilities and practices in the management and control of HID, in order to 4. Production of a final report focused on the Some deliverables of EuroNHID will integrate identify lessons that might be learned, and safe management of HIDs. the results of the previous project EUNID. In to perform a spotting of critical points. particular, EuroNHID will verify the applicability Potential applications: of the standards evidenced by EUNID as 4. Development of a final report based on In agreement with centre administrator experts’ recommendations in the field of experiences acquired during the project, authorisation, the survey results will be made minimum requirements for referral hospitals, which should represent a practical guide available for use to national authorities, and and staff safety. for handling different aspects in the public health and other professionals in EU management of highly infectious diseases Member States and elsewhere. The checklists, The added value of the project consists in hospital settings. survey results and final report will made in providing an ‘on-the-field’ evaluation of available on the Web and in EU bulletins (e.g. European capabilities that could enable Eurosurveillance), and will allow other centres

20 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: EuroNHID Contract/Grant Agreement No: 2006205 Project type: Public Health Programme EC contribution: € 374 742 Starting date: July 1, 2007 Duration: 36 months

in Europe to assess their own situations and implement either technical improvements or procedural innovations, eventually adding their experience and solutions to the common know-how. Philippe Brouqui The report could be used by health CHU Nord AP-HM Marseille, France authorities and hospital administrators for the [email protected] implementation and update of country hospital Hans-Reinhard Brodt, capability. This process should encourage Stefan Schilling health authorities in planning local initiatives J. W. Goethe Universitaet devoted to: Frankfurt am Main, Germany [email protected] [email protected] 1. building improvements in the area of Olga Adrami, Helena Maltezou infection control and HCW safety; Hellenic Center for Disease Control and Prevention 2. improving operational capacity and , Greece [email protected] arrangements that were underdeveloped; [email protected] Coordinator Francesco Maria Fusco, Gerard Sheehan 3. making the plans truly functional, and Giuseppe Ippolito University College of Dublin aligned with existing EU benchmarks and Istitut Nazionale per le Mater Misericordiae Hospital Mallatie Infettive (INMI) Dublin, Ireland standards, as well as harmonised and Padiglione Del Vecchio [email protected] consistent with EU Community policy. Via Portuense 292 00149 Rome, Italy Robert Hemmer [email protected]; Centre Hospitalier Key words: [email protected] Luxembourg, Luxembourg highly infectious diseases, isolation, infection [email protected] Norbert Vetter control, health-care workers’ safety Otto-Wagner-Spital Michael Borg Vienna, Austria St. Luke’s Hospital [email protected] Pietà, Malta [email protected] Mira Kojouharova National Center of Infectious and Parasitic Andrzej Horban Diseases Hospital of Infectious Diseases , Bulgaria Warsaw, Poland [email protected] [email protected]

Peter Skinhoj Franc Strle Rigshospitalet University Medical Center Copenhagen, Denmark Ljubljana, Slovenia [email protected] [email protected]

Heli Siikamaki Antony Trilla Helsinki University Central Hospital Hospital Clinic Aurora Hospital University of Barcelona Helsinki, Finland Barcelona, Spain [email protected] [email protected]

Christian Perronne Barbara Bannister, Gail Thomson Hopital Raymond Poincare Royal Free Hospital Hampstead Paris, France London, UK [email protected]; [email protected] [email protected] [email protected]

http://www.eunid.eu Chapter 1 - Preparedness and capacity building for Emerging Epidemics 21 Improving the diagnostic and monitoring of encephalitis viruses in Europe with the support of the European Network for Diagnostics of Imported Viral Diseases

Summary: potential pathogens for biological terrorist 4. to establish links with the European Centre A European network of collaboration was attacks. Although they are ranked with lower for Disease Prevention and Control (ECDC), established to deal with the emerging problems priority, most of them will attract the same public and other international organisations like the of imported viral diseases and the great attention as other bioterrorism (BT) threats. WHO, the Centers for Disease Control (CDC) number of viral pathogens. The improvement of and the Pan American Health Organization diagnostics of these ‘imported’ and emerging Besides WNV, several viral agents can be the (PAHO). virus infections is the most important step in cause of human encephalitis, as there are detecting and dealing with the pathogens. Herpes Simplex virus 1 and 2 (HSV1 and HSV2), Expected results: Therefore, there should be a European Epstein Barr virus (EBV), Rotavirus, Parvovirus 1. Preliminary surveys regarding the collaboration in the area of diagnostics of these B19 (PVB19), Enterovirus, Dengue virus, epidemiological situation of encephalitis virus infections through the implementation Japanese Encephalitis virus (JEV), Tick-borne viruses in Europe; using existing resources of the European Network for Diagnostics of encephalitis (TBE), Saint Louis encephalitis to facilitate a future European surveillance ‘Imported’ Viral Diseases (ENIVD). (SLE), Influenza, Mumps, Measles, Nipah and by identifying causes of unknown diagnosis Hendra. A better understanding of the clinical and improving diagnostics for viral The ENIVD project serves as a focal point for this presentation of encephalitis caused by these encephalitis for a broad European survey. initiative in Europe and is a body recognised by viral agents is required. Moreover, a quick 2. Based on the results of the External Quality the European Community and the Global Outbreak differentiation will strengthen the emergency Assurance, an overview on the diagnostic and Alert Response Network of the World Health response capacity in Europe. capacity of the European laboratories Organization (WHO). This network has been was received and the laboratories with operating for 12 years and has received partial Problem: weaker performances received help and funding for some projects from the EC. The way European countries handle the instructions to improve their work. surveillance and diagnostic of viral encephalitic Another field of interest concerns the presence diseases varies widely. Also, the diagnostic Potential applications: of the recently emerged West Nile virus (WNV) — capacities for these diseases were not For the future, there will be better insight into we have no clear information on its distribution in comparable. the European surveillance situation of viral Europe. The WNV epidemic in the USA has clearly encephalitic diseases. shown the spreading power of WNV; there are Aim: no guarantees that a similar epidemic could not The aims are as follows: Key words: occur in Europe. A certain part of neurological 1. to build up surveillance which provides early encephalitis, virus, diagnostic illness (encephalitis and meningo-encephalitis) recognition and warning for sudden changes remains without aetiological diagnosis because in the incidence of serious neurological

of the lack of understanding and/or use of diseases that may be due to encephalitis Coordinator suitable assays. Infections like West Nile or viruses and to arboviruses, especially WNV, Prof. Matthias Niedrig Sandfly Fever (SF) would be hard to diagnose TBE and Sandfly Fever infections; -Institut Nordufer 20 even though we must consider that they will be 2. to increase the capacity and improve 13353 Berlin, Germany imported occasionally. the diagnostic quality of performing [email protected]

aetiological diagnosis of encephalitis and Dr Stephan Aberle Furthermore, in most cases, Tick Borne meningo-encephalitis, especially WNV, TBE Institut für Virologie Encephalitis (TBE) will be diagnosed only if a and SF virus, within the time of the project Medizinische Universität Wien Vienna, Austria link to a tick bite and/or stay in endemic areas is in nearly all the Member States; [email protected] known. The reason for that may be twofold: the 3. to facilitate mutual help and optimise limited Dr Maria João Alves clinicians may not be aware of the disease, and resources through regular exchanges of Centro de Estudos de Vectores e Doenças that the diagnostics for these kinds of infections expertise, method, reagents, information Infecciosas-Instituto Nacional de Saúde (CEVDI- INSA) require a greater awareness and improved (in particular during meetings) and training Lisbon, Portugal diagnostic assays. All of these viruses are also of laboratory personnel; [email protected]

22 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: ENIVD Contract/Grant Agreement No: 2004206 Project type: Public Health Programme/ Surveillance Network EC contribution: € 523 218 Starting date: January 1, 2005 Duration: 39 months

Dr Tatjana Avšič University of Ljubljana Institute of Microbiology & Immunology Ljubljana, Slovenia [email protected]

Prof. Stephan Becker Institut für Virologie Dr Loredana Nicoletti Philipps-Universität Marburg Dr Jeff Connell Istituto Superiore di Sanitá Marburg, Germany Department of Medical Microbiology Department of Infectious, Parasitic and [email protected] University College Dublin Prof. Mirsada Hukič Immunomediated Diseases Dublin 4, Ireland Clinical Centre University of Sarajevo Laboratory of Virology Dr Matthias Borchert [email protected] Institute of Microbiology, Immunology and Rome, Italy Dr Antonio Tenorio London School of Hygiene & Tropical Parasitology [email protected] Centro Nacional de Microbiologia Medicine Dr Juan Garcia Costa Sarajevo, Bosnia and Herzegovina Arbovirus and Imported ITD/IDEU Laboratorio de Microbiologia [email protected] Dr Matthias Opp Viral Disease Unit London, UK C. H. Cristal-Piñor Laboratoire National de Santé Majadahonda, Spain [email protected] Hospital St. Maria Nai Dr Boris Klempa Division de Virologie [email protected] Ourense, Spain Institute of Virology/Institute of Zoology Luxembourg, Luxembourg Dr Michèle Bouloy [email protected] Slovak Academy of Sciences [email protected] Dr Hugues Tolou Unité de Génétique Moléculaire de Present address: Institut de Médecine Bunyavirides Dr Gerhard Dobler Institute of Virology Prof. Albert Osterhaus Tropicale du Service Institut Pasteur Institut für Mikrobiologie Helmut-Ruska-Haus Erasmus University Rotterdam de Santé des Armées (IMTSSA) Paris, France Munich, Germany University Hospital Charité Department of Virology Marseille Armées, France [email protected] [email protected] Berlin, Germany Rotterdam, Netherlands [email protected] [email protected] [email protected] Dr David Brown Prof. Christian Drosten Prof. Antti Vaheri Central Public Health Laboratory University of Bonn Dr Janusz Kocik Prof. Giorgio Palù University of Helsinki London, UK Institute of Virology Military Institute of Hygiene and Padua University Hospital Haartman Institute [email protected] Medical Centre Epidemiology Medical School Department of Virology Bonn, Germany Warsaw, Poland Department of Histology, Micro-biology Helsinki, Finland Dr Maria Capobianchi [email protected] [email protected] and Medical Biotechnologies [email protected] Istituto Nazionale per le Malattie Infettive Padua, Italy Rome, Italy Dr Anders Fomsgaard Dr Marion Koopmans [email protected] Dr Frank Vandenbussche [email protected] Statens Serum Institut Rijksinstituut voor Volksgezondheid CODA-CERVA-VAR Department of Virology Department of Virology Prof. Anna Papa-Konidari Department of Virology Dr Cornelia Ceianu Copenhagen, Denmark Bilthoven, Netherlands University of Thessaloniki Section Epizootic Diseases Cantacuzino Institute [email protected] [email protected] School of Medicine Uccle, Belgium Vector-Borne Diseases Laboratory Department of Microbiology [email protected] Bucharest, Romania Dr Irina Golovljova Dr Leondios Kostrikis Thessaloniki, Greece [email protected] National Institute for Health Development University of Cyprus [email protected] Dr Marjan Van Esbroeck Department of Virology Department of Biological Sciences Prins Leopold Instituut voor Trop. Dr Saulius Chaplinskas Tallinn, Estonia Laboratory of Biotechnology and Dr Baiba Rozentale Geneeskunde Lithuanian AIDS Centre [email protected] Molecular Virology Infectology Center of Latvia Centraal Laboratorium Vilnius, Lithuania Nicosia, Cyprus Riga, Latvia voor Klinische Biologie [email protected] Dr Stephan Günther [email protected] [email protected] Antwerp, Belgium Bernhard-Nocht-Institut für Tropenmedizin [email protected] Dr Remi Charrel (BNI) Dr Florigo Lista Dr Detlev Schultze Unité des Virus Emergents Hamburg, Germany Army Medical and Veterinary Research Institute for Clinical Microbiology and Dr Ildikó Visontai Faculté de Médecine [email protected] Center Immunology National Center for Epidemiology Marseille, France Rome, Italy St. Gallen, Switzerland Budapest, Hungary [email protected] Paul Heyman [email protected] [email protected] [email protected] Queen Astrid Military Hospital Dr Pascal Cherpillod Research Laboratory for Vector-Borne Dr Graham Lloyd Dr Marc Strasser Dr Hana Zelená University Hospitals of Geneva Diseases Health Protection Agency Spiez Laboratory ZÚ se sídlem v Ostravě Division of Infectious Diseases National Reference Center for Hantavirus Porton Down Biology-Virology Group Ostrava, Czech Republic Central Laboratory of Virology Infections Wiltshire, UK Spiez, Switzerland [email protected] Geneva, Switzerland Brussels, Belgium [email protected] [email protected] [email protected] [email protected] Dr Hervé Zeller Dr Åke Lundkvist Dr Marek Tomasz Szkoda l’Unité de Biologie des Dr Iva Christova Dr Olav Hungnes Swedish Institute for Infectious Disease National Institutes of Health (NIH) Infections Virales National Center for Infectious & Parasitic Norwegian Institute of Public Health Control Department of Virology Emergentes (UBIVE) Diseases Division of Infectious Disease Control Karolinska Institute Stockholm Respiratory Virus Lab Institut Pasteur Sofia, Bulgaria Oslo, Norway Solna Municipality, Sweden Warsaw, Poland Lyon, France [email protected] [email protected] [email protected] [email protected] [email protected]

http://www.enivd.org Chapter 1 - Preparedness and capacity building for Emerging Epidemics 23 European Training and Research Centre for Imported and Highly Contagious Diseases

Summary: by the Bernhard Nocht Clinic at the University Research (KCCR) will be technically upgraded To ensure that the European Union is able to Medical Centre Hamburg-Eppendorf. Thirdly, with a BSL 3 laboratory to study tropical viruses respond appropriately to the possible misuse the Ghanaian Kumasi Centre for Collaborative of the area. of biological agents or outbreaks of rare, but deadly tropical diseases, secure and safe laboratories should be provided, and they should possess the associated research competencies required to develop and maintain expertise in this field. The Bernhard Nocht Institute for Tropical Medicine (BNI) in Hamburg (Germany) is an internationally recognised centre of such expertise and is host to one of only six bio- safety level 4 labs (BSL 4) in the EU.

The BNI has received planning permission for a Fig 1: Outward design of the extension building (left) and its relation to the main building of BNI (right) 5 000 m2 building extension to house BSL 4 and The extension is slightly removed from the main building and is mainly accessed by means of a two-storey bridge which connects the old building to the new building on the first and second floor (above ground level). As a BSL 3 laboratories, and a remodelled treatment transparent steel and glass construction, this bridge has a subtle appearance to allow for the view of the gable of centre for viral haemorrhagic fevers. By that the old building. The extension of the historic main building dating from 1914 and its prominent position above the means, it would create an interdisciplinary jetty at Hamburg Port, make particular demands on the design of the building. Following on from the surrounding research centre environment unique in Europe. buildings, the walls of the building are covered with dark clinker. As this is a free-standing building with a sculptural aspect, the clinker material of the walls continues onto the roof area. Apart from uniformly covering the exterior The extension is to be financed by German surfaces on all sides with clinker, an exceptional feature of the design are the windows. All the windows on the government authorities and will receive upper floors are constructed in two parts, comprising one large window, which allows for views and daylight, and an additional financial resources from the Support additional light panel above. Drawing by Kister, Scheithauer, Gross of Cologne for Research Infrastructures Programme, which permit the optimal equipping of the facility.

Central to the project is the erection of an extension building of 5 000 m2 housing state- of-the-art BSL 3 and 4 laboratories, specific pathogen-free animal husbandry and a BSL 3 insectary. BSL 4 is the highest laboratory safety category and is reserved for diagnostics and research on highly contagious pathogens causing life-threatening disease, such as Lassa or Ebola virus. Some of these pathogens have occasionally been imported into European countries and BNI receives about 40 samples of suspect cases Europe-wide each year. The BSL 3 insectary will allow studies on mosquito- Fig 2: Section through the seven floors of the extension building The lower basement level is designed for animal breeding and features individually disinfectable stables and borne diseases like malaria, dengue or West climate control systems to achieve a specific pathogen free environment (SPF). The upper basement level is for Nile fever. animal experimentation. The ground floor is designed to host the BSL 4 and BSL 3 units for virological research. The 1st floor is designed for molecular virology studies with BSL 2 laboratories and offices. The 2nd and 3rd floors The EUTRICOD project also includes a will host parasitological research and each comprise a BSL 3 laboratory, BSL 2 laboratories, offices and cold rooms. Special constructions are fitted for a microscopy unit, the BSL 3 insectary and a video conference room located on treatment centre for management of highly the 3rd floor. Central technical installations are located on the 4th floor and the upper basement level. Drawing by contagious diseases, which is to be operated architects Kister, Scheithauer, Gross of Cologne

24 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: EUTRICOD Contract/Grant Agreement No: RICN-2004-CT-011900 Project type: Specific Support Action EC contribution: € 2 060 000 Starting date: November 1, 2004 Duration: 60 months

• enhanced accessibility, thereby offering to the scientific community an outstanding research environment, a unique assembly of know-how, excellent training conditions and support for clinical studies; • transregional impact, by opening possibilities for clinical studies in endemic areas of West Africa, including BSL 3 Work in the BSL 4 laboratory pathogens; • enhanced European preparedness for Problem: outbreaks of new and highly infectious Due to the current perceived international diseases, by extending capacities for security threats, several EU Member States are diagnostics and treatment, as well as considering establishing BSL 4 facilities. It is not capability building for qualified staff. clear that such facilities are needed or can be established in many centres around Europe, Potential applications: and indeed for security and safety reasons this may not be desirable. Instead, investment From 2009, the new facilities offer the scientific in central facilities to maintain international community a unique assembly of know-how, leadership and open up access to researchers modern high-security laboratories and excellent is, for Europe as a whole, a more optimal training conditions, as well as support for clinical strategy in line with the key objectives of the studies in West Africa. EUTRICOD will enhance programme as well as the development of the European preparedness for outbreaks of new European Research Area (ERA). and highly infectious diseases by extending capacities for diagnostics and treatment, as Aim: well as building capability for qualified staff. To sustain and extend BNI research capacities and achieve international recognition as a European Key words: Training and Research Centre for Imported and infectious diseases, virology, parasitology, Highly Contagious Diseases (EUTRICOD). emerging diseases, mosquito-borne diseases, high security Expected results: The project will contribute to the development Coordinator of the European research area in the following Prof. Dr Bernhard Fleischer ways: Bernhard-Nocht-Institut fuer Tropenmedizin • improved attractiveness for researchers Bernhard-Nocht-Str. 74 20359 Hamburg, Germany seeking to conduct a specific project [email protected] involving BSL 3 and BSL 4 pathogens, Universitätsklinikum animal models, insect experiments or field Hamburg-Eppendorf studies in West Africa; Hamburg, Germany

http:/www.bni-hamburg.de/eutricod Chapter 1 - Preparedness and capacity building for Emerging Epidemics 25 European Network of P4 Laboratories

Summary: on the operation of a deployable laboratory maintenance of which is very expensive; The European Network of P4 Laboratories for outbreak investigations within or outside 2. the absence of reference samples for the (ENP4Lab) will build on experience gained from Europe. diagnosis of group 4 agents; the previous Euronet-P4 project — preserving 3. the lack of commercially available and strengthening collaboration among Problem: diagnostic tests for these pathogens, European P4 laboratories — and will undertake The group 4 infectious agents must be handled whose identification relies on the use of in- efforts to further enhance preparedness. The in high containment laboratories classified as house reagents that need to be constantly project partners will do so by focusing on the Biosafety Level 4. To date, such facilities in verified and validated. harmonisation and standardisation of existing the European Community are operative in five practices, biosafety and biosecurity issues that countries only: Germany, France, Italy, Sweden, Furthermore, the network recognises that are connected with the laboratory diagnosis of and the UK. Over the past two years, cooperation there is a strong need to provide assistance to group 4 agents, as well as by considering the has been initiated under the Euronet-P4 project, the new European laboratories that are being European enlargement process that will lead and has led to the creation of a European built, as well as to establish a common strategy to the inclusion of new laboratories in the pre- network of P4 laboratories (Euronet-P4), to provide diagnostic assistance to European existing network. for the exchange of procedures (regarding countries that do not have such costly facilities. diagnostics and biosafety), reagents and staff Lastly, a European mobile BSL-4 laboratory is There are three means to achieve this: (1) for training, which need to be reinforced. urgently needed to provide support to outbreak organisation of meetings of network partners investigations carried out by the World Health and invited experts on biosafety or diagnostic Activities are directed towards filling the Organization (WHO) and the European Centre issues for group 4 agents; (2) design and gaps identified in the area of group 4 agents for Disease Prevention and Control (ECDC), in evaluation of a biosafety checklist to be used diagnostics: and outside Europe, in endemic areas or during as an assessment tool for audits of new P4 1. the need to manipulate such agents in outbreaks, and to collect samples to be used laboratories; and (3) implementation of Quality high-containment laboratories that are not as reference biological materials to validate the Assurance exercises and a feasibility study present in all European countries and the new diagnostic tests.

26 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: ENP4Lab Contract/Grant Agreement No: 2006208 Project type: Public Health Programme EC contribution: € 697 165,84 Starting date: October 1, 2007 Duration: 36 months

Aim: The goal of ENP4Lab is to enhance European preparedness for emerging pathogens through efforts aimed at increasing collaboration among reference P4 laboratories in different and validated diagnostic methods, agreed European countries. The aim is also to make background biosafety measures and increased such experience available to other European field investigation capability. In particular, the countries, where new P4 laboratories are being execution of a feasibility study for a deployable planned or are under construction. laboratory will allow EU health organisations to evaluate the overall effort needed for outbreak This will be achieved through the harmonisation investigations in endemic areas or in case of Coordinator of biosafety/biosecurity procedures and the an outbreak of a disease caused by a group 4 Carla Nisii Giuseppe Ippolito, standardisation of viral diagnostics. As a result, agent. For example, the study will also assess the Maria R. Capobianchi, biosafety audits and diagnostic assistance will advisability of either establishing a deployable Antonino Di Caro INMI IRCCS L. Spallanzani be made available to other European countries laboratory or increasing the number of P4 Padiglione Del Vecchio upon request. Support will also be offered to laboratories within Europe in order to increase Via Portuense 292 international organisations or agencies, such preparedness for group 4 agent threats. 00149 Rome, Italy [email protected]; as WHO and ECDC, for outbreak investigations [email protected]; in or outside Europe. Key words: [email protected]; [email protected]; BSL-4, biosafety, laboratory network, biosafety, [email protected] Expected results: viral diagnostics Stephan Günther The following are the main results expected Bernhard Nocht Institut from project activities: für Tropenmedizin 1. lists of existing European P4 laboratories Hamburg, Germany [email protected] and experts associated with each laboratory and diagnostic capabilities that Markus Eickmann Philipps-Universität Marburg are constantly updated and available on Institut für Virologie the project’s website; Marburg, Germany 2. development of a biosafety and biosecurity [email protected] checklist, to be used to perform internal Graham Lloyd and external biosafety audits; Health Protection Agency Porton Down 3. external Quality Assurance exercises Wiltshire, UK for the diagnosis of Arenaviruses, [email protected] Orthopoxviruses, Filoviruses, and Nipah, Ali Mirazimi, Hendra, and Crimean-Congo haemorrhagic Tuija Koivula fever (CCHF) viruses. Smittskyddsinstitutet SMI Solna Municipality, Sweden 4. feasibility study for establishing a European [email protected]; mobile laboratory, including cost estimates [email protected]

and definition of a road map. Hervé Raoul, Marie-Claude Georges Courbot Potential applications: National Institute for Health and Medical Research In the coming years, the work of the network Laboratoire P4 Inserm Jean Mérieux will offer a concrete opportunity to strengthen Lyon, France [email protected]; the global capacity of the European Community [email protected] to face high-threat infections, based on reliable

http://www.euronetp4.eu Chapter 1 - Preparedness and capacity building for Emerging Epidemics 27 Response to Emerging infectious disease: Assessment and Development of core capacities and tools

Summary: of International Health Regulations (IHR): Only a few reports on validated surveillance The EU coordinated response to communicable Reporting from local to intermediate/national systems for healthcare workers (HCWs) diseases has experienced major challenges level; and (4) international contact tracing after focusing on infectious diseases that are likely in the past. Differences in public health exposure to infectious disease. to cause outbreaks have been published. Close preparedness and response, which have surveillance of HCWs is an important source repeatedly been seen within the EU, are difficult Problem: of information on emerging pathogens with a to explain to EU citizens and result in delayed The more persons, goods and media information serious public health impact. public health interventions. The project focuses that move within Europe, the greater the need on areas of generic response which are crucial for improved and coordinated response to The World Health Organization (WHO) has to be for international cooperation for the prevention infectious diseases within the European Union. notified of events that may constitute a public of international spread of infectious diseases, Different responses to similar health threats health emergency of international concern. The and where the necessities of a European effort in various EU countries are likely to negatively decision instrument in Annex 2 of the IHR can to develop a common basis for action have affect the acceptance of the general public and be used as a guide for assessing events. It is up been identified. the compliance by health professionals. One of to the Member States to construct systems for the major reasons for the differences is that the detecting and reporting focal points and events REACT will assess existing and generate new evidence does not yet exist or has not yet been that need to be assessed to the national IHR. evidence. In the framework of the project, the critically assessed. partners will establish tools and best practices, Little evidence is available on the risk of and will in part define core capacities for four So far, there are no procedures available to infectious diseases transmission in conveyances specified areas that are likely to be applicable assist individual countries to decide what core other than aircrafts. Consequently, there is no and acceptable throughout the EU: (1) enhanced capacities are needed for the implementation guidance on when and to what extent contact surveillance during international mass gathering of enhanced surveillance of infectious diseases tracing of passengers should be initiated. events; (2) surveillance of infectious diseases during a specific mass gathering event. in healthcare workers; (3) implementation

28 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: REACT Contract/Grant Agreement No: 2007211 Project type: Public Health Programme EC contribution: € 800 000 Starting date: April 1, 2008 Duration: 30 months

Aim: REACT seeks to provide evidence and tools towards a common European standard for the response to emerging public health threats that are likely to be applicable and acceptable stage in an emergency. The guidance given throughout the EU, for responding rapidly for local health authorities with regard to the and coordinately to public health threats in reporting of IHR relevant events will facilitate Europe. The project addresses specific areas the implementation of the IHR in a harmonised where harmonised best practices and tools are manner throughout Europe. Providing the not in place, but where the need for EU-level scientific basis for the necessity of contact harmonisation has been identified. These areas tracing in ground travel conveyances might be are crucial for international cooperation on the a basis for recommendations of the EC. prevention of the global spread of infectious diseases. Key words: surveillance, preparedness, mass gathering, Expected results: infectious diseases, healthcare workers, The project will provide instruments and tools international health regulations, contact to detect and respond to public health threats tracing in the following areas: • a tool box of core capacities essential for covering surveillances needs in Technical Coordinator mass gathering situations and a training Ekkehardt Lang module; Gesellschaft für Technische • a framework model and indicator list Zusammenarbeit (GTZ) GmbH Reichpietschufer 20 for detecting unusual or clusters of 19785 Berlin, Germany communicable illness in HCWs; [email protected]

• a tool for reporting events from the local Scientific Coordinator to the national level, relevant to the Gabriele Poggensee, Tim Eckmanns, International Health Regulations (2005); Gérard Krause Robert Koch-Institut • a criteria list for the necessity and extent Nordufer 20 of contact tracing after exposure to 13353 Berlin, Germany [email protected] infectious diseases (ground travel and ship [email protected] travel), and definition of a minimum set of variables for international contact tracing Mike Catchpole, Fortune Ncube Health Protection Agency (all conveyances other than those used for London, UK air travel). [email protected] [email protected]

Potential applications: Andrzej T. Zielinski Narodowy Instytut Zdrowia Publicznego The products of REACT will help advance the (National Institute of Public Health) integration of the surveillance of infectious Warsaw, Poland diseases as a component of the management [email protected] of mass gathering events by the event Preben Aavitsland organisers. The surveillance of outbreaks in Nasjonalt Folkehelseinstittut (Norwegian Institute of Public Health) HCWs is an important tool for the recognition Oslo, Norway of exposure to a new pathogen at an early [email protected]

Chapter 1 - Preparedness and capacity building for Emerging Epidemics 29 Rapid SPR for parallel detection of pathogens in blood

Summary: to improve the technologies used for screening During the signal processing, the signals from In the RaSP project, the partners will develop a diseases such as HIV and hepatitis C. The same all (or numerous selected) reference and sensor fast, cheap and at the same time very sensitive need exists to test donor blood in a cheap and spots are taken into account. This leads to a method, which has the potential to detect more fast way, especially in less developed countries decrease in temperature fluctuations (as well as than 100 blood pathogens simultaneously. A where the rate of infected blood is high due to in pressure, reagent concentrations and other new type of surface plasmon resonance (SPR) high prevalence of diseases. parameters). The level of these fluctuations is transducing principle will be exploited, which less than that between two miniaturised sensing allows an essential increasing of the sensitivity Aim: and reference spots, while the total surface of the compared to the state-of-the-art SPR systems. The RaSP partners are proposing an spots remains macroscopic, thus suppressing The consortium aims at the simultaneous immunosensing diagnostic assay, which can be shot noise and other noise sources caused by detection of the pathogens HIV, hepatitis C, used without labels and amplification. A new type miniaturisation of the sensor surface. hepatitis B and to demonstrate the of SPR transducing principle will be exploited capabilities of the system. In parallel, a simple which allows very fast and sensitive testing: the The described innovations will be realised and will version of the system will be set up that will development of most transducers for chemical lead to a highly sophisticated SPR system capable allow for the detection of the presence of any and biological sensors has reached the level of detecting numerous analytes simultaneously of the mentioned blood pathogens. at which they are limited by fluctuations of with a high resolution. Thus, numerous pathogens physical (temperature, pressure) and chemical in a blood sample can be detected speedily, and Problem: (concentrations of reagents) parameters in the in parallel. Sophisticated transducer chips with Biological materials like blood, tissues and close vicinity of the sensing spots. an array of capture molecules are needed in this organs now represent a daily routine material system. The to four pathogens will be that our hospitals and research institutes handle In the RaSP project, the partners apply a new randomly distributed through the transducer chip. for many preventive, therapeutic, and research solution providing a breakthrough for these The output of the system provides information applications. They represent hope for many limitations. The approach is based on the use on whether any of these four pathogens is medical situations, but at the same time they of distributed sensing and reference spots. present in the blood sample. This information pose a risk of transmitting diseases via blood Instead of single macroscopic reference spots, is sufficient for many applications and will lead transfusion, tissue transplantation or organ numerous miniaturised reference spots placed to the exclusion of blood, tissue or organs for transplantation. Thus, there is an urgent need between miniaturised sensing spots are used. transfusion or transplantation.

inlet (sample injection) rotation platform temperature outlet (waste) control laser diode thermo stabilisation current microfluidic measurement cell

power supply control expanding prism transducer chip laser optics imaging optics transducer analytical device unit ccd computer camera Fig 3: RaSP System Concept Overview.

30 Chapter 1 - Preparedness and capacity building for Emerging Epidemics Acronym: RaSP Contract/Grant Agreement No: SP5A-CT-2006-044515 Project type: Specific Targeted Research Project EC contribution: € 1 556 702 Starting date: January 1, 2007 Duration: 36 months

(typically 10 to 20 minutes). The system will be tested in two countries against standard testing methods like ELISA. The resulting diagnostic system will represent a revolution in the field of Coordinator rapid diagnostics. Its applications in the medical Dr Thomas Velten Fraunhofer Institute for Biomedical sector will reduce the risk of dealing with Engineering (IBMT) Fig 4: Experimental setup for testing the improved RaSP contaminated biological materials and will help Ensheimer Strasse 48 transducer chips. The setup is based on a Biosuplar to prevent persons from becoming severely 66386 Sankt Ingbert, Germany 6.321 SPR Reflectometer provided by Mivitec GmbH. [email protected] ill. The system and test will be suited for easy detection of the four most prevalent blood- Dr Hunor Sántha Budapest University of Technology and borne infections that matter in the process of Economics The biological idea of the biosensor will depend blood transfusion. It can be conducted in one Budapest, Hungary mainly on the - reaction. In step, on location where the blood is collected [email protected] contrast to methods like the linked from donors, and it does not need any Dr Kyle Jiang immunosorbent assay (ELISA), the detection sophisticated laboratory preparation. University of Birmingham Birmingham, UK will be performed without any time-consuming [email protected] reaction and with minimal human error and/or Potential applications: Prof. Vladimir Mirsky risk by detection of layer growth due to coupling The RaSP system could become a standard University of Regensburg between the antigen and its antibody on the system for screening donor blood. Furthermore, Regensburg, Germany transducer chip. The main achievement will be other bioanalytical applications are conceivable [email protected] the multiple specificity of the chip as it will have for this system, such as the detection of Dr Waleed Nazmy El-Mazny specificity for all the pathogens required, unlike emergency markers, food monitoring (detection Holding Company for Biological Products and Vaccines (VACSERA) other methods that can be used for only one of food-related pathogens) and monitoring Agouza pathogen at a time. of environmental pathogens and biological Giza, Egypt warfare agents. [email protected] Expected results: Dr Róbert Deák The expected outcome of RaSP is a desktop Key words: MikroMikoMed Kft Budapest, Hungary system, which is easy to use and leads to HIV, hepatitis C, hepatitis B, syphilis, blood [email protected] accurate results within a limited reaction time screening, surface plasmon resonance Dr Alexander Zybine Gesellschaft zur Förderung der Analytischen Wissenschaften e.V. Dortmund, Germany [email protected]

Thomas Hirsch Mivitec GmbH Sinzig, Germany [email protected]

Dr Anton Samoylov V. Lashkaryov Institut of Semiconductor Physics National Academy of Sciences Kiev, Ukraine [email protected]

http://www.rapid-spr.com Chapter 1 - Preparedness and capacity building for Emerging Epidemics 31

CHAPTER 2 DENGUE AND OTHER HAEMORRHAGIC FEVERS

33 Towards successful dengue prevention and control

Summary: to improve our understanding of the natural diseases benefiting from global climate change The DENCO (dengue control) research history of the disease, necessary for vaccine and its consequences. programme covers a wide spectrum of applied and drug development and evaluation). research including clinical research (i.e. case Problem: classification and management, evaluation Partners of the DENCO study include institutions An alarming global spread of dengue disease of new diagnostics), vector research (i.e. from Europe, from Disease Endemic Countries has been ongoing in the last decades with a development of user friendly and effective (DECs) as well as TDR — the research arm substantial social and economic burden placed vector control tools), strategy research (i.e. of the World Health Organization (WHO) for on both individuals and their societies. This identification of cost-effective partnership Tropical Diseases. mosquito-borne disease is a major threat to approaches in the control of the disease and public health throughout South-East Asia and its vectors), and pathogenesis research (i.e. First results will be available in the course of Latin America. the year 2008. A large research platform has been created to foster collaborative research Aim: Basic research, implementation research and the interface of research and policy are components on this important disease. Dengue also has The comprehensive research agenda is aimed of the DENCO study (WP=Work Package; P1-9 = a high probability of being one of the major at advancing our understanding of dengue partners 1-9) pathogenesis and providing better tools for dengue control. Implementation Basic research research Expected results: 1. Objective 1: Viral and host determinants (WP1) Virology, contributing to the pathogenesis of disease immunology Providing well will be identified through the correlation of characterized clinical disease progression, dengue virus genetic Partners: P2, P1, P3, (WP2B) Clinical/ cases and blood samples markers and human immune factors. P4, P5, P8, P9 Public health 2. Objective 2: The case classification for (WP2A) Partners: dengue disease will be improved and Clinical sciences P1, P2, P5 - P9 clinical management guidelines reviewed. 3. Objective 3: The efficacy of novel vector Partners: Delivering tools for field (WP4) Public health/ control methods will be demonstrated. P1, P2, P5 - P9 studies (improved case entomological 4. Objective 4: Acceptability, sustainability, classification of severe cost and effectiveness for implementation (WP3) dengue and guidelines Partners: of different vector control tools will be Entomology for case management; P4, P1, P3, P5, P6, P9 novel vector control tools) determined and the superior strategy or Partners: strategies identified. P3, P4, P5, P6, P9 5. Objective 5: Approval of revised dengue classification/case management and inclusion of the new vector control methods into modified guidelines by WHO regional offices and headquarters will be facilitated. Translating research into policy and practice Potential applications:

(WP5) Public health The process of updating the global dengue Partners: P5, P1 - P4, P6 - P9 guidelines was initiated by the WHO in late 2006 and is continued through 2008. The

34 Chapter 2 - Dengue and other Haemorrhagic Fevers Acronym: DENCO Contract/Grant Agreement No: INCO-CT-2005-517708 Project type: Specific Targeted Research Project EC contribution: € 2 499 779 Starting date: November 1, 2005 Duration: 48 months

findings of the clinical part of the DENCO study can contribute to the re-shaping of dengue prevention and control in the near future. The empirically based outcome of severe disease, which is being validated in the clinical studies, will also have implications on the design of Prof. Axel Kroeger pathogenesis studies and vaccine studies. Special Programme for Research and Training in Tropical Diseases (TDR) Geneva 27, Switzerland The findings of the studies on vector control [email protected]

efficacy and acceptability will be important in Dr Siripen Kalayanarooj order to inform policy in DECs. Pathogenesis Queen Sirikit National Institute of Child studies will lead to an increase in knowledge Health Bangkok, Thailand about viral factors correlated with severe [email protected] disease over a wide geographic range (seven Dr Efren Dimaano countries in two continents). San Lazaro Hospital Department of Vector-Borne/Blood Borne Key words: Infections Manila, Philippines dengue, vector control, case classification, [email protected] pathogenesis, immune response, acceptance, Dr Jeremy Farrar cost effectiveness Oxford University Clinical Research Unit Hospital for Tropical Disease Ho Chi Minh City, Vietnam [email protected]

Dr Elci Villegas Centro Trujillano de Investigaciones Parasitologicas Trujillo, Venezuela [email protected]

Subcontracted Partners Prof. Steffen Fleßa Ernst Moritz Arndt University Greifswald, Germany [email protected]

Dr Maria Guzman Coordinator Instituto Pedro Kouri (IPK) Dr Thomas Jaenisch Havana, Cuba University Hospital Heidelberg [email protected] Section Clinical Tropical Medicine, INF 324 69120 Heidelberg, Germany Affiliated Partners [email protected] Dr Angel Balmaceda Children’s Hospital Manuel Jesús de Revera Dr Philipp McCall Department of Virology Liverpool School of Tropical Medicine National Diagnostics and Reference Center Liverpool, UK Ministry of Health [email protected] Managua, Nicaragua [email protected] Dr Patrick van der Stuyft Prince Leopold Institute of Tropical Dr Lucy Lum Medicine University of Malaya Department of Public Health/Epidemiology Department of Paediatrics Antwerp, Belgium Kuala Lumpur, Malaysia Aedes albopictus : Photo by Michel Dukhan, IRD [email protected] [email protected]

Chapter 2 - Dengue and other Haemorrhagic Fevers 35 Innovative diagnostic tools and therapeutic approaches for dengue disease

Summary: of dengue, there is no specific prevention or control procedures; Dengue disease is a mosquito-borne viral treatment. Thus, there is an urgent need for 3. to transfer technological activities. disease that is one of the foremost public reliable rapid diagnostic and new therapeutic health issues in developing countries. Up to tools for people at risk of DV infection. Expected results: 100 million cases are reported each year. Over Concerning WP1, standardisation of collection 500 000 cases of a life-threatening form of the Aim: of well-characterised sequential clinical data illness, known as dengue hemorrhagic fever The overall objective of DENFRAME is to make and biological samples from dengue patients (DHF), occur each year, with about 25 000 a fundamental contribution to the management (children and adults, with different dengue fatalities (mainly children under 15). To date, of dengue disease in the human populations of patterns) in Asia and South America has been there is no specific prevention or treatment. Latin America and Asia. established. An electronic database has been The consortium has defined three scientific created and data analysis has already started. The main aim of the DENFRAME project is to objectives: The partners have now selected the reference improve the management of dengue disease 1. to develop and implement new diagnostic techniques for virological and immunological in the human populations of Latin America and tools using ligand binding molecules and diagnosis of dengue infections, and tests such Asia. The goals of the project are to develop chemiluminescent biosensor technique; as RT-PCR, viral culture, antigen detection and and implement new diagnostic tools, to devise 2. to devise a comprehensive approach of in-house ELISA, are currently used. a comprehensive approach of innate immune innate immune response to DV infection; response to the infection and to develop 3. to develop lead compounds inhibitors of The consortium has produced recombinant lead compounds inhibitors of Dengue virus DV replication; DV envelope proteins that can be used for (DV) replication. Additional goals include The following are some additional goals: serological assays, in a microtitre plate format the collection of well-characterised data, 1. to collect well-characterised clinical and or as part of chemiluminescent biosensors. identification of prognosis factors involved in biological data, identify prognosis factors They also analysed the interactions between the disease severity, and standardisation of current involved in disease severity, and prepare a envelope protein and a neutralising antibody diagnostic assays. genetic sub-study; strictly specific for DV, to the exclusion of the 2. to standardise the current diagnostic other Flaviviruses. The partners constructed To reach these goals, two complementary Work assays and implement inter-laboratory several derivatives to this antibody to better Programmes (WPs) are being developed: 1. WP1 concentrates on the standardisation and validation of the current diagnostic assays, and the development of new diagnostic tools. 2. WP2 aims at developing an integrated approach to understand the DV-host interactions focusing on key components of innate , and identifying potential therapeutic agents.

Problem: Dengue has emerged as the most important vector-borne viral disease in tropical areas. The four serotypes of DV each cause human disease and are transmitted by mosquitoes. Epidemics with a high frequency of life-threatening DHF continue to expand geographically. Despite the increased health and economic impacts IRD Photo by Michel Dukhan, Aedes albopictus :

36 Chapter 2 - Dengue and other Haemorrhagic Fevers Acronym: DENFRAME Contract/Grant Agreement No: INCO-CT-2005-517711 Project type: Specific Targeted Research Project EC contribution: € 2 550 000 Starting date: November 1, 2005 Duration: 36 months

understand the molecular mechanisms by which it interacts with DV and neutralises its four serotypes. They might prove useful as therapeutic molecules against DV. The strategy of immobilisation of on optical fibres is providing new knowledge on biology and and its reproducibility have been validated. epidemiology, as well as new diagnostic tools The consortium constructed and validated and therapeutic approaches for dengue Philippe Dussart Institut Pasteur de Guyanne such biosensors for several viruses and is disease. It might help to implement appropriate , French Guinea now progressing in the application of this strategies and policies for control and treatment [email protected]

technology to DV. of dengue. Andrea Gamarnik Fundacion Instituto Leloir Concerning WP2, the partners have produced Key words: Buenos Aires, Argentina [email protected] many of the tools necessary for the study of dengue, innate immunity, diagnostic tools DV-host interactions, such as cell lines inducible Michael Jacobs Royal Free and University College Medical for the expression of the secreted form of School the dengue envelope protein of the four DV London, UK serotypes and cell lines producing recombinant [email protected] retrovirus expressing each dengue type-2 Beate Kümmerer non-structural (NS) protein separately. They Bernhard Nocht Institute of Tropical Medicine constructed recombinant bicistronic vectors co- Hamburg, Germany expressing the green fluorescent protein and [email protected]

dengue NS proteins, as well as an infectious Robert Marks, full-length dengue type-2 genome expressing Angel Porgador gene reporters. The consortium demonstrated Ben Gurion University of the Negev Beer Sheva, Israel that dengue NS proteins play a major role in [email protected]; the blocking of innate immunity response of [email protected]

DV-infected cells. They showed that DV NS Béatrice Nal-Rogier proteins upregulate expression of MHC-class Hong Kong University I molecules at the infected cell surface. Their Coordinator Pasteur Research Centre Nathalie Pardigon Pokfulam, Hong Kong studies of the innate immune responses to DV Laurence Baril, [email protected] infection at the skin level show that fibroblasts Hugues Bedouelle, Philippe Despres, Johan Neyts are targets for viral replication, and that some Jean-Claude Manuguerra Rega Institute for Medical Research toll-like receptors are upregulated on these Institut Pasteur Leuven, Belgium cells. A lead compound was identified and novel 25 rue du Dr. Roux [email protected] 75724 Paris, France analogues are being synthetised and tested [email protected]; Pedro Vasconcelos against DV type 2. They recently identified an [email protected]; Instituto Evandro Chagas [email protected]; Pará, Brazil antibiotic derivative that can inhibit selectively [email protected]; [email protected] DV replication in primary screening assays. [email protected]; Thi Que Huong Vu Philippe Buchy Institut Pasteur de Ho Chi Minh Ville Potential applications: Institut Pasteur du Cambodge Ho Chi Minh, Vietnam Dengue disease has considerable impact on , Cambodia [email protected] [email protected] the economic development perspectives and Jian-Ping Zuo is a major childhood infection in the affected Leticia Cedillo-Barron Institute for Materia Medica – Centro de Investigacion y de Estudios Chinese Academy of Sciences communities. The DENFRAME project, through Avanzados, Mexico Shanghai, China an integrated multidisciplinary approach, [email protected] [email protected]

http://www.denframe.org Chapter 2 - Dengue and other Haemorrhagic Fevers 37 Development of rapid field diagnostics for identification, control and management of haemorrhagic fever outbreaks

Summary: to produce and has a long shelf life. This tool Problem: The VHF Diagnostics project aims at developing will help to improve outbreak detection in Control of viral hemorrhagic fever (VHF) and validating diagnostic tools for early Africa. The project includes a long-term field outbreaks critically depends on early detection, viral haemorrhagic fever outbreak detection trial in local hospitals. A mobile integrated and an early alert, to allow, define, and deliver and control. A frontline line-assay carrying fluorescent real-time-PCR (F-RT-PCR) for an appropriate response. To improve the early antigens of all African haemorrhagic fever outbreak investigation teams is also to be detection of cases, adequate tools have to be viruses is to be developed and validated for developed. It will consist of a panel of F-RT- developed to allow early detection in the basic widespread use in local hospitals. Line assays PCRs covering all haemorrhagic fever viruses, (field) conditions of local hospitals. Once are third-generation (3G) immunoblots using a robust simple nucleic acid extraction protocol the outbreak is identified, case management purified recombinant proteins sprayed onto and ready-to-use lyophilised PCR mixes. This also needs on-site tools, such as viral membranes irrespective of their molecular tool will help outbreak investigation teams to genome detection, to contain the spread weight. This means that highly concentrated improve their ability to manage and control of the outbreak by carefully identifying and protein can be arranged onto membranes in haemorrhagic fever outbreaks. monitoring viraemic patients able to transmit the manner of a barcode. the virus. A consortium of three European laboratories There are no problems with contaminating and four African laboratories will provide the The general objective of VHF Diagnostics is extra bands, or with spacing of target expertise for the development, validation and to make adequate tools available to identify molecules. This assay is easy to use and the adaptation to filed use of both tools. VHF outbreaks on-site at an early stage, and results are easy to interpret. It is also cheap to support and complement the control of an outbreak. To reach this general objective, the consortium will develop: 1. line assays (LA LA) for antibody detection as an easy-to-use frontline detection assay for healthcare workers in local hospitals; 2. F-RT-PCR assays that can be used at the scene of the outbreak, to be used by specialised mobile outbreak investigation teams.

Both assays will cover Ebola-Virus (EBOV), Marburg Virus (MRGV), Crimean-Congo-Virus (CCHFV) Lassa virus (LASV), Rift Valley Fever Virus (RVFV), virus (YFV) and Dengue virus 1-4 (DENV). The F-RT-PCR will additionally cover the most important viral differentials Influenza A virus (FLUAV) and Influenza B virus (FLUBV).

Aim: LA: To develop LA, purified recombinant proteins will be expressed in the in vitro RTS-500 system (Roche) and sprayed onto immunoblot strips in the manner of a barcode. The LA will be designed for VHF circulating in Africa. Validation of the LA will be achieved

38 Chapter 2 - Dengue and other Haemorrhagic Fevers Acronym: VHF Diagnostics Contract/Grant Agreement No: INCO-CT-2006-32180 Project type: Specific Targeted Research Project EC contribution: € 853 000 Starting date: December 1, 2006 Duration: 36 months

by using available sera in the consortium of laboratories, which will be centralised in a repository for VHF diagnostics development.

F-RT-PCR: The consortium will validate existing Potential applications: F-RT-PCRs for field use (EBOV, MBGV 12, CCHFV LA: A fully functional and validated VHF-line 13, RVFV 14, DENV 15, FLUAV, FLUBV16). assay can be used in regional hospitals and by Additionally, F-RT-PCRs not yet described for outbreak investigation teams. Coordinator LASV and YFV will be designed and validated Dr Manfred Weidmann Bereich Humanmedizin der Georg-August- for field use. To assess the sensitivity of F-RT.-PCR: A fully functional and validated set of Universitaet Goettingen Stiftung des each assay, the partners will generate RNA- VHF F-RT-PCRs could increase the efficiency of Oeffentlichen Rechts standards for each aetiological agent derived outbreak investigation teams. Department of Virology Am Kreuzbergring 57 from sections of the respective genomes. The 37075 Göttingen, Germany specificity of the assays will be evaluated with Key words: [email protected]

recent isolates of each aetiological agent and viral haemorrhagic fevers, diagnostics, line Dr Jean-Claude Manugerra patient and/or rodent samples provided by the assay, mobile real-time PCR Institut Pasteur collaborating laboratories. They will adapt the Cellule d’intervention Biologique d’Urgence Paris, France extraction of nucleic acids from blood samples [email protected] to field conditions. The partners will also Dr Ali Mirazimi develop lyophilised ready-to-use PCR mixes Swedish Institute for Infectious Disease for each aetiological agent to allow field PCR Control without the need for refrigeration facilities. Centre for microbiological preparedness Solna Municipality, Sweden [email protected] Expected results: Dr Amadou Alpha Sall LA: The partners expect to be able to Institut Pasteur de Dakar produce the envisioned line assay and test Arbovirus Unit Dakar, Senegal its applicability in local hospitals in Mali and [email protected] Guinea. They hope to prove that an easy-to- use frontline test indeed is a tool to reduce Dr Laurent Toe Multi Disease Surveillance Centre World alert time in the case of an outbreak. The Health Organization / African Region consortium hopes to detect either a YFV, a Laboratoire de Biologie Moleculaire Ouagadougou, Burkina Faso RVFV or a LASV outbreak during the evaluation [email protected] period. Dr Youssouf Issabre Foundation Merieux Mali F-RT-PCR: The partners expect to develop Laboratoire Rodolphe Merieux an integrated toolbox for mobile outbreak Bamako, Mali investigation teams that will enable them to [email protected] perform initial differential diagnostics and Dr Lamine Koivogui follow up patients during the containment of Université de Conakry, Faculté de Médecine Institut de Microbiologie the outbreak. This will contain a field-evaluated Conakry, Guinea set of lyophylised PCR mixes for VHFV plus [email protected] FluA and B virus detection in combination with Dr Klaus-Ingmar Pfrepper a field-evaluated simple extraction protocol. If Mikrogen-molekularbiologische Entwicklungsgesellschaft mbH successful, it may be possible to produce the Neuried, Germany LA assay for the African market. [email protected]

http://www.vhf-diagnostics.eu Chapter 2 - Dengue and other Haemorrhagic Fevers 39 Development and commercial pro- duction of standardised PCR-assays for detection of haemorrhagic fever viruses and variola virus and their implementation in the diagnostic service of EU P4 laboratories

Summary: CCHF virus), prototypes of ready-to-use kits infectious agents. Significant attention was The main objective of the VHF/VARIOLA-PCR were developed by a small or medium-sized paid to demonstration activities and inter- project was the development and distribution enterprise (SME). They will also be made laboratory quality control measures to ensure of a set of high-quality, standardised, and available to experienced laboratories in that the novel technologies emerging from evaluated PCR-based detection methods Member States (e.g. those of the European the project are implemented in high quality for viral haemorrhagic fever (VHF) viruses Network of Imported Viral Diseases (ENIVD)) in the diagnostic service of all participating and variola virus. The implementation of that do not have direct access to P4 facilities. laboratories. these assays in the diagnostic service of all existing European P4 laboratories established A different set of PCR assays was developed Problem: a laboratory infrastructure that can provide for confirmatory testing. These are not Common methods for laboratory diagnosis of high-quality diagnostic services to all EU produced as a kit and are to be used mainly smallpox and VHF are isolation of the virus in Member States. by the P4 laboratories. The development of cell culture or laboratory animals, polymerase these assays required the concerted action chain reaction (PCR), virus antigen detection, Furthermore, in order to facilitate wide of all European laboratories experienced electron microscopy, as well as detection distribution and safe handling of PCR assays in handling and diagnosing VHF and pox of specific antibodies in the serum of the for the most relevant viruses (variola virus, viruses, as well as of a company experienced patient. Ebola and Marburg viruses, Lassa virus, and in developing and producing PCR kits for

40 Chapter 2 - Dengue and other Haemorrhagic Fevers Acronym: VHF/VARIOLA-PCR Contract/Grant Agreement No: SSP-CT-2003-502567 Project type: Coordinated Action EC contribution: € 700 000 Starting date: January 1, 2004 Duration: 36 months

Virus detection and isolation in cell culture is still the gold standard for establishing a definitive diagnosis. However, it takes days to weeks to isolate a virus. Furthermore, P4 facilities are required in case of VHF and smallpox. PCR additional sequences of the PCR target regions and other nucleic acid amplification techniques were generated: 30 sequences for Lassa virus (NAT) meet the need to rapidly identify VHF or GPC gene PCR; 22 sequences for Lassa virus L biological warfare agents. These techniques are gene PCR; 7 sequences for Ebola/Marburg virus suitable for identification of viruses, , L gene PCR; and 14 sequences for variola virus parasites and fungi. 14-kDa fusion protein gene PCR. Corresponding assays were revised or developed de novo using In contrast to classical diagnostic methods, which the new sequence data. Sufficient published are based on the detection and identification of sequences were available for designing a the intact organism, PCR detects the genetic New World Arenavirus NP gene real-time PCR. Coordinator Stephan Günther material of a pathogen and thus reduces the Two reliable orthopox virus real-time PCRs Bernhard-Nocht-Institute for Tropical contact with infectious material to a minimum. were selected as second-line assays from the Medicine So, even laboratories of lower security level literature based on evaluation with a large Department of Virology Bernhard-Nocht-Str. 74 than P4 can perform PCR diagnostics for VHF number of Orthopox virus strains. 20359 Hamburg, Germany and smallpox. [email protected] Real-time probe detection was developed for Stephan Becker Aim: the following assays: Ebola/Marburg virus L Philipps-University of Marburg Institut für Virologie VHF/VARIOLA-PCR targeted the development gene PCR, CCHF virus NP gene PCR, Orthopox Marburg, Germany and distribution of a set of standardised and viruses 14-kDa fusion protein gene PCR, and [email protected] evaluated PCR-based detection methods for New world Arenaviruses NP gene PCR. All RT- Marie Claude Georges VHF viruses and variola virus. In order to PCR assays were developed in 1-step format. Institut Pasteur facilitate wide distribution and safe handling The protocols were evaluated by the consortium Unit of Biology of Emerging Viral Infections Lyon, France of PCR assays for the most relevant viruses and integrated into the diagnostic service of [email protected] (variola virus, Ebola and Marburg viruses, the BSL-4 laboratories. Lassa virus, and CCHF virus) the assays will be Graham Lloyd Health Protection Agency manufactured by the small-sized enterprise as Prototypes of the Orthopox PCR kit, Ebola/ Porton Down, GPM Special Pathogens ready-to-use kits. They will be made available to Marburg virus L gene PCR kit, and CCHF virus NP Salisbury, UK experienced laboratories in Member States that gene PCR kit were produced by artus/QIAGEN [email protected] do not have direct access to P4 facilities. Hamburg GmbH and successfully evaluated by Åke Lundkvist the consortium. Swedish Institute of Infectious Disease Control Results: Center for Microbiological Preparedness Initially, assays available in the consortium were Potential applications: (KCB) Solna Municipality, Sweden evaluated using an inactivated virus. Based on Use of the established assays in diagnostic [email protected] the quality assessment study and published service of BSL4 laboratories and public health Hermann Meyer evaluation data, assays for Lassa virus, Ebola/ laboratories in Member States. Institute of Microbiology of the German Marburg virus, and Orthopox (variola) viruses Armed Forces were selected for further optimisation. Other Key words: Munich, Germany [email protected] assays were developed de novo. viral haemorrhagic fever; variola virus; molecular diagnostics; PCR Thomas Grewing Artus GmbH/Qiagen In order to design reliable primers and Hamburg, Germany hybridisation probes for real-time PCR, [email protected]

Chapter 2 - Dengue and other Haemorrhagic Fevers 41

CHAPTER 3 SARS

43 Sino-European Project on SARS Diagnostics and Antivirals

Summary: groups made important contributions to Potential applications: The Sino-European Project on SARS Diagnostics our understanding of the replication and 1. Further development into approved drugs and Antivirals (SEPSDA) brought together four transcription mechanisms of the coronaviral of the anti-SARS lead compounds that were European and four Chinese research groups RNA. Furthermore, the knowledge gained discovered (in case of a new outbreak). working on the Severe Acute Respiratory was used for designing drugs that would 2. Some of the anti-SARS inhibitors that were Syndrome (SARS) Coronavirus. The consortium interfere with these mechanisms. This was discovered also have good activity against determined the three-dimensional structures supported by structure-based drug design; other positive-strand RNA viruses and may of many replicase proteins of the virus by within SEPSDA, the crystal structures of the be developed into broad-spectrum antiviral X-ray crystallography. Based on these target following components of the Coronavirus drugs. structures, it discovered about 50 non-toxic replicase complex were determined: X-domain 3. Differential diagnostics (distinction from chemical compounds with activity against the of Nsp3, SARS-unique domain, Nsp5, Nsp7/8, other respiratory viruses) virus; five of these were developed into lead Nsp9, Nsp10, and Nsp15. compounds and are ready for preclinical and clinical testing in case of a new outbreak of The main target for anti-SARS drug discovery SARS or another Coronavirus-caused epidemic. was the protease, Nsp5. Many crystal structures Also, SEPSDA has significantly improved the of complexes between Nsp5 and inhibitors existing diagnostics for SARS and introduced identified within SEPSDA were determined. differential diagnostics allowing the rapid and SEPSDA researchers elucidated more crystal reliable distinction between the disease and structures of coronaviral proteins than any other forms of viral pneumonia. other consortium working in this field. They also found about 50 compounds that were Problem: active against the virus. These were either When SARS emerged in China, Hong Kong, discovered by virtual screening, by de novo Vietnam, Taiwan and Canada in 2003, little design, or by screening libraries of Chinese was known about the molecular biology of medicinal compounds. The best of these ‘hit Coronaviruses. In particular, reliable diagnosis molecules’ were then optimised, resulting in was not available (no rapid differential five ‘lead compounds’, which would be ready diagnostics) and no therapy existed. for preclinical and clinical testing in case of a new outbreak. Aim: SEPSDA was set up to achieve breakthroughs in In addition to SEPSDA’s efforts at discovering both the development of better diagnostics of antiviral compounds, the consortium also SARS and structure-based discovery of small- worked on improved diagnostics of the virus. molecule compounds with anti-SARS activity. Antibodies against the individual components of In order to achieve the latter goal, the three- the replicase were raised and a new antibody- dimensional structures of many components of based SARS-CoV assay was developed. Since it the Coronavirus replicase complex had to be is difficult to quickly decide whether a patient determined. suffering from pneumonia is infected by the SARS virus or other respiratory viruses (such Results: as influenza), advanced differential diagnostics SEPSDA brought together the European were developed, allowing this decision to be and Chinese research groups that had done taken with confidence. Also, non-infectious seminal work on the SARS Coronavirus virus-like particles were developed within the when this new pathogen emerged in 2003. project, for various purposes. During the four years of SEPSDA, these

44 Chapter 3 - SARS Acronym: SEPSDA Contract/Grant Agreement No: SP22-CT-2004-003831 Project type: Specific Targeted Research Project EC contribution: € 1 887 608 Starting date: May 1, 2004 Duration: 48 months

Coordinator Prof. Rolf Hilgenfeld University of Lübeck Institute of Biochemistry Ratzeburger Allee 160 23538 Lübeck, Germany [email protected]

Dr Peter Kristensen University of Aarhus Department of Molecular Biology Aarhus, Denmark [email protected]

Dr Leszek Rychlewski Polish Academy of Science Bioinformatics Laboratory Poznan, Poland [email protected]

Karin Sonnenberg Euroimmun AG Tropical Diagnostics Department Lübeck, Germany [email protected]

Prof. Zihe Rao Tsinghua University Laboratory of Structural Biology Beijing, People’s Republic of China [email protected]

Prof. Hualiang Jiang Chinese Academy of Science Shanghai Institute of Materia Medica Drug Discovery and Design Center Shanghai, People’s Republic of China [email protected]

Prof. Jinming Li National Center for Clinical Laboratory Division of Immunoassay and Molecular Diagnosis Beijing, People’s Republic of China [email protected]

Prof. Huanming Yang Beijing Genome Institute Division of Immunoassay and Molecular Diagnosis Beijing, People’s Republic of China [email protected]

http://www.sepsda.eu Chapter 3 - SARS 45 Development of intervention strategies against SARS in a European-Chinese taskforce

Summary: formation was achieved by the co-expression From this cDNA, a replicon was derived that is An attenuated live recombinant vaccine, in the baculovirus system of three proteins: very useful for screening anti-virals without the inactivated vaccines, different antivirals, and M, E, and S. These VLPs induced a neutralising need to use infectious virus. E, 6, 7a, 7b, 8a, immune strategies to prevent and protect immune response to SARS-CoV and elicited 8b and 9b proteins were not essential for virus against Severe Acute Respiratory Syndrome protection in a mice model. replication in vitro or in vivo. In a transgenic (SARS) have been developed. In addition, a mice model highly sensitive to the virus, the microarray system to diagnose SARS patients Several plant expression systems based on Plum DISSECT partners have shown that a SARS- has been designed. The efficacy of these tools pox potyvirus (PPV) and Potato virus X (PVX) CoV E protein deletion mutant was attenuated, has been tested in animal models developed by have been developed to express at low cost whereas removal of genes 6 to 9b reduced the consortium. SARS-CoV antigens. SARS-CoV S, S1, E, M, N, 3a very little pathogenicity. A virus mutant missing proteins alone or linked to a cell compartment all these seven genes provided protection Problem: retention signal, to increase expression, were against SARS-CoV. The potential re-emergence of SARS, mostly also obtained. In addition, several transgenic due to the presence of recent ancestors of the lines expressing constitutively tagged S, S1, M, The attenuated rSARS-CoV engineered is an virus in the bat population. N and 3a proteins were produced. Furthermore, excellent starting point for the production of expression of SARS-CoV antigens in plants, with a chemically . This type Aim: modified glycosylation systems mimicking the of vaccine will include two safety guards, the To prevent, diagnose, and cure SARS mammalian glycosylation pattern, has been chemical inactivation, and the attenuated Coronavirus (SARS-CoV) infections. obtained. phenotype, in case the chemical inactivation is incomplete inside a virus aggregate. Results: The first recombinant vaccine for SARS-CoV A collection of viral proteins expressed mainly has been constructed. The efficacy of this The partners have shown that inactivated in baculoviruses and plants has been obtained. vaccine has been shown in two animal model SARS-CoV vaccines protect macaques and This collection includes proteins S, S1, S2, M, E, systems, and has provided protection against ferrets against an intratracheal challenge with N, 3a, 6, and 7a. To increase the immunogenicity homologous and heterologous viruses. The SARS-CoV, and that the induction of neutralising of these proteins, virus-like particles (VLPs) morphogenesis of the vaccine virus missing antibodies may suffice to protect against SARS- protein E is shown in comparison with that of CoV. The inflammatory response in SARS-CoV Electron microscopy of the recombinant SARS-CoV the parental full-length virus (Figure 1). To infected vaccinated and naïve macaques was engineered. Left panel: viral factory of the parental assemble a recombinant vaccine for SARS-CoV, analysed. A wide range of cytokines including virulent virus (SARS-CoV). Right panel: viral factory of the attenuated deletion mutant vaccine candidate an infectious cDNA of SARS-CoV was constructed IL-1, IL-6, IL-8 and IFNs, several chemokines (SARS-CoV-îE) using a bacterial artificial chromosome (BAC). such as monocyte chemotactic protein genes like CCL8, CCL7, and also CCL11 (eotaxin), a chemotactic protein for eosinophils were identified. These results provided a rationale for using live attenuated vaccines.

Both ferret and macaque have been developed as animal models for SARS-CoV. Polyvalent antibodies of human origin protect against SARS in macaques. In addition to the description of pegylated interferon alpha as an antiviral, two other antivirals have been identified: IL-4 and interferon-gamma. The mechanism of action of IL-4 includes a reduction in the expression of the ACE-2 receptor of SARS-CoV.

46 Chapter 3 - SARS Acronym: DISSECT Contract/Grant Agreement No: SP22-CT-2004-511060 Project type: Specific Targeted Research Project EC contribution: € 2 375 892 Starting date: October 1, 2004 Duration: 36 months

The identification of genes that may contribute to SARS-CoV virulence was studied as their removal may lead to safer SARS-CoV vaccines. The role of accessory 3, 6, and 8 proteins in virus host interaction has been determined. 3a protein is O-glycosylated, and that interacts with the viral M protein. ORF 8 acquired a deletion Prof. Albert D. M. E. Osterhaus early after SARS-CoV jumped from the animal Erasmus University Rotterdam reservoir to the human population and this Department of Virology Rotterdam, Netherlands deletion was found in all later human isolates. [email protected] The 29nt deletion plays a role in the efficient spread or the high pathogenicity of SARS-CoV Prof. Anlong Xu Professor in Molecular Biology and in the human population. Protein 6 was involved Immunology in virus replication and virulence. Dean, College of Life Sciences Sun Yat-Sen University Guangzhou, People’s Republic of China The consortium has shown that IFN-a inhibits [email protected] SARS-CoV replication in macaques and has Prof. Zhihong Hu identified IL-8 as one of the pathogenic Wuhan Institute of Virology (WIV) cytokines induced at high levels in macaques. Chinese Academy of Sciences Wuhan, People’s Republic of China These studies emphasised that IFN production [email protected] inversely correlated with IL-8 induction. As IL-8 Dr Pilar Perez Breña is a central mediator of inflammatory responses, Instituto de Salud Carlos III including acute respiratory distress and acute Centro Nacional de Microbiologia lung injury, modulation of its expression by the Madrid, Spain [email protected] IFNs may reveal an important new intervention strategy to suppress pathogenic responses. Dr Juan Plana Durán Fort Dodge Veterinaria SA Girona, Spain A new genomic approach to diagnose SARS- [email protected] CoV, based on microarray technology, is being Coordinator Prof. Luis Enjuanes Dr Han van den Bosch developed, which is independent of hybridisation Prof. Juan Antonio García Intervet UK Ltd techniques, and uses primer extension (APEX) Centro Nacional de Biotecnologia Milton Keynes, UK Department of Molecular and Cell Biology [email protected] technology. Campus Universidad Autónoma, Cantoblanco [email protected] 28049 Madrid, Spain Potential applications: [email protected]; Collaborators [email protected] Prof. 1. diagnosis and protection of the population The in case of SARS re-emergence by Prof. Qi Xie Department of Microbiology Institute of Genetics and Developmental Pokfulam, Hong Kong vaccination; Biology [email protected] 2. therapeutic strategies for SARS, including Laboratory of Plant Molecular Signaling Chinese Academy of Sciences Prof. Wilina Lim antivirals and immunotherapy. Beijing, People’s Republic of China Government Virus Unit [email protected] 9/F Public Health Laboratory Center Key words: Kowloon, Hong Kong Prof. Peter J. M. Rottier [email protected] SARS, vaccines, antivirals, immunotherapy, Utrecht University Coronavirus Department of Infectious Diseases and Prof. Ding Xiang Liu Immunology Institute of Molecular and Cell Biology Utrecht, Netherlands Singapore, Singapore [email protected] [email protected]

http://www.cnb.csic.es/~webcoron/EUprojectdissect Chapter 3 - SARS 47 Complementary research action to support SARS-related diagnostic tests, therapeutic interventions and vaccine development

Summary: The 2003 SARS outbreak, caused by a Results: Severe Acute Respiratory Syndrome (SARS) is Coronavirus, was a clear example of the latter With other Coronaviruses, SARS-CoV uses a life-threatening form of pneumonia caused situation. Still, less virulent Coronaviruses replicative machinery that is unique among by an emerging Coronavirus (SARS-CoV) that (causing common colds) were already known RNA viruses because of the large number of likely circulates in bats. The prevention and/ to circulate among humans and several others enzymatic subunits and the use of several or containment of future outbreaks of this were detected in the post-SARS era, together enzymes that are rare or lacking in other virus virus, or any of its relatives, will depend on our with many novel Coronaviruses circulating in groups. Both individually expressed subunits and understanding of their biology, pathogenesis bats and a variety of other animal species. This the integral enzyme complex in the living infected and evolution. To aid in designing an overall underlines the widespread nature and zoonotic cell were studied. This resulted, for example, strategy, the SARS-DTV project focused its potential of the Coronavirus group. The SARS- in two novel crystal structures of important attention on the development of reliable DTV project aimed to dissect the biology of SARS-CoV enzymes (NendoU and ADRP), in the diagnostic tools, specific antiviral compounds, SARS-CoV and increase our general knowledge discovery of a unique secondary RNA-dependent and a SARS-CoV vaccine. of Coronaviruses, in order to be well prepared RNA polymerase activity (the nsp8 ‘primase’), when the SARS virus (or any of its relatives) in the more detailed description of several Problem: would (re-)emerge. other viral enzymes, and in the ultrastructural Due to their high mutation frequency, RNA characterisation of an elaborate network of viruses are the most common source of Aim: modified membranes with which viral RNA unanticipated virus outbreaks, which are caused The SARS-DTV consortium consists of a balanced synthesis is associated in the infected cell. either by novel variants of known viruses of by mixture of coronavirologists and specialists in the introduction into the human population of other fields from Europe and Asia. The overall Furthermore, an initial screening for antiviral previously unknown viruses, often transmitted objective of the SARS-DTV network was to lead compounds targeting SARS-CoV enzymes from an animal source. contribute to the development of candidate was performed. In addition, a 30 000-compound anti-SARS-CoV drugs, vaccines and diagnostic library was purchased for (ongoing and future) assays, by collaborative and complementary screening campaigns using biochemical assays Plaque assay to determine the infectivity titer of SARS- research in five Work Packages (WPs). In the developed during the characterisation of various CoV on Vero-E6 [monkey kidney] cells. A dilution of a ‘Molecular Targets’ WP, SARS-CoV proteins — in enzymes. In a similar screening approach, but SARS-CoV stock was used to infect a cell monolayer, which was subsequently covered with a solid medium particular the Spike protein and the replicative now targeting the viral life cycle as a whole, to prevent spread of newly produced virus throughout enzymes that are primary targets for antiviral over 2 000 potential antiviral compounds were the cell layer. The local spread of the virus gives rise to drug development — were studied both in vitro screened and several were found to show antiviral clusters of dead cells [plaques], which were visualized and in vivo. A combination of structural biology, activity. Derivatives of selected anti-Coronavirus after 2 days [using crystal violet staining of living cells ] and counted to determine the virus titer. biochemistry and molecular virology was used. compounds were synthesised to assess their In the WP ‘Correlates of Humoral and Cellular antiviral activity in more detail. Furthermore, Protection’, vaccine development and SARS an animal model was used to study the in vivo immunopathology were addressed. The WP activity of chloroquine against Coronaviruses. ‘Model Systems’ developed a reverse genetics system for SARS-CoV in order to establish In the consortium’s analysis of SARS-CoV Spike biosafe cell culture-based model systems to protein functions, the interactions with the study virus replication and its inhibition by ACE-2 receptor protein and the fusion process specific compounds. The ‘Diagnostics and of viral envelope and cellular membrane were Standardization’ WP aimed to develop rapid and investigated. Efforts were made to obtain small reliable diagnostic methods and to promote the molecules (e.g. peptides) that might be used to exchange of SARS-CoV-specific data and reagents inhibit receptor-binding and entry of the virus. between partners. Finally, the ‘Management’ WP took care of internal management issues, as well In the immunological WP, antigenic sites on SARS- as contacts with the EC and the general public. CoV proteins were characterised and the role of

48 Chapter 3 - SARS Acronym: SARS-DTV Contract/Grant Agreement No: SP22-CT-2004-511064 Project type: Specific Targeted Research Project EC contribution: € 2 386 860 Starting date: October 1, 2004 Duration: 36 months

the humoral and cellular immune response in SARS infection was studied. Using an antibody- phage library approach, genes-encoding neutralising human monoclonal antibodies were Prof. Dr Georg Herrler cloned and expressed as IgG molecules. Virus Potential applications: Tieraerztliche Hochschule Hannover neutralisation epitopes and escape were studied Clearly, because a second episode of SARS has Hannover, Germany using these reagents and transient expression not occurred (yet), the partners’ newly acquired [email protected] systems required to rapidly produce anti-SARS- knowledge and SARS-DTV prototypic assays Prof. John Ziebuhr CoV antibodies were developed. In terms of and reagents have not been put to the test, in Queen’s University Belfast Belfast, UK cellular immunology, SARS-CoV T cell epitopes practice. In the meantime, also supported by [email protected] were defined and fine mapping was performed SARS-DTV reagents and technical advancements, (55 new CD4 and CD8 epitopes). The magnitude basic research of Coronaviruses continues with Dr Bruno Canard Université de la Méditerranée of the responses to the novel epitopes in patient a clear purpose and enhanced possibilities. Marseille, France samples was determined. Researchers’ knowledge of Coronaviruses was [email protected]

already expanded enormously over the past five Prof. Marc van Ranst Partners in the SARS-DTV ‘Model Systems’ WP years, largely as spin-off of the SARS outbreak. Katholieke Universiteit Leuven successfully developed a vaccinia virus-based As during the 2003 SARS outbreak, previous Leuven, Belgium [email protected] reverse genetic systems for SARS-CoV and other studies on Coronaviruses will be the basis for a Coronaviruses. This important new research swift and adequate response in the case of any Dr Volker Thiel Kantonsspital St Gallen tool will enable the development (in progress) new outbreaks. In that case, assays to detect St Gallen, Switzerland of biosafe, cell culture-based systems that can and identify the virus are in place, several [email protected]

be used for antiviral testing. Furthermore, these targets for antiviral drug development have Prof. Gavin Screaton systems allow the site-directed mutagenesis been clearly defined, and candidate vaccines Imperial College of Science, Technology of Coronavirus RNA and protein sequences, a will be available. and Medicine London, UK technique commonly essential for probing the [email protected] importance of these elements and functions in Key words: Dr Thierry Leclipteux the viral life cycle and in virus-host interactions. SARS, coronaviruses, molecular biology, structural Coris BioConcept Several Coronavirus replicase subunits and also genomics, antiviral drugs, vaccines, human Coordinators Gembloux, Belgium the nucleocapsid protein are currently targeted monoclonal antibodies, T-cell epitopes, reverse Prof. Dr Willy J. M. Spaan, [email protected] Prof. Dr Eric J. Snijder using this approach. genetics, replicon cell lines, rapid diagnostics Leiden University Medical Center Dr Jerome Weinbach, Center of Infectious Diseases Ibrahima Guillard Department of Medical Microbiology INSERM Transfert SA SARS-DTV partners developed prototype Molecular Virology Laboratory Paris, France immunochromatography assays for the detection P. O. Box 9600 [email protected]; of SARS-CoV antigens in patient specimens, 2300 RC Leiden, Netherlands [email protected] [email protected] which could be developed into assays for rapid Prof. Leo Poon bedside testing. Also, rapid tests to detect Prof. Wolfgang Garten University of Hong Kong Philipps-Universität Marburg Pokfulam Road, Hong Kong SARS-CoV-specific nucleic acid sequences Marburg, Germany [email protected] were developed, including a novel isothermal [email protected] Prof. Weizhi Ji amplification method. Finally, the SARS-DTV Prof. Stuart G. Siddell Kunming Institute of Zoology partners have created a Biobase and Database University of Bristol Chinese Academy of Sciences for central storage and exchange of reagents Bristol, UK Kunming, People’s Republic of China [email protected] [email protected] and information, respectively. Dr Menzo Havenga Dr Shiou-Hwei Yeh Crucell Holland BV Institute of Molecular Biology Leiden, Netherlands Taipei, Taiwan [email protected] [email protected]

http://www.sars-dtv.nl Chapter 3 - SARS 49 Immunoprevention and immunotherapy of SARS infection

Summary: and formulate optimal treatment protocols circulating in an unknown animal reservoir, making The 114-day long epidemic wave of Severe to reduce morbidity and mortality. The SARS the development of preventive and therapeutic Acute Respiratory Syndrome (SARS) swept Coronavirus is believed to have jumped over strategies against it a pressing need. 29 countries, sickened a reported 8 096 from an animal host to people in Guangdong people, left 774 patients dead in its wake, and province, southern China, in November 2002 Aim: almost completely paralysed Asia’s economy. and then to have spread rapidly throughout the The Novartis Research Group in Siena (Italy) Aggressive measures and rising world via air travel. Following unprecedented promptly reacted to the global emergency and summer temperatures successfully terminated collaboration between laboratories worldwide, was among the first to isolate the virus and the first eruption of SARS and provided at the virus could be isolated and its sequence sequence its genome. Two other research least a temporal break, allowing scientists to was published in April 2003. groups started to collaborate with Novartis, consolidate what they have learned so far and i.e. the Institute of Virology at the University plan for the future. The association of the virus with the disease of Marburg (Germany), to provide expertise was confirmed when macaques that were in virology, and the Istituto di Ricerche The SARSVAC project proposal was prepared inoculated with the virus developed symptoms Biomediche in Bellinzona (Switzerland), to in response to urgent medical and societal similar to those observed in human cases of provide expertise in the production of human needs for immunopreventive (vaccination) SARS. When the epidemic finally waned, WHO monoclonal antibodies against the SARS and immunotherapeutic measures for SARS. counted a cumulative number of 8 096 probable Coronavirus. An integrated strategy for developing effective SARS cases and 774 deaths in a geographical vaccines and for establishing effective area spanning 29 countries. Economists have Building on this previous experience, a therapeutic treatment will be developed. The estimated that the overall cost of the outbreak research project is proposed targeting three strategy for vaccine development will follow two may approach USD 100 billion — mostly as main objectives: parallel approaches: (1) the preparation of a a result of cancelled travel and decreased 1. a killed virus vaccine that protects from classical inactivated vaccine (as already done investment in the affected region. SARS Coronavirus infections; for other Coronaviruses); and (2) the definition 2. a recombinant vaccine based on SARS- of potential antigens and T/B protective SARS is mainly characterised by flu-like CoVLPs; epitopes through the study of SARS-CoV symptoms including high fever, headache, 3. human monoclonal antibodies against derived virus-like particles (VLPs), pivotal to chills, rigors, dizziness, myalgia, sputum SARS-CoV for immunotherapy. the understanding of SARS-CoV morphogenesis production, sore throat, coryza, nausea, and virion maturation. vomiting and diarrhoea. The incubation period The results of this project could be measured is at least 2 days but no longer than 10 days. for points 1 and 2 (above) as: The immunotherapeutic strategy will rely on The overall mortality rate was about 10%, but 1. a candidate vaccine proved to elicit the development and validation of neutralising varied profoundly with age; although SARS specific immunity in animal models; and human antibodies to SARS-CoV. Under this affected relatively few children and generally for point 3 project, academia experts in immunology, appeared to be milder in the paediatric 2. a potentially therapeutic human monoclonal vaccinology, and molecular biology have group, the mortality rate in the elderly was antibody to be used in patients. joined forces with industrial vaccine production as high as 50%. Any pre-existing lung ailment experts, in order to develop preventive and complicates the disease, and conditions such Expected results: therapeutic measures for SARS. as emphysema are more common in the The project has already concluded, with the elderly. Although it is now well established following final results: Problem: that the SARS virus can kill on its own, other 1. Preparation of an inactivated vaccine The evolution and spread of the etiological agent co-infection with different pathogens can that protects from SARS Coronavirus of SARS, a novel Coronavirus, has resulted in exacerbate the illness. infections (Patent PCT, C12N7/00; an unparalleled international effort coordinated Stadler, K., Roberts, A., Becker, S., Vogel, by the World Health Organization (WHO) to While SARS did not re-emerge in the human L., Eickmann, M., Kolesnikova, L., Klenk, characterise the virus, develop diagnostic tests, population in 2004, most likely the virus is still H-D., Murphy, B., Rappuoli, R., Abrignani,

50 Chapter 3 - SARS Acronym: SARSVAC Contract/Grant Agreement No: SP22-CT-2004-511065 Project type: Specific Targeted Research Project EC contribution: € 1 200 000 Starting date: March 1, 2004 Duration: 36 months

S., Subbarao, K., ‘SARS vaccine protective in mice’, Emerging Infectious Diseases, 2005, 11, pp. 1312-1314).); 2. Preparation of human monoclonal antibodies against SARS-CoV that can be used for passive immunotherapy (Traggiai, E.; Becker, S., Subbarao, K., Kolesnikova L., Uematsu Y., Gismondo, M.R., Murphy, B.R., Rappuoli, R., Lanzavecchia, A., ‘An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus’, Nature Medicine, 2004, 10:871-5). 3. Development of a recombinant vaccine based on SARS virus-like particles (VLPs) which are non-infectious but will stimulate the production of antibodies and immune T-cells. For this part of the study, a collaboration with the National Institutes of Health (NIH) is ongoing.

Potential applications: Results obtained within the scope of the project will be enhanced by two factors. The first is the further development of SARS vaccines by partner 1 (Novartis) which will comprise clinical testing of the vaccine. This will guarantee that the seed money of the EU Commission will serve to promote important applications and products. Along the same line, the therapeutic Coordinator Dr Mariagrazia Pizza monoclonal antibodies will be industrialised for Novartis Vaccines and Diagnostics S.r.l. process development. Via Fiorentina 1 53100 Siena, Italy [email protected] This result could also become an applied tool first, and probably a product within the strategies Prof. Stephan Becker Philipps-Universitat Marburg proposed by the EU Commission in FP6. On the Marburg, Germany whole, the scientific outcomes of this project are [email protected]

expected to have a very high potential impact Prof. Antonio Lanzavecchia reinforcing the competitiveness of the European Istituto di Ricerca in Biomedicina researcher in the vaccine field. Bellinzona, Switzerland [email protected]

Key words: Dr Peiying Ouyang Fudan University SARSVAC, vaccine development, therapeutic Shanghai, China monoclonal antibodies [email protected]

http://www.altaweb.eu/sarsvac Chapter 3 - SARS 51 Control policy optimisation for SARS and other emerging infections: characterising transmission dynamics and estimating key epidemiological parameters

Summary: Problem: of epidemic trends and the impact of The Severe Acute Respiratory Syndrome Database structures, analytical tools and interventions for future outbreaks; (SARS) outbreak of 2003 demonstrated the mathematical models were rapidly developed 3. develop mathematical models to study potential for the rapid global spread of a novel in response to the outbreaks and contributed optimal control policies for airborne respiratory infection, whilst also showing how to the effective control of SARS. However, respiratory infections. effective international scientific collaboration there were still lessons to be learned for and simple public health measures could bring future similar outbreaks, such as how best to Results: such an outbreak under control. SARSTRANS identify the similarities and differences between SARS 2003: Data from Taiwan, Hong Kong brought together data and public health outbreak epidemiology in different regions, the and Beijing was brought together into a expertise from the three largest SARS outbreaks underlying causes of super-spreading events combined dataset which allowed comparative (in Beijing, Hong Kong and Taiwan) with experts and which control measures are likely to be analysis of the three epidemics. There were on infectious disease epidemiology from most effective for future outbreaks. similar patterns in incubation periods and age- outbreak areas themselves and from France, distribution of cases in all three settings, but the Netherlands and the United Kingdom. The Aim: discrepancies in case fatality ratios. Reanalysis shared experience of the whole project team The aims of the SARSTRANS project were to: of a ‘super-spreading’ event suggested that led to new insights into the optimal control of 1. characterise and quantify key the large number of cases attributed to a single SARS, new generic tools for outbreak analysis, epidemiological factors for SARS and source was likely to have been an overestimate and new epidemiological theory. These insights develop novel statistical methods for caused by biased reporting. This highlighted are already informing public health policy for analysing outbreak data; the difficulty in identifying sources of exposure future outbreaks. 2. define ideal structures for case databases, for a novel infection early in an outbreak. and facilitate rapid analysis, interpretation Novel methods and tools for the analysis of outbreaks: Ideal database structures, methods

WHO issue travel advisory (Apr 23) 22 universities and 2610 schools closed (Apr 24) for correctly estimating the case fatality ratio, 120 Fever checks at airports begin (Apr 22) Libraries, bars, theaters closed (Apr 26) the distribution of times from exposure to Quarantine of close contracts (Apr 21) Start to group patients with SARS Outbreak announced publicy in designated wards (Apr 27) onset of symptoms and for real-time estimation 100 by government (Apr 20) HCW training in PPE and management New 1000-bed SARS of the potential scope of an outbreak, and 80 of patients with SARS (Apr 18) hospital opens (May 1) the effectiveness of control measures from 123 fever clinics open (Apr 17) MOH issue infection control guidelines (May 4) incidence data on a novel disease were 60 66 designated fever

Number clinics (May 6) developed and applied to existing datasets. 40 SARS made reportable (Apr 10) Contact tracing begins (Apr 9) An online tool for uploading and analysing 20 outbreak data was developed for quantification of epidemics. 0 Mar 1 Mar 8 Mar 15 Mar 22 Mar 29 Apr 5 Apr 12 Apr 19 Apr 26 May 3 May 10 May 17 May 24 May 31 (a) Number of cases of SARS in Beijing by date Date of symptom onset, 2003 of onset (n=1896) and dates of important control 6 measures, March–May 2003. (b) Daily estimates of the effective reproductive number Rt with 5 95% confidence intervals where the grey region 4 indicates Rt<1. HCW, Health-care worker; PPE, 3 personal protective equipment; WHO, World Health 2 Organisation; MOH, China Ministry of Health. Estimated Rt Estimated 1 Reproduced from Cowling BJ, Ho LM, Leung GM. 0 Effectiveness of control measures during the SARS Mar 1 Mar 8 Mar 15 Mar 22 Mar 29 Apr 5 Apr 12 Apr 19 Apr 26 May 3 May 10 May 17 May 24 May 31 epidemic in Beijing: a comparison of the Rt curve Date, 2003 and the epidemic curve. Epidemiology and Infection (2008), 136: 562-566.

52 Chapter 3 - SARS Acronym: SARSTRANS Contract/Grant Agreement No: SP22-CT-2004-511066 Project type: Specific Targeted Research Project EC contribution: € 1 700 000 Starting date: August 1, 2004 Duration: 41 months

Other epidemiological analyses and lessons for future pandemics: During the course of this project, the collaborators were called upon to contribute to public health policy discussions during an outbreak of Chikungunya that there is a reduction in transmission of a global , the database in Réunion. They were also called upon to during these periods, and that school structures, epidemiological analysis tools and inform international planning for possible closure could contribute to mitigating the the insights gained during this project will future outbreaks of influenza, smallpox or novel effects of a global influenza pandemic. contribute substantially to the development of zoonoses. This led to many novel contributions • International travel: Models of international effective control programmes within the EU and to the theory of epidemics, including a new travel and the spread of infectious disease elsewhere. method of characterising the infectious potential showed that control of epidemics within of a disease which spreads between species. source areas was a highly effective measure Key words: SARS, epidemiology, emerging The public health policy options considered in controlling the international spread of infection, pandemic planning include the following. SARS, and that only extremely effective • Contact tracing: A study on the effectiveness travel restrictions rapidly implemented will of contact tracing showed that long latent be effective in controlling a global influenza Coordinators periods (e.g. smallpox) make tracing pandemic. Tracking diseases in European Prof. Sir Roy M. Anderson, Prof. Christl A. Donnelly insensitive to delays in finding contacts, that travellers could be used to detect Imperial College London variability in how infectious individuals are emerging diseases in developing countries London, UK [email protected]; increases tracing effectiveness (e.g. SARS), and may play a significant role in aiding the [email protected] and that tracing will not be very effective for international public health community to Prof. Alain-Jacques Valleron infections with high levels of infectiousness improve infectious disease control. Institut National de la Santé et de la prior to symptoms (e.g. influenza). Recherche Médicale (INSERM) • School closure: Control strategies based Potential applications: Paris, France [email protected] on non-pharmaceutical interventions These results are informing public health are potentially attractive policy options. planning for future outbreaks of airborne Prof. J. A. P. Heesterbeek University of Utrecht School closure is the measure most often respiratory infections and furthering the Utrecht, Netherlands considered. Reanalysis of data on influenza understanding of such epidemics. In the event [email protected] transmission during school holidays showed of a novel outbreak of emerging infection, or Prof. Anthony Hedley, Prof. Gabriel Leung The proportion of contacts University of Hong Kong of diseased and detected Department of Community Medicine individuals that should be Pokfulam Road, Hong Kong traced to contain epidemics [email protected]; of influenza, SARS, and [email protected] smallpox. It is assumed that the diseased cases Dr Chao Agnes Hsiung National Health Research Institutes (NHRI) are perfectly isolated Taipei, Taiwan upon detection and that [email protected] the average numbers of Influenza secondary infections before Prof. Chen Liang An detection were 1.5, 1.5, and General Hospital of the PLA Smallpox 3, respectively. Respiration Department, Adapted from Klinkenberg Beijing, People’s Republic of China SARS [email protected] Proportion of contracts to be traced D, Fraser C, Heesterbeek H. The effectiveness of Dr Michiyo Shima contact tracing in emerging IC Consultants Tracing delay (days) epidemics. PLoS ONE 2006; London, UK 1: e12. [email protected]

http://www.sarstrans.org Chapter 3 - SARS 53 Prevention of future SARS epidemics through the control of animal and human infection

Summary: Researchers and public health specialists around of the palm civets as intermediate hosts, This project, whose aim was the prevention the world were mobilised to develop drugs and allowing the study of human SARS-CoV of future Severe Acute Respiratory Syndrome and vaccines, to contribute to surveillance of right after transmission from animals (Song (SARS) epidemics through the control of animal emerging diseases, and to propose ways of et al., PNAS, 2005). and human infections, led to very significant preventing future SARS pandemics. 3. Two amino-acid substitutions in the SARS- discoveries: (1) the identification of horseshoe CoV spike protein appeared sufficient for a bats as the natural reservoir of infections, (2) At the time this project proposal was submitted virus adapted to palm civets to cross species the confirmation of the role played by masked (September 2003), it was very difficult to and to bind to human cellular receptors palm civets as intermediate hosts, and (3) predict what the future of this new emerging angiotensin converting enzyme-2 (ACE-2) the prevention of future epidemics by well- disease would be: Would a new pandemic (Li W., Nature, 2003; Nie et al., Biochem coordinated hospital-based surveillance and restart during the 2003/04 winter season? Biophys Res Commun, 2004; Qu X.X. et al., field investigations. Would the elimination from the markets of J Biol Chem, 2005). masked palm civets, the animals that most 4. Neutralising antibodies, induced by an Problem: likely infected men during the first epidemic, antigenic determinant on the S2 domain In November 2002, a previously unrecognised prevent future epidemics? Was there another of the spike glycoprotein (Zhang H. et al., animal Coronavirus (CoV) emerged from the ‘wet animal source for the virus? Were there other J Virol, 2004), could be detected 5 to 10 markets’ (i.e. meat and fish market) of China to ‘human’ CoVs able to induce respiratory days after infection, and persist for 2 to 3 pose a worldwide threat to public health systems. diseases? Would we have the appropriate years, although titres declined markedly at Within 8 months, more than 8 000 people had diagnostic tools to differentiate SARS from the 24-month follow-up visit (Nie et al., J been infected in 25 countries spread over 5 the flu, during acute respiratory infections? Infect Dis, 2004; Liu W et al., J Infect Dis, continents, and 774 had died from the disease. Would neutralising antibodies play a role in 2006; Li T et al., PLoS One, 2006; Cao WC Although the number of fatalities was small protecting against re-infection? If yes, would et al., N Engl J Med, 2007). compared to deaths related to HIV or malaria, such immunity be long term, knowing the rapid 5. New human Coronaviruses were described, the short-term impact of SARS was much wider. decline in protective immunity associated with HCoV-NL63 (Van der Hoek L. et al., Nat other human CoVs? Med, 2004) and HCoV-HKU1 (Woo PC et al., J Virol, 2005), and new diagnostic tools Aim: developed (Vabret A. et al., Emerg Infect The main aim of the EPISARS project was the Dis, 2005; and Vabret et al., Clin Infect Dis, prevention of future SARS epidemics through 2006). control of animal and human infections. 6. Other important findings of the network included the study of long-term excretion of Results: virus in sputum and stools of convalescent Three years later, much progress has been patients (Liu W. et al., Emerg Infect Dis, made in understanding the emergence and 2004), the comparison of the molecular spread of this new viral disease. Several of switches in key nucleotides of the human the important discoveries involved partners of SARS-CoV between the Beijing and the the EPISARS collaborative network (EPISARS worldwide epidemics (Liu W et al., Emerg publications in bold). Infect Dis, 2005), the quantitative detection 1. Horseshoe bats were identified as a natural of SARS-CoV by a multi-target real-time reservoir for SARS-like coronavirus (SARS- Taqman reverse transcription-PCR (RT- CoV) (Li et al., Science, 2005; Lau et al., PCR) assay (Hu W et al. J Clin Microbiol, The masked palm civet (Paguma larvata), a small PNAS, 2005). 2005), and the use of a two-step screening viverrid eaten in restaurants of Guangdong, China, 2. Masked palm civets were again at the method to identify small molecules derived and at the source of transmission of SARS-like coronaviruses to humans (Drawing by François source of the small 2003/04 human from Chinese herbal medicine interfering Moutou, EPISARS partner). outbreak in Guangdong, confirming the role with viral entry (Yi L et al., J Virol, 2004).

54 Chapter 3 - SARS Acronym: EPISARS Contract/Grant Agreement No: SP22-CT-2004-511063 Project type: Specific Targeted Research Project EC contribution: € 1 596 556 Starting date: April 1, 2004 Duration: 36 months

Potential applications: The SARS epidemic has been exemplary in that it gave the scientific and public health communities the opportunity to study the emergence of a virus in human populations at a time when both epidemiological and virological tools were available for in-depth studies. The Jose M. Sanchez-Vizcaino Universidad Complutense de Madrid results were remarkable, with the epidemic Zhang Shuyi Departamento de Sanidad Animal placed under control within six months. Center for Animal Ecology and Madrid, Spain Conservation Biology [email protected] Institute of Zoology, the Chinese Academy EPISARS has markedly contributed to this of Sciences He Xiong outcome, notably with the identification of the Beijing, People’s Republic of China Beijing Center for Disease Prevention and [email protected] Control horseshoe bats as reservoirs for SARS-like Beijing, People’s Republic of China coronaviruses, and with the documentation François Moutou [email protected] Unité d’Epidémiologie of the crucial role played by the masked palm AFSSA LERPAZ Laurent Abel civets in the spread of the disease to humans. Maisons-Alfort, France Génétique Humaine des Maladies Needless to say, the consortium’s contribution, [email protected] Infectieuses Institut National de la Santé et de la although very significant, is one piece of a Wang Jianwei Recherche Médicale (INSERM) Unité U 550 gigantic effort putting together international Institute for Viral Disease Control and Hôpital Necker Prevention Paris, France organisations such as the World Health China CDC [email protected] Organization, national sentinel surveillance Beijing, People’s Republic of China [email protected] Cao Wuchun systems, and first-class laboratories. Beijing Institute of Microbiology and Ettore Randi Epidemiology The partners’ work had direct impact on public Istituto Nazionale per la Fauna Selvatica Department of Epidemiology Conservation Biology and Genetics Beijing, People’s Republic of China health policies, with the control of farming Ozzano dell’Emilia, Italy [email protected]; and selling of masked palm civets in China. [email protected] [email protected]

It also showed the value of multidisciplinary Francisco Palomares Li Taisheng approaches to emerging viruses, combining, Estacion Biologica de Donana Peking Union Medical College Hospital among others, zoologists, , Consejo Superior des Investigationes Department of Infectious Diseases Cientificas Chinese Academy of Sciences virologists, epidemiologists, clinicians and Seville, Spain Beijing, People’s Republic of China public health specialists. Their findings have [email protected] [email protected]

been disseminated through participation in Hu Zhihong Deng Hong-Kui international conferences and more than 30 Wuhan Institute of Virology College of Life Science scientific publications in peer-reviewed journals, Coordinator Chinese Academy of Sciences Peking University Arnaud Fontanet Wuhan, People’s Republic of China Beijing 100871 including 5 editorial papers. Jean-Claude Manuguerra [email protected] Beijing, People’s Republic of China Institut Pasteur [email protected] 25, rue du Docteur Roux Zhao Guo-Ping Key words: 75015 Paris, France. Chinese National Human Genome Center emerging infections, SARS, Coronavirus, China [email protected]; at Shanghai Hong Kong University [email protected] Zhang Jiang High Tech Park Pasteur Research Centre Shanghai, People’s Republic of China Pokfulam Road, Hong Kong Géraldine Veron [email protected] [email protected] Unité Origine, Structure et Evolution de la Biodiversité François Freymuth Giuseppe Ippolito Laboratoire Mammifères et Oiseaux Laboratoire de Virologie Istituto Nazionale per le Malattie Infettive Département Systématique et Evolution UPRES EA 2128 IRCCS Muséum National d’Histoire Naturelle CHU de Caen Lazaro Spallanzani Paris, France Caen, France Rome, Italy [email protected] [email protected] [email protected]

http://www.pasteur.fr/recherche/episars/accueil Chapter 3 - SARS 55 Effective and acceptable strategies for the control of SARS and new emerging infections in China and Europe

Summary: will receive particular attention. SARSControl is control of SARS in China and to additionally The epidemic of Severe Acute Respiratory therefore an integrated multidisciplinary project develop protocols for standardised recording of Syndrome (SARS) showed that new infections to aid European policy on emerging infections. epidemiological data. transmitted through close contact are able to spread rapidly across international borders Problem: Mathematical modelling resulting in significant morbidity. They can even New infections transmitted through close contact A range of transmission dynamic models of cause widespread public alarm and economic loss are able to spread rapidly across international SARS and pandemic influenza was developed, in unaffected countries. It is therefore crucial to borders resulting in significant morbidity. The capable of simulating both the local and global assess the likelihood of similar occurrences and public health response to such emerging spread. They can also model the impact of their possible impact on public health, economic infections (pandemic preparedness) needs to be various interventions identified in other Work performance and public concern. improved. Packages (WPs) of the project and estimate their effectiveness. This was achieved by a series of SARSControl aims to improve the public health Aim: stochastic models for assessing the community response to emerging infections, such as SARS SARSControl aims at improving: transmission of influenza within countries and and influenza, through better knowledge of • knowledge about the spread of SARS in by evaluating the effectiveness of local control the spread of these viruses, improved risk various affected countries, with special measures and travel restrictions to impede assessment, mathematical modelling, and reference to mainland China (the epicentre global spread. economic analysis and risk communication of the epidemic), and assessment of the strategies. All of these activities will be performed impact of various determinants on this Risk perception in conjunction with policymakers and key spread; Risk perceptions were analysed in relation to stakeholders in Europe, thus helping to improve • control of possible future outbreaks of SARS SARS, influenza and other infectious diseases the quality of decision-making. A database with all and other emerging diseases by developing in Europe and Asia. This was achieved with a SARS cases from mainland China, in conjunction appropriate intervention strategies based survey questionnaire developed to measure with World Health Organization (WHO) data, will on epidemiological and economic modelling; risk perceptions, precautionary actions, sources be used to help develop models for the local and • surveillance and risk communication of information used, etc. In addition, focus geographical spread of SARS. strategies for effective control of SARS. group interviews of Chinese communities in two European countries were conducted to explore A toolbox of models will be developed covering Expected results: the reactions to risk communications and the the range of alternative approaches. By Risk assessment models impact of SARS on vulnerable communities standardising epidemiological and control Risk assessment models were developed based living in unaffected regions. Finally, strategies parameters, a consensus view on model-based on international travel, and they assess the risk of were developed for effective risk communication policy recommendations will be derived. These introduction of new infectious diseases like SARS directed at realistic risk perceptions and model results will be combined with analyses of and influenza. To achieve this, data sources of precautionary actions in the populations. the micro- and macroeconomic consequences international travel were identified and analysed. of SARS-like infections to evaluate the potential Different risk assessment scenarios were Risk communication economic impact of different control options. developed to estimate the risk of importation of Risk communication strategies used by affected infections by air travel under different scenarios. Asian countries and other professional bodies Because the acceptance of interventions like the WHO and EU during the SARS outbreak depends on social, cultural and psychological Chinese data analysis were developed and the media response was factors, SARS-related risk perceptions and An optimally complete database with nearly analysed. The institutional structures within precautionary practices will be studied along with all epidemiological data on the 2002/03 SARS which government communication occurred were the risk communication strategies adopted during outbreak in mainland China was developed analysed, as well as the content and timeliness the outbreak to help improve future strategies to estimate key parameters in the spread of communication from governments and public for communicating with the public. Vulnerable and control of SARS, as well as to assess the health authorities to the public. In addition, communities, such as the Chinese in Europe, (economic) impact of interventions used in the critical ethical issues were identified in the

56 Chapter 3 - SARS Acronym: SARSControl Contract/Grant Agreement No: SP22-CT-2004-003824 Project type: Specific Targeted Research Project EC contribution: € 2 500 000 Starting date: January 1, 2005 Duration: 39 months

communication of risks and it was determined whether discrimination or stigmatisation of groups identified as a special risk source played a role, in both the Asian and European context. Key words: Economic analysis SARS, pandemic influenza, avian influenza, public The partners analysed the macro- and micro- health, infectious disease control, epidemiology Dr Petri Ruutu National Public Health Institute economic impact of the SARS outbreak of 2003 Helsinki, Finland and of potential scenarios of pandemic influenza [email protected]

and future SARS outbreaks on European Dr Matthew-James Keeling countries. In addition, an economic analysis Coordinator Warwick University of strategies to control and prevent new and Dr J.H. Richardus Coventry, UK Erasmus MC, [email protected] emerging communicable diseases, such as SARS University Medical Center Rotterdam and pandemic influenza, was undertaken. Department of Public Health Jacco Wallinga P.O. Box 2040 CA National Institute of Public Health and the Rotterdam, Netherlands Environment Policy evaluation [email protected] Bilthoven, Netherlands The research objectives were achieved by the [email protected] Dr John Edmunds preparation of an inventory of the main SARS Health Protection Agency Dr Onno de Zwart control strategies implemented by European and London, UK Municipal Health Service Rotterdam Area [email protected] Rotterdam, Netherlands non-EU countries, including China and Canada, [email protected] during the 2002/03 SARS epidemic and the Dr Jean-Claude Desenclos Institut de Veille Sanitaire Yuwen Yang identification of critical ethical issues associated Département Maladies Infectieuses Center for Disease Control with the implementation of such measures. It also Saint-Maurice, France Taipei, Taiwan included the application of the Hazard Analysis [email protected] [email protected]

and Critical Control Points (HACCP) Model Dr Wuchun Cao Dr Richard Smith to identify critical control points in pandemic Beijing Institute of Microbiology and University of East Anglia Epidemiology School of Medicine, Health Policy and management and a qualitative Delphi analysis with Beijing, China Practice questionnaire rounds and face-to-face meetings [email protected] Norwich, UK to assess the current preparedness situation [email protected] Prof. Thomas Abraham and feasibility of intervention strategies. University of Hong Kong Dr Stefania Salmaso Journalism and Media Studies Centre Instituto Superiore di Sanita Pokfulam Road, Hong Kong Rome, Italy Multidisciplinary workshops and seminars [email protected] [email protected] provided additional insight for generating and appraising scientific advice. Finally, the results Dr Philippe Beutels Jorge Benages Nozal University of Antwerpen World Health Organisation for Europe from the policy evaluation analysis, along with Centre for the Evaluation of Vaccination, Communicable Disease Surveillance and the outcomes generated from research in the Epidemiology and Social Medicine Response (CSR) Antwerp, Belgium Copenhagen, Denmark other WPs of SARSControl, the experiences [email protected] [email protected] gained from the 2002/03 SARS outbreak and Prof. Ralf Reintjes Dr Marianne van Genugten information gained at SARSControl meetings Hamburg University of Applied Sciences MAPI Values and workshop have been compiled in this policy Hamburg, Germany Houten, The Netherlands evaluation report. [email protected] [email protected] Dr Martin Eichner Prof. Arja R. Aro Potential applications: Eberhard-Karls Universität Tübingen University of Southern Denmark Inst. für Medische Biometrie Unit for Health Promotion Research Pandemic preparedness plans in Europe and Tübingen, Germany Esbjerg, Denmark elsewhere. [email protected] [email protected]

http://www.sarscontrolproject.org Chapter 3 - SARS 57

CHAPTER 4 TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHIES

59 European Creutzfeldt-Jakob Disease surveillance

Summary: BSE infection and cases caused by secondary incubation period in relation to human growth The European Creutzfeldt-Jakob disease iatrogenic transmission. The project aimed to hormone-related CJD. Surveillance System (EUROCJD) has achieved all provide an early warning system for new cases the objectives in the original grant application to of vCJD and to disseminate information via a An important issue in relation to the non-UK DG SANCO (Directorate-General for Health and website and through scientific publications. cases of vCJD is whether they were exposed Consumers). The ability to continue to coordinate to BSE infection in exports from the UK or to CJD surveillance in Europe has had major benefits Results: indigenous BSE. This issue is discussed in a and, in particular, the facility to provide real-time During the period of the project, cases of variant paper form the EUROCJD group1. The conclusion data on variant Creutzfeldt-Jakob disease (vCJD) CJD have been identified (see Table) in a number is that it is possible that non-UK variant cases internationally. Through the EUROCJD system, it of regions with additional cases of vCJD having were exposed to UK exports rather than to has been possible to establish travel history in also been identified in Japan (1) and USA (2). indigenous BSE and this may be consistent with all cases of vCJD internationally, and to confirm in the relative delay in the peak of onsets of vCJD each case the country of likely human exposure Some cases of vCJD, including cases in Ireland, cases in France in comparison to the UK. The to bovine spongiform encephalopathy (BSE). Canada and the USA, had a history of extended temporal development of outbreaks of vCJD is Cases of secondary iatrogenic transmission residence in the UK during the period of maximal an important issue in relation to predictions of of vCJD through blood transfusion have been human exposure to the BSE agent and it is likely the future course of any epidemic. In the UK, identified in the UK. that the causal exposure to BSE took place in the data indicates that the numbers of deaths the UK rather than the country of residence. By per annum from vCJD may have peaked in 2000 Aim: using the known periods of residence of these and there may also have been a peak in non-UK The primary objective of this project has been cases in the UK, it is possible to estimate a mean cases in 2005. the identification and characterisation of all cases incubation period and the figure compares this of vCJD in participating countries by establishing with incubation period estimates in iatrogenic One important aspect of vCJD epidemiology is surveillance systems for all forms of human prion CJD in kuru. It is apparent that the estimated that there have been a number of cases of vCJD disease in these countries. Another objective of incubation periods in relation to vCJD are identified in recent years in France, although the system has been to identify novel forms of consistent with both the minimum incubation this is consistent with a previous mathematical human prion disease that might be related to period in iatrogenic CJD and kuru and the median prediction model2. One aspect of the French cases that differentiates them from the UK cases Total Number of is that they are older on average, although this is Total Number of Secondary Cases: Cumulative Residence Country Primary Cases Blood Transfusion in UK >6 Months During of only borderline significance. (Number Alive) (Number Alive) Period 1980 to 1996 UK 163 (5) 3 (0) 166 During the period of the project, four instances France 22 (2) - 1 of presumed transmission of vCJD infection through blood transfusion were identified in Republic of Ireland 4 (0) - 2 the UK, including three clinical cases and one Italy 1 (0) - 0 subclinical or preclinical infection3. USA 3† (0) - 2 Canada 1 (0) - 1 † The third US patient with vCJD was born and raised in Saudi Arabia and has lived permanently Saudi Arabia 1 (1) - 0 in the United States since late 2005. According Japan 1* (0) - 0 to the US case report, the patient was most likely infected as a child when living in Saudi Arabia. Netherlands 2 (0) - 0 Portugal 2 (1) - 0 *The case from Japan had resided in the UK for 24 Spain 1 (0) - 0 days in the period 1980 to 1996.

1 Sanchez Juan P et al., ‘Sources of Variant Creutzfeldt-Jakob Disease outside the United Kingdom’, EID, 13, pp. 1166-1169 2 Chadeau-Hyam, M., Alperovitch, A., ‘Risk of variant Creutzfeldt-Jakob disease in France’, Int J Epidemiol, 2005, 34, pp. 46-52 3 Hewitt, P.E., Llewelyn, C.A., Mackenzie, J., Will, R.G., ‘Creutzfeldt-Jakob disease and blood transfusion: results of the UK Transfusion Medicine Epidemiology Review study’, Vox Sanguinis, 2006, 91, pp. 221-230

60 Chapter 4 - Transmissible spongiform encephalopathies Acronym: (N)EUROCJD Contract/Grant Agreement No: 2003201 Project type: Public Health Programme/ Surveillance Network EC contribution: € 176 645 Starting date: September 1, 2004 Duration: 36 months

Further analysis suggested that transfusion transmission of vCJD was relatively efficient and that infectivity was present in blood during the incubation period and prior to the onset of clinical disease. This is an important issue Potential applications: for public health and individuals with vCJD who The project has had important implications Prof. Cornelia van Duijn had previously donated blood; they have also for public health policy in the EU and other Erasmus University Medical School Department of Epidemiology been identified in France, Spain, Ireland and countries. Prof. Pauli Leinikki & Biostatistics Saudi Arabia. National Public Health Institute Rotterdam, Netherlands Department of Infectious [email protected] Key words: Disease, Epidemiology In addition to the study of vCJD, other forms of Creutzfeldt-Jakob disease; epidemiology; Helsinki, Finland Dr H. Blystad human prion disease are also ascertained and risk factors [email protected] Nasjonalt Folkehelseinstituttet Adveling for Infeksjonsovervaking annual mortality rates per million for sporadic CJD Dr Annick Alperovitch Oslo, Norway (definite and probable) in participating countries Institut National de la Santé et de la [email protected] Coordinator Recherche Médicale (INSERM) U.360 are listed online (see www.eurocjd.ed.ac.uk). Prof. Robert G. Will Paris, France Dr A. Zielinski National CJD Surveillance Unit [email protected] National Institute of Hygiene The major activity is achieving and sustaining Western General Hospital Epidemiological Department Crewe Road Prof. Inga Zerr Warsaw, Poland systematic surveillance for human prion diseases Edinburgh EH4 2XU, UK Georg-August-Universität Göttingen [email protected] in participating countries. This involves a regular [email protected] Neurologische Klinik und Poliklinik Prionforschungsgruppe Göttingen Dr Judite Catarino review of methodologies, of diagnostic criteria Prof. Herbert Budka Göttingen, Germany General Directorate of Health and of available diagnostic investigations. Medical University of Vienna [email protected] Division of Epidemiology & Biostatistics Clinical Institute of Neurology Lisbon, Portugal Vienna, Austria Prof. D. Vassilopoulos [email protected] An important activity for the group has been the [email protected] University of Athens Medical School review and, if necessary, updating of diagnostic Department of Neurology Dr Eva Mitrova Dr S. Quoilin Athens, Greece Institute of Preventative and Clinical criteria for the various forms of human prion Scientific Institute of Public Health [email protected] Medicine disease. A decision was made to revise the Epidemiology Department National Reference Centre Brussels, Belgium Dr Molnár Zsuzsanna of Slow Virus Neuroinfections variant CJD diagnostic criteria to take account of [email protected] National Center for Epidemiology Bratislava, Slovakia two cases, in Italy and Japan, in which the EEG Department of Communicable Diseases [email protected] had shown an appearance that was consistent Dr Savvas Papacostas Budapest, Hungary Institute of Neurology and Genetics [email protected] Dr Alenka Kraigher with sporadic CJD. The revised criteria have Nicosia, Cyprus Communicable Diseases Center been adopted in an amended form as the case [email protected] Prof. Elias Olafsson Institute for Public Health Slovenia National University Hospital Ljubljana, Slovenia definition for the European Centre for Disease Dr Radek Matej (Landspitalinn) [email protected] Prevention and Control’s (ECDC) Designated Thomayer University Hospital Reykjavik, Iceland Surveillance Networks. The National Reference Lab for Diagnostics Dr Jesus de Pedro Cuesta of Human CJD/TSE Dr Michael Farrell Instituto de Salud Carlos III Department of Pathology Beaumont Hospital Centre Nacional de Epidemiologia The results of a questionnaire circulated to Prague, Czech Republic Dublin 9, Ireland Departamento de Epidemiologia Aplicada [email protected] [email protected] Madrid, Spain determine public health policies in participating [email protected] countries in relation to the potential of secondary Dr Kåre Mølbak Prof. Maurizio Pocchiari Statens Serum Institut Instituto Superiore di Sanita Margareta Löfdahl transmission of vCJD are being analysed. Department of Epidemiology Laboratory of Virology Smittskyddsinstitutet (SMI) Copenhagen S, Denmark Rome, Italy Solna Municipality, Sweden An Early Warning System was provided by [email protected] [email protected] [email protected] the EUROCJD system during the course of the Dr Kuulo Kutsar Dr Irina Lucenko Prof. Adriano Aguzzi project. Each new case of vCJD has been notified Health Protection Latvian State Agency ‘Public Health Agency’ Institut fur Neuropathologie Inspectorate Surveillance of Infectious Diseases University Hospital of Zurich following identification through the Early Warning Tallinn, Estonia Department of Epidemiological Zurich, Switzerland and Response System (EWRS). [email protected] Riga, Latvia [email protected]

http://www.eurocjd.ed.ac.uk Chapter 4 - Transmissible spongiform encephalopathies 61 Development of a blood screening assay for diagnosis of prion diseases in humans

Summary: WP1: For many decades, Creutzfeldt-Jakob disease (CJD) was thought to be transmissible among WP2: humans only via contact with infectious WP3: nervous system tissue. However, recently it was shown that variant Creutzfeldt-Jakob WP4: disease (vCJD) is transmissible by blood donation. The transmission of the disease WP5: occurred in the incubation period of the donors, which demonstrates that this route is WP6: highly efficient. Precautionary measures such as leucodepletion and donor deferral increase detection of disease-specific early markers Aim: the costs of blood and blood products, reduce or abnormal protein aggregation. This work The aim is the development of easy applicable the donor population, and might lead to willWP1: be directedIdentification towards of ea therly maidentificationrkers or risk of facto testsrs for CJ forD . prion diseases in humans and shortage of available blood products. specific interacting partners on a protein, potentially in animals. A suitable blood test can mRNAWP2: andIdentification DNA level. of potential biomarkers of CJDbe using used S T forrEP™ diagnostic techno lo purposes,gy and pr oteomic whereass . a Undetected subclinically infected blood WP3: Identification of specific TSE-biomarkers inscreening blood samples assay will be a relevant tool for the donors bear a great risk for secondary vCJD Problem:by MALDI-TOF-Mass-spectrometric techniques.analysis of blood samples. transmission, persistence and or even spread TheWP4: amplificationIdentification of o f thePrP inte abnormalracting memb prionr ane proteins. of vCJD epidemic within the human population. protein Microfiltration by PMCA (Proteinassay for Misfoldingthe detection of disease-associated prion protein WP5: This demonstrates the urgent need for a Cyclic Amplification)aggregates in isblood one of ofexperimentally the 263K scrapie-infected hamsters. screening method, which is applicable and most challenging methods. WP6: Microfiltration assay for the detection of disease-associated prion protein repeatable in easily accessible tissues and Particularlyagg r withegates regard in blood to o thef human CJD. fluids such as blood. prevention of artefacts, this method demands much There is a need to identify new biochemical effort to achieve accuracy markers, since conventional tests require brain in discriminating between autopsy or biopsy and surrogate markers are the normal and abnormal often positive in advanced disease stages only. prion protein. Furthermore, A test in blood would be more favourable for the identification of putative diagnostic purposes and as a screening assay prion protein interaction in blood donors. It needs to reflect disease partners may include pathology in the early stages and therefore a risk potential. be able to indicate a prion infection. The The instability of tests may be based on PrPSc detection or on some proteins and surrogate markers reflecting the reaction of the occurrence of the organism to the disease process. high abundant proteins, which can mask other The development of such assays requires proteins, are possible the study of cell culture systems and animal sources for the production experiments under controlled conditions. of unspecific artefacts. Due They have to be verified on human biological to the sensitivity to protein samples, which are collected at early disease degradation of human fluids, the stages. The goal is the development of a storage and handling of the samples test using multimodal approaches such as must be consistent.

62 Chapter 4 - Transmissible spongiform encephalopathies Acronym: Prionscreen Contract/Grant Agreement No: SP5A-CT-2007-044438 Project type: Specific Targeted Research Project EC contribution: € 1 602 000 Starting date: March 1, 2007 Duration: 36 months

Expected results: The table on the left gives an overview on the Work Packages in this study.

Potential applications: Results of the project on diagnostic markers can be used by public health services and blood banks for blood donor testing. They may be also used by the medical community for individual diagnosis in suspected cases of human spongiform encephalopathies. In addition, the results can be used in potential studies on the treatment of human CJD and can be used in the protocols for monitoring of disease activity or

progress. Coordinator Prof. Dr Inga Zerr Key words: Prof. Dr Victor Armstrong Dr Walter Schulz-Schaeffer TSE, CJD, biomarker, PMCA, test, blood Georg-August University of Göttingen Departments of Neurology, Clinical Chemistry and Neuropathology National Reference Center for TSE Robert-Koch-Str. 40 37075 Göttingen, Germany [email protected]; [email protected]; [email protected]

Prof. Dr Dieter Naumann, Dr Michael Beekes Robert-Koch Institut Berlin, Germany [email protected]; [email protected]

Prof. Dr Maurizio Pocchiari Istituto Superiore di Sanitá National Register of CJD and related syndromes Rome, Italy [email protected]

Prof. Cornelia van Duijn Erasmus University Medical School Department of Epidemiology & Biostatistics Rotterdam, Netherlands [email protected]

Eva Mitrová MD Slovak National Reference Centre of Slow Virus Neuroinfections Bratislava, Slovakia [email protected]

Prof. Dr R. G. Will, Dr Alison Green National CJD Surveillance Unit Edinburgh, UK [email protected]

http://www.prionscreen.de Chapter 4 - Transmissible spongiform encephalopathies 63 An integrated immunological and cellular strategy for sensitive TSE diagnosis and strain discrimination

Summary: sensitive tools for TSE diagnosis and strain scrapie sick sheep). Therefore, not only are Prion infections result in progressive, fatal discrimination. Field tests will validate the new tools to detect PrPSc in various body fluids neurodegeneration. No effective therapies are partners’ recently identified secreted surrogate or organs at various stages of disease needed, available, and medical interventions, possibly markers, whose levels are profoundly increased but new surrogate markers that would ‘sense’ including blood transfusions, have resulted in preclinical prion infections, for identifying the appearance of prion disease are needed in human-to-human transmission of prions. potentially contaminated body fluids. Immuno- as well. However, no biomarkers are available for PCR technology will be explored as a means to preclinical diagnosis of prion infection in body enhance the sensitivity threshold of each assay. Therefore, in order to detect affected individuals fluids. All approved methods of diagnosis Finally, the partners will extend the scrapie at the subclinical stage, it will be of great rely exclusively on the detection of the cell assay technology for rapid and sensitive importance to find other surrogate markers pathological prion protein (PrPSc), which may detection of bona fide prion infectivity in a than PrPSc. Moreover, the appearance of new not be present in all Transmissible spongiform variety of paradigms. prion strains that do not differ in the primary encephalopathies (TSEs). amino acid sequence but are believed to vary Problem: in the three-dimensional structure has made it The TSEUR consortium develops, validates, and The current need for sensitive tests to detect clear that there is also a big demand for tools exploits innovative reagents and technologies prions or surrogate markers of the prion that enable scientists to differentiate those that will address the above problems in three diseases in affected individuals before the prion strains. Prions strains have different areas: (1) enhanced detection of PrPSc, (2) clinical onset of disease has intensified the organ tropisms, can be replicated in different direct measurement of prion infectivity, and (3) search for new technologies and tools. Currently, hosts with different efficiency and can induce validation of new TSE biomarkers in body fluids. diagnosis relies exclusively on the detection of diseases with varying incubation times, lesion PrPSc, which may not be present in all TSEs. profiles, etc. As a consequence of this, it will By using and establishing powerful new panels Importantly, even by using detection methods be of high importance to generate tools to of picomolar-affinity anti-PrP monoclonal specifically for PrPSc, no sensitive tests are differentiate various prion strains. antibodies to a variety of PrP domains, this available to detect prions in blood or urine of consortium aims at generating new, highly affected individuals (e.g. human CJD patients; Aim: The TSEUR consortium proposes to develop, validate, and exploit innovative reagents and technologies that will address the current problems of prion diagnostics in three areas: 1. to develop innovative diagnostic technologies addressing the current gaps in prion detection; 2. to provide minimally invasive diagnostics of human and animal TSEs (e.g. detection of prions in blood and urine of affected individuals, surrogate markers found in urine or blood that can be used to identify subclinically infected individuals); 3. to develop highly sensitive tools for discrimination of prion strains.

Expected results: The expected result of Work Package (WP) 1 is to significantly improve the currently available scrapie cell assay technique and

64 Chapter 4 - Transmissible spongiform encephalopathies Acronym: TSEUR Contract/Grant Agreement No: LSHB-CT-2005-018805 Project type: Specific Targeted Research Project EC contribution: € 1 750 000 Starting date: January 1, 2006 Duration: 36 months

develop cell-based assays using heterologous tagged PrP variants for the rapid and sensitive determination of bona fide prion infectivity in biological tissues and fluids. WP2 will exploit a powerful new panel of picomolar-affinity anti- milk and mammary gland tissue from scrapie- PrP monoclonal antibodies to a variety of PrP affected sheep harbouring Maedi-visna viral domains. These will provide the basis for highly infection. WP6 ensures the establishment, sensitive detection of PrPSc and discrimination maintenance, and quality control of the of prion strains by the consortium’s original infrastructure needed for sample collection and technology termed ‘epitope coding’. WP2 will clinico-biological correlations in sheep tissues. deliver PrPSc-based diagnostic reagents and technology with significantly lower limits of Overall, the TSEUR programme will result in the detection sensitivity. provision of innovative diagnostic technologies with the ultimate goal to enhance the safety WP3 will provide and exploit newly identified of the blood supply, to provide minimally biomarkers by one member of the TSEUR invasive diagnostics of human and animal prion consortium. RNA levels of these two biomarkers diseases, to develop highly sensitive tools for are profoundly altered as a result of prion discrimination of prion strains, and to advance Coordinator disease; early in pathogenesis, encoded basic prion science. Prof. Adriano Aguzzi University Hospital Zurich proteins are known to be present in a variety Institut of Neuropathology of body fluids. Highly sensitive monoclonal Potential applications: Schmelzbergstr. 12 8091 Zurich, Switzerland antibodies directed against human and ovine Many potential applications are planned from the [email protected] cystatin 7 and ovine serpinA3 utilising Virus- results that emerge from this EU consortium: Like Particle (VLP) technology should overcome 1. a highly sensitive and reliable test for Dr Ina Vorberg Technical University of Munich problems of immuno-tolerance of immunised detecting preclinically affected individuals; Institute of Virology mice. Such biomarkers should prove valuable 2. the use of surrogate markers in various Munich, Germany as tools to monitor efficacy of future therapeutic body fluids may enable to detect [email protected] intervention strategies for prion diseases. those preclinically affected individuals, Prof. Roman Jerala independent of the low amounts of PrPSc National Institute of Chemistry Ljubljana, Slovenia WP 4 will deliver a technological platform in in the respective body fluid; [email protected] which sensitivity of detection of low levels 3. discrimination of strains may enable to Dr Ciriaco Ligios of antigen is amplified by PCR technology screen natural scrapie sick sheep for the Istituto Zooprofilattico (quantitative immuno-PCR). WP5 utilises an existence of other prion strains (e.g. BSE). Sperimentale della Sardegna existing experimental set-up whereby several Sassari, Italy [email protected] groups of sheep are managed in controlled Key words: conditions and have been experimentally TSE, epitope typing, surrogate markers, body Dr Martin Bachmann Cytos Biotechnology AG infected with scrapie and are either harbouring fluids, scrapie cell assay, immuno-PCR Schlieren, Switzerland Maedi-visna virus infection or not. The partners [email protected]

will use highly sensitive and cross-species Dr Ingolf Lachmann reactive POM anti-PrP monoclonal antibodies AJ Roboscreen GmbH characterised in WP2 to assess PrPSc load in Leipzig, Germany [email protected] mammary gland and milk of these groups of animals. Additionally, they will use ovine TraSCA Dr Max Basagni Prion Diagnostica Srl technology developed in WP1 to determine Rho (MI), Italy whether prion infectivity can be detected in [email protected]

Chapter 4 - Transmissible spongiform encephalopathies 65 Development of a preclinical blood test for prion diseases

Summary: Problem: end-users, a national blood bank, a There are currently no tests for early prion Prions are infectious proteins. There is currently national biosafety regulatory agency, and a diagnosis. Such tests would help: no effective therapy for prion diseases — centre for neurodegenerative diseases. 1. to prevent transmission through blood, collectively called the transmissible spongiform biologicals, the food chain, and medical encephalopathies (TSEs) — and the disease Four types of activities can be discerned in procedures, and is lethal. There is no sensitive and reliable AntePrion: 2. identify candidates for emerging anti-prion preclinical or even ante-mortem diagnostic test 1. Collection and preparation of human and therapies and prophylactic procedures, for the detection of prions in blood or other animal samples. especially among silent carriers of body fluids. Post-mortem diagnosis relies on 2. Analysis of samples (preparing fractions pathogenic PrP mutations. pathological findings in the CNS and especially enriched in PrPSc, discovering surrogate on the detection of PrPSc. Due to the difficulty markers). Current tests are based on the identification of detecting low levels of prion infectivity and 3. Development of novel detection systems of PrPSc or of characteristic pathologies in PrPSc, little is known about prion infectivity and (e.g. cultured cells), reagents (e.g. brain samples collected post mortem. Recent PrPSc in peripheral tissues. antibodies) and novel software. advances have shown that minute amounts 4. Integration and assessment of the of PrPSc exist in body fluids such as blood. The sensitivity of existing PrPSc detection developing technologies. The principal aim Although these PrPSc levels are too low to methods is insufficient for the identification is to devise a preclinical blood test to: be detected reliably by existing methods, they of PrPSc in body fluids (blood, CSF, milk) a. identify human TSE cases early point to the feasibility of using these fluids with or in non-neural tissues. 14-3-3 and S-100 enough so that emerging therapies improved methods. have been proposed as surrogate markers can be administered on time (prior to to PrPSc as the basis for diagnostic TSE extensive neurodegeneration), Backed by a powerful consortium of partners tests, but such markers are not very specific. b. prevent transfusion of tainted human with proven clinical, experimental and industrial Therefore, the current project will endeavour blood, and achievements, the AntePrion partners want to to find new TSE-specific markers using novel c. remove TSE-tainted meat and animal develop methods for the preclinical detection mass spectrometric and genomic approaches, products from the food chain. of prions in body fluids, based on (1) PrPSc as well as immunological methods. and (2) novel surrogate (non-PrP) markers of Expected results: prion diseases. Thus, the search for non-PrP markers that Subpopulations of WBCs from humans and is being carried out in parallel with improved animals enriched for PrPSc will be isolated. PrPSc detection in body fluids will be achieved procedures for detecting both the protease- The subcellular localisation of the PrPSc will by systematically optimising every step in the sensitive (s) and -resistant (r) PrPSc may give be studied. A number of new antibodies and process: rise to a reliable preclinical test. methods for concentrating and detecting PrPSc 1. Fractionation, to identify fractions enriched are being developed and tested. Enrichment in PrPSc; Aim: of blood fractions containing high levels of 2. PrPSc concentration; AntePrion’s goal is to use a combination of PrPSc, combined with optimisation of methods 3. PrPSc amplification; and research and engineering approaches to: for detecting PrPSc, may yield a blood test 4. PrPSc detection. 1. improve PrPSc detection in blood and at a phase before any clinical symptoms of fluids; prion disease appear. Mass spectrometry will Surrogate markers and molecular ‘signatures’ 2. discover novel proteomic, genomic and be used to obtain profiles of molecules from of prion diseases will be identified using novel immunologic surrogate markers of TSE; and body fluids and tissues from prion-infected sensitive proteomic and genomic approaches, 3. integrate these advances into a preclinical animals that bind to different chromatographic including SELDI, MALDI and DNA microarrays. test for TSEs. To achieve these goals, surfaces. The aim is to identify prion-infection Proprietary software will be developed to experts in the field of prions, cell biology, specific biomarkers, most likely proteins. analyse these emerging signatures. antibody production, and diagnosis Measurements of such a biomarker might comprise the consortium, together with provide a target for development of a non-PrP

66 Chapter 4 - Transmissible spongiform encephalopathies Acronym: AntePrion Contract/Grant Agreement No: LSHB-CT-2006-019090 Project type: Specific Targeted Research Project EC contribution: € 2 450 000 Starting date: June 1, 2006 Duration: 36 months

based ante-mortem test. Alternatively, specific patterns of protein expression or ‘signatures’ detected by mass spectrometry might be used as the basis of such a test.

Potential applications: European countries aim at high standards of consumer protection and for high standards Prof. Dr R. G. Will concerning the safety of blood and blood University of Edinburgh National CJD Surveillance Unit products. The presence of prion infections in Edinburgh, UK cattle (sheep and goats) and the transmission [email protected] of the disease to human beings are serious Prof. Dr Markus Otto dangers to public health. Low levels of PrPSc University Ulm, Medical Faculty have been detected in white blood cells (WBC) Department of Neurology Ulm, Germany in the blood circulation of prion-infected [email protected] animals. Moreover, recent data suggest that variant Creutzfeldt-Jakob disease (vCJD) can be Prof. Dr Eva Mitrova Slovenska Zdravotnicka Univerzita transmitted from humans to humans via blood Department of Prion Diseases and National or blood products. The consortium’s initiative Reference Centre for Prion Diseases Institute of Preventive and Clinical Medicine will help to establish markers and methods Bratislava, Slovakia for the early, preclinical diagnosis of prion [email protected]

infections in animals and human beings, and will Prof. Dr Chiara Zurzolo lead to the development of a new and sensitive Institute Pasteur ante-mortem diagnostic test for prion diseases. Coordinator: Department of Cell Biology and Infection/ Prof. Dr Peter J. Peters Unité Trafic Membranaire et Pathogenese Since several partners are involved in national Nederlands Kanker Instituut Paris, France and international research activities through Department of Tumor Biology [email protected] Plesmanlaan 121 – H4 networks and control/surveillance programmes 1066 CX Amsterdam, Netherlands Dr Carsten Korth on other infectious or transmissible diseases, [email protected] Heinrich Heine Universität Düsseldorf AntePrion has a large impact on public health. Department of Neuropathology Dr Albert Taraboulos Düsseldorf, Germany The Hebrew University of Jerusalem [email protected] Key words: Department of Molecular Biology Hebrew University Dr Michael Baier blood, MALDI, preclinical, prions, proteomics, Hadassah Medical School Robert-Koch-Institut PrPSc, SELDI, surrogate marker, TSE Jerusalem, Israel Berlin, Germany [email protected] [email protected]

Prof. Dr Krister Kristensson Prof. Dr Lothar Stiz Karolinska Institutet Friedrich-Loeffler-Institut (Federal Institute Department of Neuroscience for Animal Health) Division of Neurodegenerative Diseases Greifswald - Insel Riems, Germany Research [email protected] Stockholm, Sweden [email protected] Dr Martin Wiesenfeldt Matrix Advanced Solutions Germany GmbH Dr Jesus Requena Göttingen, Germany Universidade de Santiago de Compostela [email protected] School of Medicine Department of Microbiology Dr Peter L. Hordijk Prion Research Unit Stichting Sanquin Bloedvoorziening Santiago, Spain. Amsterdam, Netherlands [email protected] [email protected]

http://www.anteprion.eu Chapter 4 - Transmissible spongiform encephalopathies 67 Prevention, control and management of prion diseases

Summary: establish a long-lasting leadership that will one of the goals of NeuroPrion is to enhance NeuroPrion – Science at the Service of protect and improve human and animal health. dialogue between researchers, the general public Society NeuroPrion has identified areas where greater and policymakers, raising public awareness of NeuroPrion is the European Network of coordination of research would be beneficial and prion research. NeuroPrion’s annual international Excellence (NoE) dedicated to research on others where novel, applied research is needed. conferences have become a major forum for prion diseases. It involves 52 public research Based on these assessments, NeuroPrion has knowledge dissemination within and beyond the organisations in 20 different countries and implemented a joint programme of activities scientific community. With over 800 participants, federates over 120 individual research groups, that is built on the following four research these conferences — organised each year in a corresponding to more than 90% of the pillars: PREVENTION, TREATMENT, CONTROL different European country — are recognised leading researchers in Europe. The combined and RISK. These four themes were agreed as the as the main ones in the world. know-how and the synergies between the common basis to develop coordinated research main European research teams constitute a programmes to provide the knowledge necessary Moreover, their scientific impact is now increased unique core of expertise strengthening the against future prion crises. by an original video streaming of all the scientific role of science in our society to prevent future presentations accessible to all the participants prion crises. NeuroPrion constitutes a first Expected results: (NeuroPrion’s Online Conferences). These approach towards a new European Research Today, NeuroPrion represents the strongest technologies are now used to communicate Area (ERA) open to collaboration with prion research community ever constituted in the prion information to the public at large, and researchers from all over the world to protect prion field. Its members have implemented a NeuroPrion is also supporting patient families human and animal health against prions and new culture of collaboration among its partners, with information. related diseases. characterised by trust and the equitable exchange of information. In 2004, this cooperation between Potential applications: Problem: scientists, national and European authorities In order to maintain this mobilisation and avoid Since the appearance of the first cases of ‘mad averted an unjustified economic crisis in relation possible crises in the future, NeuroPrion is cow disease’ in the 1980s, prion diseases have to the detection of BSE in a French goat. By exploring new opportunities to enhance the become a major problem for society, both in using new Web technologies, researchers of joint research efforts of project members Europe and worldwide, with important health the network can have access to almost all the through public funding and private investors. and economic consequences. The recent information available on prions: key documents Through its coordinator, NeuroPrion has notably discovery of atypical cases of scrapie in sheep (including journal articles, other reports, promoted the creation of Alliance Biosecure, a and atypical bovine spongiform encephalopathy relevant multimedia, inventories of ongoing non-profit foundation. Its mission is ‘to enable (BSE) in cattle in Europe and the US has raised research, key policy documents); the private progress in the analysis, comprehension and concerns that previously unidentified strains exchange area (where participants can discuss management of risks for public health, linked to of prions may pose new risks for public health. findings, imminent publications and activities at microbiological agents, current or emerging, in Furthermore, the compelling evidence that their institution); a virtual bank of tissues area particular prions’. prion diseases are transmissible through blood (combining the information of several national transfusion, serves as a reminder that crucial and local tissue banks and respecting all the As a consequence of the structuring and information on prion diseases to ensure the required ethical issues related to the human integrating activities of NeuroPrion, the scientific safety of public health is still missing. tissues in order to simplify access to critical collaboration of the NeuroPrion partners have samples for researchers). NeuroPrion is also strongly contributed to scientific progress in the Aim: supporting the Training & Mobility of researchers prion field, which is reflected by the numerous Protection of human and animal health and promotes the exchanges between partners. articles published by NeuroPrion members against prions and related diseases Communication within and beyond the network is (892 articles since 2004). Among the different The primary objective of NeuroPrion is to of clear importance in spreading the knowledge potential applications, original decontamination structure and integrate the efforts of the main concentrated in NeuroPrion. In recognition of techniques could have very interesting European prion research teams in order to the damage the BSE crisis did to public trust in developments in limiting the impact of prions on reduce the fragmentation of the research and government and governmental scientific advice, animal food and the environment.

68 Chapter 4 - Transmissible spongiform encephalopathies Acronym: NeuroPrion Contract/Grant Agreement No: FOOD-CT-2004-506579 Project type: Network of Excellence EC contribution: € 14 400 000 Starting date: September 1, 2003 Duration: 64 months

Coordinator Dr Jean-Philippe Deslys Prof. Jean-Jacques Hauw Dr Stefania Thorgeirsdottir Dr Herman J. W. van Roermund Prof. Krister Kristensson Commissariat à l’Energie Atomique Institut National de la Santé et de la Institute for Experimental Instituut voor Dierhouderij en Karolinska Instituet CEA/DSV/iMETI/SEPIA Recherche Médicale (INSERM) Pathology of the University of Iceland Diergezondheid BV Stockholm, Sweden 18, route du Panorama, BP6 Paris, France Reykjavik, Iceland Lelystad, Netherlands [email protected] 92265 Fontenay-aux-Roses, France [email protected] [email protected] [email protected] [email protected] Dr Dolores Gavier-Widen Prof. Jean-Louis Laplanche Dr Mark Rogers Dr Sylvie Benestad National Veterinary Institute of Sweden Dr Heinz Schimmel Université René Descartes National University of Ireland National Veterinary Institute Uppsala, Sweden Institute for Reference Materials Paris, France Dublin, Ireland Oslo, Norway [email protected] and Measurements [email protected] [email protected] [email protected] Geel, Belgium Prof. Adriano Aguzzi [email protected] Dr Kai Frölich Dr Ruth Gabizon Prof. Martha Ulvund University of Zürich Institute for Zoo and Wildlife Research Hadassah Medical Organization Norwegian School of Veterinary Science Zurich, Switzerland Dr Rikke Hoff-Joergensen Berlin, Germany Jerusalem, Israel Oslo, Norway [email protected] Danish Institute for Food [email protected] [email protected] [email protected] and Veterinary Research Dr Danny Matthews Copenhagen, Denmark Prof. Martin H Groschup Dr Fabrizio Tagliavini Prof. Pawel Liberski Veterinary Laboratories Agency [email protected] Federal Research Institute Instituto Nazionale Neurologico Carlo Besta Medical University of Lodz Addlestone, UK for Animal Health Milan, Italy Lodz, Poland [email protected] Prof. Liisa Sihvonen Institute for Novel and [email protected] [email protected] National Veterinary and Emerging Infectious Diseases Dr Jean Manson Food Research Institute Insel Riems, Germany Dr Gianluigi Forloni Dr Alexandre Galo Institute for Animal Health Helsinki, Finland [email protected] Istituto di Ricerche Farmalogiche Mario Laboratorio Nacional de Investigacao Edinburgh, UK [email protected] Negri Veterinaria [email protected] Prof. Detlev Riesner Milan, Italy Lisbon, Portugal Dr Thierry Baron Heinrich-Heine-Universität Düsseldorf [email protected] [email protected] Dr Neil Raven Agence Française de Sécurité Düsseldorf, Germany Health Protection Agency Sanitaire des Aliments [email protected] Prof. Maurizio Pocchiari Prof. Tibor Hianik Devizes, UK Lyon, France Istituto Superiore di Sanita Comenius University [email protected] [email protected] Prof. Hans Kretzschmar Rome, Italy Bratislava, Slovakia Ludwig-Maximilian-Universität München [email protected] [email protected] Prof. John Collinge Dr Franck Guarnieri Munich, Germany University College London Association Pour la Recherche et [email protected] Dr Maria Caramelli Dr Maria Gasset London, UK le Développement des Méthodes et Istituto Zooprofilattico Sperimentale del Consejo Superior de Investigaciones [email protected] Processus Industriels Dr Michael Beekes Piemont, Liguria e Valle d’Asota Cientificas Sophia Antipolis, France Robert Koch Institute Turin, Italy Madrid, Spain Prof. Alun Williams [email protected] Berlin, Germany [email protected] [email protected] Royal Veterinary College [email protected] Hatfield, UK Prof. Sylvain Lehmann Dr Piero Parchi Dr Juan Maria Torres [email protected] Centre National de la Prof. Hermann Schätzl Alma Mater Studiorom - Universita di Instituto Nacional de Investigacion y Recherche Scientifique (CNRS) Technische Universität München Bologna Tecnologia Agraria y Alimentaria Dr Francesca Chianini Montpellier, France Munich, Germany Bologna, Italy Madrid, Spain Moredun Research Institute [email protected] [email protected] [email protected] [email protected] Edinburgh, UK [email protected] Prof. Jeanne Brugère-Picoux Dr Thorsten Kuczius Dr Gianluigi Zanusso Prof. Isidro Ferrer Ecole Vétérinaire d’Alfort Westfälische Wilhelms-University University of Verona Institut Neuropatologia/ Prof. William Keevil Maisons-Alfort, France University Hospital Münster Verona, Italy Hospital Universitari Bellvitge University of Southampton [email protected] Münster, Germany [email protected] Barcelona, Spain Southampton, UK [email protected] [email protected] [email protected] Dr Hubert Laude Dr Jan Langeveld Institut National de la Recherche Prof. Theodoros Sklaviadis Centraal Instituut voor Prof. Juan José Badiola Prof. Alan Archibald Agronomique (INRA) Institute for Agrobiotechnology Dierziekte Controle-Lelystad Univesidad de Zaragoza Roslin Institute Jouy en Josas, France Thessaloniki, Greece Lelystad, Netherlands Zaragoza, Spain Edinburgh, UK [email protected] [email protected] [email protected] [email protected] [email protected]

http://www.neuroprion.com Chapter 4 - Transmissible spongiform encephalopathies 69 Immunological and structural studies of prion diversity

Summary: An important parameter in cross-species to humans. The tropism of human prions is IMMUNOPRION is a project at the cutting-edge infection resides in the degree of molecular studied in vivo by means of a dedicated mouse of current scientific knowledge on Transmissible homology between the infectious PrPSc and model combining transgenic expressions of Spongiform Encephalopathies (TSEs). The the host prion protein (PrPC). Cell-free systems PrpC from various origins and the graft of a project is built around three key issues: the confirmed the importance of molecular matching human . This model allows strain diversity of TSE agents; the crossing of for efficient conversion of PrPC into PrPSc. Yet, direct testing on prions of concern, including the species barrier; and the evaluation of the such in vitro systems parallel only partially the in BSE, CWD (Chronic Wasting Disease, in deer) host innate and acquired immune responses. vivo reality, suggesting that molecular matching and other emerging prions strains. TSEs are diseases that affect the brain and is not the unique parameter involved and that the nervous system of humans and animals, additional factors might control the species Several lines of evidence support that the among which we find what is commonly termed barrier effect. One of those factors could be the immune system plays a key role during the Mad Cow Disease and its human equivalent, host immune system which is known to react stages of the disease. The project aims to Creutzfeldt-Jakob disease (vCJD). TSEs are vigorously against xenogeneic PrP and which, understand how innate immunity, including propagated by prions (a type of infectious in doing so, could reduce the pathogenicity of dendritic cells and complement, mediates agent made exclusively of protein) through the foreign TSE agents. interactions with specific strains of prions. food chain. There are good reasons to believe that the Aim and expected results: host immune system is tolerant to all (or most) IMMUNOPRION is investigating the fundamental The diversity of strains epitopes except those that are buried in PrPC features of TSEs to develop the detection of prion The strain properties of TSE agents are thought and are revealed only in transconformed strains for diagnostic procedures and for the to be enciphered in the structural conformation PrPSc. On the basis of PrPsc structure models, control of their dissemination through the food of the pathogenic form of PrPSc. The project peptides buried inside the native PrpC are used chain. The project’s objectives are organised will provide a better definition of prion strains in dedicated immunisation protocols to test around the idea that a rational food safety based on their structural and biochemical for their ability to raise antibody responses in strategy must prevent, predict and protect. properties, and will establish relations with mouse models. their physiological and pathological features. Problem: IMMUNOPRION began by producing in vitro Potential applications: The passage of TSE agents, scrapie form of synthetic variants of prions because they A rational food safety policy cannot be attained the prion (PrPSc), from one species to another constitute a reliable and homogenous source, without a detailed scientific knowledge of is limited by a so-called species barrier. When mimicking natural strain diversity. Then, the TSE pathogenesis. This is the reason for the it occurs, this cross-species passage presents project will switch to naturally infectious strains importance of mouse models in many of the the risk for introducing new prions into the in mice, hamsters and sheep. A new imaging research activities. The project emphasises human food chain. technique was set up to identify structures immunological parameters since it appears of prion strains, by means of electron cryo- that the immune system is an accomplice of the The strength of this barrier varies considerably tomography reaching a four-nanometres TSE agent during lympho-invasion. However, it according to the mammalian species: in some resolution, which is not achievable with other seems that it may also act as a highly sensitive combinations, the passage is almost inexistent, methods. Macromolecular prion assemblies alarm and first line of defence. or requires more infectious material and longer will then be analysed in gut follicular dendritic incubation periods than within members of a cells (FDCs), which are infected following oral The potential development of an acquired same species. Under natural conditions too, contamination with different prion strains. immune response against uncovered epitopes the species barrier is highly variable: no of PrPSc may serve as a witness of infection evidence of human contamination by ovine The prion contagion and a tool for early diagnosis. Access to the scrapie has been reported so far whereas IMMUNOPRION aims to acquire a better structural features of various sources of prions hundreds cases of the human new variant vCJD understanding of the species barrier by will allow for determining the exact cartography have been attributed to the bovine spongiform carrying out research using rodents, to probe of the major strains of prions, and will result encephalopathy (BSE) agent. the transmission of TSE agents of animal origin in a well-standardised map of prion diversity,

70 Chapter 4 - Transmissible spongiform encephalopathies Acronym: IMMUNOPRION Contract/Grant Agreement No: FOOD-CT-2006-023144 Project type: Specific Targeted Research Project EC contribution: € 1 960 000 Starting date: June 1, 2006 Duration: 48 months

which will be used to relate the morphological specificities to the pathogenic profile. This will help European countries to define the highest possible standards of consumer protection, through better safety of food products. Therefore, the results of this research will have Robert Sim a major impact on the development of improved The Chancellor, Masters and Scholars of the University of Oxford food safety measures. Department of Biochemistry MRC Immunochemistry Unit Oxford, UK Key words: [email protected] food safety, prion, Transmissible Spongiform Encephalopathies, strain diversity, structural Gordon MacPherson Sir William Dunn School of Pathology biology, immune system, dendritic cells, Oxford, UK complement, data mining. [email protected]. ac.uk

Adriano Aguzzi, Mathias Heikenwaelder University of Zurich Institute of Neuropathology Zurich, Switzerland [email protected]

Peter Peters Het Nederlands Kanker Institut Division Tumor Biology Amsterdam, Netherlands [email protected]

Christophe Lecante TecKnowMetrix S.A.R.L. Voiron, France [email protected]

Philippe Derreumaux Centre National de la Recherche Coordinator Scientifique (France) Patrice Marche UPR 9080 Institut Albert Bonniot Paris, France Centre de Recherche INSERM-UJF U823 [email protected] Equipe Immunologie Analytique des Pathologies Chroniques Ernst Heinen UJF Site Santé, BP 170 Université de Liège 38042 Grenoble, France Institute of Human Histology [email protected] Liège, Belgium [email protected] Claude Carnaud, Pierre Aucouturier Institut National de la Santé et de la Philippe Arhets Recherche Médicale Institut National de la Santé et de la INSERM Unité 712, Hopital Saint-Antoine Recherche Médicale Paris, France Paris, France [email protected], [email protected] [email protected] Pierre Espinasse Jean-Pierre Liautard The Chancellor, Masters and Scholars of INSERM Unité 431- Université Montpellier II the University of Oxford Montpellier, France Oxford, UK [email protected] [email protected]

http://immunoprion.vitamib.com Chapter 4 - Transmissible spongiform encephalopathies 71 Understanding prion strains and species barriers and devising novel diagnostic approaches

Summary: Problem: Specific goals are as follows. Prions: The added complexity and unpredictability of • To study biological properties of field strains Transmissible spongiform encephalopathies prion strains is unsettling. New strains can emerge of scrapie and BSE and of their crossing (TSEs) are fatal neurodegenerative diseases unheralded, with novel clinical presentation and of the species barrier. These studies are that include Creutzfeldt-Jakob disease (CJD) unexpected epidemiological properties. performed in transgenic mice expressing of humans, scrapie of sheep and goats, bo- heterologous PrP of various species. vine spongiform encephalopathy (BSE) or The BSE case: • To examine strain-dependent biochemical ‘Mad cow disease’, chronic wasting disease Based on its typical neuropathology, clinical and biophysical properties of PrPSc. (CWD) of deer in North America, and others. signs, and the biochemical properties of associ- • To determine the 3-D structure of PrPSc TSEs are caused by prions (Prusiner, 1982), ated PrPSc, BSE is a distinct strain. Its emergence of various strains using advanced electron unique proteinaceous pathogens that appear in the late 1980s was unpredictable, as no TSE tomographical techniques. to propagate without the help of nucleic acid cases had ever been observed in cattle. Disqui- • To study strain-specific features of prion genes. Rather, prions ‘replicate’ by refolding etingly, BSE is very infectious, transmitting easily infection and pathogenesis in infected cells a normal protein of the host, PrPC, into a among cattle. Even more worrisome is the ease in culture. For instance, one goal is to find a pathogenic protein called PrPSc. This exclu- with which it infects other species, thus cross- strain-specific ‘signature’ of prion infection sive mechanism explains how TSE can be ei- ing the so-called ‘species barrier’. Upon infection of cells, a device that could help identify ther inherited, acquired through infection, or of sheep, BSE establishes a novel and distinct field strains. occur sporadically. sheep prion strain different from scrapie. While • To create strain-specific monoclonal there have been no reports of ‘classical’ sheep antibodies to be used in research and The emergence of BSE in the late 1980s and its scrapie having infected humans, this may not be diagnosis. subsequent transmission to humans (as variant true for the more ‘promiscuous’ sheep BSE. CJD) has illustrated the grave risks that prions Expected results: pose to public health. Because incubation time Problems presented by prion strains: These efforts are expected to provide many ap- is exceedingly long, most diagnosis methods Prion strains appear to be much more numerous plicable results. First, the consortium will obtain rely on the immune detection of PrPSc (which is and unstable than once thought. Sheep scrapie a better understanding of the natural his- often distinguished from PrPC by its resistance may comprise several substrains, such as tory of strains, of their infectious to proteolysis). the newly discovered Nor98. PrPSc denoting potential, and of their epide- ‘atypical’ and perhaps ‘latent’ TSE have been miology. This should help Prion strains: detected by veterinary surveillance facilities and health, veterinary and A puzzling property of prions is that they occur in research laboratories. However, in most cases, food safety authorities in different ‘strains’ within a given host. Prion distinguishing between strains by biochemical in their efforts to keep strains differ in clinical features and disease tests is not yet possible. In some strains, the the food chain safe. course, and also in their contagious potential. properties of PrPSc (e.g. its sensitivity to Second, the idiosyn- The current view is that prion strains differ proteolysis) may preclude its detection by current crasy of strains will be in the three-dimensional folding of PrPSc. methods. In summary, prion strains increase the better understood Strains greatly complicate the prion problem risk of contaminating the food chain and are and characterised and increase the dangers presented by TSE, difficult to diagnose at present. at the molecular, because they are difficult to diagnose and since structural and some strains are ‘promiscuous’, they jumpwith Aim: cellular levels. ease among species. StrainBarrier is an EU- StrainBarrier’s aims are to study fundamental Third, the consor- funded consortium that strives to achieve and applied aspects of prion strains and tium hopes to cre- the following: (1) to better understand the their relationship to the species barrier, to ate novel, strain- structure, biology and epidemiology of prion use this knowledge to devise strain-specific specific monoclonal strains, and (2) to devise accurate methods to diagnostic methodologies and to predict the antibodies and other distinguish between them. epidemiological behaviour of strains. reagents such as cell-

72 Chapter 4 - Transmissible spongiform encephalopathies Acronym: StrainBarrier Contract/Grant Agreement No: FOOD-CT-2006-23183 Project type: Specific Targeted Research Project EC contribution: € 2 158 500 Starting date: November 1, 2006 Duration: 36 months

based bioassays. Last, the knowledge and re- agents generated by StrainBarrier will be used to devise novel methodologies to diagnose prion strains. Key words: Potential applications: prion, strain, species barrier, atypical, biological Coordinator Several findings and products of this project products Albert Taraboulos The Hebrew University-Hadassah should be readily applicable. Novel diagnostic Medical School methods and reagents (e.g. monoclonal Department of Molecular Biology 91120 Jerusalem, Israel antibodies and cell culture-based bioassays) will [email protected] find their use in veterinary screening programmes and perhaps in hospitals. Novel epidemiological Peter J. Peters Vereniging Het Nederlands Kanker Instituut knowledge will be used by veterinary planning Amsterdam, Netherlands authorities. Reagents and fundamental knowledge [email protected]

will help life science researchers to further their Krister Kristensson understanding of prions. Karolinska Institutet Stockholm, Sweden [email protected]

Jesus R. Requena Universidade de Santiago de Compostela Santiago de Compostela, Spain [email protected]

Chiara Zurzolo Institut Pasteur Paris, France [email protected]

Juan Maria Torres Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria Madrid, Spain [email protected]

Ayub Darji MabGenics GmbH Giessen, Germany [email protected]

Olivier Andreolotti Institut National de la Recherche Agronomique (INRA) Paris, France [email protected]

Dolores Gavier-Widen Statens Veterinarmedicinska Anstalt i Uppsala, Sweden [email protected]

Marion Simmons Veterinary Laboratories Agency Department for Environment, Food and Rural Affairs (Defra) London, UK [email protected]

http://StrainBarrier.huji.ac.il Chapter 4 - Transmissible spongiform encephalopathies 73 Goat BSE: proposal for improvement of goat TSE discriminative diagnosis and susceptibility based assessment of BSE infectivity in goat milk and meat

Summary: Aims: CNS tissues, peripheral nervous tissues, Prion diseases are fatal transmissible The main objective of GoatBSE is to determine lymph nodes, intestines, muscle tissues neurodegenerative diseases that are currently the tissue distribution of BSE after oral and milk. incurable. Although the risk to humans is exposure of goats, and to do this while 2. To determine the influence of PrP genotype generally considered low, cases of Creutzfeldt- simultaneously generating indispensable data on susceptibility of goats for transmissible Jacob disease (CJD) in humans are a fact, and on genetic susceptibility in the most commonly spongiform encephalopathies (TSEs) and the recent discovery of two bovine spongiform used production breeds. The project has the in particular BSE. This will involve case- encephalopathy (BSE) cases in goats has following aims: (1) providing data for the control studies in scrapie-infected herds, shown that the species barrier is not watertight. evaluation of human risk associated with experimental inoculations of goats having The GoatBSE project aims at providing goat BSE passage in goat; (2) providing different PrP genotypes with different sound scientific information to allow the risk pathogenesis data and biological material TSE inoculums and work addressing assessment of human exposure to BSE via goat from first and second passage BSE in goats; the transmissibility/species barriers by milk, meat and products thereof. (3) evaluating the possibility of BSE self- different goats and transgenic caprinised maintenance in goat herds through maternal mice inoculations, as well as rapid in vitro Problem: or horizontal transmission; (4) validating and systems. In light of the known ability of the BSE agent improving our ability to detect caprine BSE 3. To generate/collect data and materials to cross the animal/human species barrier, and discriminate it from scrapie in goats. that will allow quantifying the risk posed to recent evidence establishing the presence humans by the consumption of milk (and of BSE in goat is especially alarming, as it The project itself has been designed to address milk products) and meat of goats. represents a new potential risk of food-borne the following specific objectives: 4. To improve animal models as acceptable contamination to human consumers of goat 1. To determine the tissue infectivity diagnostic assays for TSEs (in particular milk and meat products. distribution of BSE after oral exposure of BSE) in small ruminants. This will involve goats. This will involve work focusing on the generation of caprinised transgenic

74 Chapter 4 - Transmissible spongiform encephalopathies Acronym: GoatBSE Contract/Grant Agreement No: FOOD-CT-2006-36353 Project type: Specific Targeted Research Project EC contribution: € 3 849 994 Starting date: December 1, 2006 Duration: 48 months

mice carrying the PrP alleles making them highly susceptible to small ruminant TSEs and their comparison to the classical mouse bioassays. In addition, goats harbouring the most susceptible PrP alleles will be on scrapie and BSE susceptibility so that it assessed as a rapid/sensitive model for could potentially be used for the control of small ruminant TSEs. field TSE outbreaks in goats. The partners Dr Juan Maria Torres Centro de Investigacion en 5. To assess currently standard diagnostic will also document European field TSE strain Sanidad Animal (CISA-INIA) methods and optimised methods thereof variability in goats by recruiting a large Laboratorio de Biologia Molecular y Celular de Priones for the detection and strain differentiation number of TSE goat isolates from affected Madrid, Spain of TSEs in goats. European countries. [email protected] 6. To assess the feasibility of breeding Dr Cristina Acín programmes to improve existing prevention Already established or specifically created Universidad de Zaragoza and control strategies for TSEs in goat. animals models (strain typing) and biochemical Centro Nacional de Referencia de las EET en España 7. To determine the geographical mapping tools (PrPSc typing) will be investigated for Zaragoza, Spain of prions in goats. This will involve the their ability to efficiently discriminate goat [email protected] collection of a panel of TSE goat cases BSE/scrapie in goats. Finally, by measuring Dr Martin H. Groschup covering the European geographical infectivity in various tissues (including skeletal Friedrich-Loeffler-Institut zone and select amongst them cases for muscle) and secretions (milk), collected from Institute for Novel and Emerging Infectious Diseases strain-typing with biochemical methods and goats at different stages of BSE infection, the Greifswald-Insel Riems, Germany biological bioassays. consortium will provide indispensable essential [email protected]

valuable data for quantitative risk assessment. Dr Pier Luigi Acutis Expected results: Istituto Zooprofilattico It is expected that the project will have a Key words: Sperimentale del Piemonte Centro di Referenza number of important outcomes with immediate goats, TSE, prion, scrapie, BSE, early detection, per le Encefalopatie Animali relevance to the ‘European’ problem of BSE in genetics Turin, Italy goats: [email protected] 1. BSE infectivity distribution in goats and Coordinator Dr Umberto Agrimi goat products; Dr Alex Bossers Istituto Superiore di Sanità Central Veterinary Institute of Wageningen Department of Food Safety 2. improved animal models for detection UR and Veterinary Public Health and discrimination of BSE from other TSE Department of Bacteriology and TSEs Unit of Transmissible Spongiform P.O. Box 65 Encephalopathies and Emerging Infectious strains (in goat); 8200 AB Lelystad, Netherlands Diseases of Animals 3. improved and validated (existing) [email protected] Rome, Italy diagnostics for goat BSE and scrapie; [email protected] Deputy Coordinator 4. additional guidelines to actively control Dr Olivier Andréoletti Prof. T. Sklaviadis TSEs in goats by breeding or selected UMR INRA ENVT 1225 Aristotle University of Thessaloniki Interactions Hôtes Agents Pathogènes, School of Health Sciences culling strategies (also suitable to end- ENVT Department of Pharmaceutical Sciences users and producers); 23 Chemin des capelles Laboratory of Pharmacology 31076 Toulouse, France Thessaloniki, Greece 5. TSE in goat reference point for all stake- [email protected] [email protected] holders including consumers, producers, scientific community and policymakers. Dr Wilfred Goldmann Dr J. Grassi Roslin Institute and R(D)SVS Commissariat à l’Énergie University of Edinburgh Atomique (CEA)/Saclay Potential applications: TSE Genetics group Service de Pharmacologie et Neuropathogenesis Unit d’Immunologie The consortium’s approach will integrate the Midlothian, UK Gif-sur-Yvette, France predicted influence of PrP gene polymorphisms [email protected] [email protected]

http://www.goatbse.eu Chapter 4 - Transmissible spongiform encephalopathies 75

CHAPTER 5 ZOONOSES, FOOD- AND WATERBORNE EMERGING EPIDEMICS

77 Network for the prevention and control of zoonoses

Summary: been emphasised by separate education, training of human and veterinary medicine in order to Med-Vet-Net (MVN) is a five-year EU- and research institutes, and compounded by promote an understanding of the driving forces funded project (2004-2009) targeted at the different governmental ministries for animal in their work and fields of expertise. New and development of a Network of Excellence (NoE) and human health, with different strategies and re-emerging threats to the health of humans for the integration of veterinary, medical and food overall direction. and food animals can be rapidly recognised as sciences, in the field of food safety, at European a precursor to the development of appropriate level. It is based on a ‘virtual institute’ structure A further contributory factor has been the intervention strategies at European level. comprising 15 public health and veterinary discrepancies in the overall direction of institutes in 10 countries plus a small and research, with veterinary objectives often Results: medium-sized enterprise (SME) to disseminate linked to the enhancement of food production, The activities of MVN have been implemented knowledge, and encompasses the activities of whereas research in human medicine may be within a series of WPs. There are three overarching over 300 scientists. more directed to the health of the patient and WPs with different responsibilities: Virtual Institute community. Although some countries in Europe structure (WP1); Strategic Scientific Integration The activities of MVN have been implemented have attempted to bring together research in (WP2); and Spreading Excellence (WP3). WP1 within a series of Work Packages (WPs) the spheres of veterinary and human medicine, is led by the Administration Bureau responsible with three overarching WPs and a range further integration is essential in order to develop for the administrative and financial aspects of of scientific activities falling within four key meaningful intervention strategies. the network, and also has responsibility for the thematic areas: epidemiology; detection and project finances, reporting and developing and control; host-microbe interactions; and risk Aim: taking forward proposals for sustainability. WP2 is research. Within these thematic areas there MVN seeks to develop an NoE in order to improve led by the Project Manager and has responsibility are a number of scientific WPs encompassing research on the prevention and control of for scientific coordination and strategic planning, a wide range of scientific topics and organisms zoonoses, including food-borne diseases, whilst development of research skills, inter-network of major medical and veterinary importance. taking into account the public health concerns of scientific communications and extension of the High priority is afforded to training and there consumers and other stakeholders throughout network by external collaborations. WP3 is led is a well-attended annual three-day scientific the food chain. by the Communications Unit and is responsible conference, with both invited speakers and for the strategy for network communications, speakers from within the network. The network brings together researchers and involving coordination of all aspects of public health experts in diverse agricultural communicating information about the activities Problem: and public health environments in the field of of the network to the scientific community and Of the more than 1 400 microbes known to food safety throughout the European Union, other key stakeholders by means of regular cause infectious disease in humans, over 60% with several overall objectives: (1) enhancing newsletters, a web-based notice board, annual are transmissible from animals. Many of these an understanding of transmission routes reports and training. infections occur following consumption of of pathogens from animals to humans, and contaminated food products or from direct contact of complex host-pathogen interactions; (2) The scientific activities fall within four key with food-producing animals. The resurgence of increasing knowledge of the contribution of thematic areas: epidemiology; detection and diseases, such as bovine tuberculosis, and the external factors such as the use of antimicrobials control; host-microbe interactions; and risk emergence of new infections, much as Severe in their development and spread; (3) developing research. Within these thematic areas there are Acute Respiratory Syndrome (SARS) and avian methods for the rapid identification of zoonotic a number of scientific WPs (31 in total, WP4 to influenza, serve as a reminder of the importance food-borne pathogens and their routes of WP34), some of which have been completed, of animals in human disease. transmission and spread; and (4) producing some of which are ongoing, and some of meaningful risk assessments of key contributory which are scheduled to start later in 2008. The Within Europe, research on zoonotic diseases factors in both human and veterinary medicine. scientific WPs cover several areas: development has, to a large extent, been fragmented, with of a linked molecular surveillance database major divisions between researchers in human A further aim of the NoE is to enhance system for food-borne pathogens; molecular and veterinary medicine. This fragmentation has communication between scientists in the fields epidemiology of European bat Lyssaviruses;

78 Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics Acronym: Med-Vet-Net Contract/Grant Agreement No: FOOD-CT-2004-506122 Project type: Network of Excellence EC contribution: € 14 400 000 Starting date: September 1, 2004 Duration: 60 months

development and application of geographical information systems (GIS) for key food-borne pathogens; pathogenesis of Vero cytotoxin- producing Escherichia coli; identification

of molecular markers for pathogenicity in Potential applications: Bela Nagy Salmonella, Escherichia coli and Campylobacter • improvements in detection and control Veterinary Medical jejuni; validation and standardisation of of zoonotic pathogens, particularly Research Institute (VMRI) Budapest, Hungary PCR methods for pathogen detection and food-borne, in Europe, as well as risk [email protected] quantitative risk assessment; formation assessment and risk analysis; Alfredo Caprioli of European networks for Trichinella and • prioritisation of food-borne and zoonotic Istituto Superiore di Sanita (ISS) Cryptosporidium; harmonisation of Trichinella hazards at EU level; Dipartimento di Sanità, infection control; integrating risk assessment; • better understanding of role of antibiotics Alimentare e Animale Rome, Italy epidemiology and economics to support in development and spread of resistance [email protected] decision making in food safety, pre-harvest in zoonotic pathogens; Johan Bongers, risk assessment; molecular epidemiology of • increased understanding of factors Jaap Wagenaar resistance genes in Salmonella; surveillance of contributing to pathogenicity of key food- Central Veterinary Institute emerging antimicrobial resistance; prioritisation borne zoonotic pathogens; of Wageningen UR, CVI Lelystad, Netherlands of food-borne and zoonotic hazards at EU • identification of new and re-emerging [email protected]; level; improvement of diagnostics for Q fever, zoonotic pathogens; [email protected] host-microbe interactions in Campylobacter; • use of online databases of molecular Arie Havelaar food animals as a source of viral zoonoses; and characteristics of a range of pathogenic Coordinator/ Rijksinstituut voor Deputy Project Manager Volksgezondheit en Milieu (RIVM) Campylobacter risk assessment. micro-organisms for outbreak detection André Jestin Bilthoven, Netherlands and control; Agence Française de [email protected] Each scientific WP holds meetings to discuss • rapid communication between public Sécurité Sanitaire des Aliments 27/31 av du Général Leclerc Tad Dzebenski and decide priorities, and all WPs follow health and veterinary institutions for 94700 Maisons-Alfort, France Panstwowy Zaklad Higieny (PZH) programmes of strictly monitored milestones. outbreak control. [email protected] Warsaw, Poland [email protected] Regular publication of results is encouraged and Project Manager to date over 100 papers have been published Key words: Prof. E. J. Threlfall Lucas Dominguez in scientific journals. Additionally, a number zoonoses, food borne pathogens, prevention, Health Protection Agency Complutense University Madrid (UCM) Centre for Infections Madrid, Spain of ‘Special Interest’ groups have convened in control, network communication 61 Colindale Avenue [email protected] areas such as new, emerging and neglected London NW9 5EQ, UK [email protected] Aurora Echeita zoonoses, Lyssaviruses, host pathogen Instituto de Salud Carlos III (ISCIII) interactions and Campylobacter epidemiology. Henrik Caspar Wegener Madrid, Spain High priority is afforded to training, with training Danish Technical University [email protected] formerly Danish Institute for workshops held within and between WPs, with Food and Veterinary Research Bo Sundqvist exchange programmes (short-term missions) The National Food Institute National Veterinary Institute (SVA) Copenhagen, Denmark Uppsala, Sweden and with support for attendance at relevant [email protected] [email protected] scientific conferences. A further key activity of Kaare Molbak Peter Silley the network is an annual three-day scientific Statens Serum Institut (SSI) Society for Applied Microbiology (SfAM) conference, with both invited speakers and Copenhagen, Denmark c/o Science Communications Ltd speakers from within the network. So far, three [email protected] Milton Keynes, UK [email protected] conferences have been held: Italy, Malta and the Annemarie Kaesbohrer UK have hosted them, with a fourth scheduled Federal Institute for Roberto La Ragione Risk Assessment (BfR) Veterinary Laboratories Agency (VLA) to take place in France in June 2008 and a fifth Berlin, Germany Surrey, UK in Spain in 2009. [email protected] [email protected]

http://www.medvetnet.org Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics 79 International Network for Capacity Building for the Control of Emerging Viral Vector Borne Zoonotic Diseases

Summary: Problem: Aim: West Nile (WN) fever, Crimean-Congo The virgin soil-epidemic raises the threat The ARBO-ZOONET project aims at creating haemorrhagic fever (CCHF) and Rift Valley of expansion into other parts of Asia and common knowledge of these diseases, as well fever (RVF) are arthropod-borne diseases Europe. The general public concern regarding as sharing and exchanging data, expertise, of domestic and wild animals that can affect emerging zoonotic disease has gained interest experiences and scientific information. The humans, posing a great threat to public and relevance in light of global warming. This surveillance systems will be maintained and health because of their epidemic et zoonotic is especially true regarding the spread of the expanded, monitoring disease occurrence potential. Their geographical distribution Arboviruses such as RVFV, CCHFV and WNV, and vaccine use. The disease detection and has expanded greatly in recent decades. WN which are transmitted by mosquitoes or ticks. control tools will be introduced, distributed outbreaks have occurred in Europe, CCHF is It is therefore imperative to work out integrated and harmonised. The consortium will also endemic in many countries including Europe, control measures that include vector control, disseminate knowledge and train staff of and RVF which was endemic/epizootic in the and vaccination programmes, which improve relevant third countries. The project partners African continent, spread for the first time in therapeutic strategies, as well as diagnostic think it is also important to interlink different Yemen and Saudi Arabia in 2000, causing two tools and surveillance, public awareness, scientific disciplines which approach the simultaneous outbreaks. capacity building and the infrastructures in problems from different angles. endemic regions.

Vector control Pathogen Vaccination programme Improved - therapy strategies - diagnostic tools - surveillance - public awareness - capacity building

Human Medecine

Vector

Veterinary Host Zoonosis Medecine

Schematic representation of the consortium as a whole

80 Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics Acronym: ARBO-ZOONET Contract/Grant Agreement No: 211757 Project type: Coordinated Support Action/ Coordinated Action EC contribution: € 998 470 Starting date: May 1, 2008 Duration: 36 months

Expected results: The coordinated research programme — comprising key laboratories in Europe and neighbouring countries — will address K. De Clercq questions of joint interest, thus enabling the Veterinary and Agrochemical development of effective control measures Research Centre that will improve the EU’s response to disease Brussels, Belgium V. Chevalier [email protected] outbreaks. Centre de Coopération Internationale en Recherche Agronomique R. Moorman pour le Développement Stichting Dienst Landbouwkundig Potential applications: Montpellier, France Onderzoek The ARBO-ZOONET consortium hopes this [email protected] Wageningen, Netherlands network will be continued beyond the timeframe [email protected] C. Drosten of the project, and will be extended to address University of Bonn A. Sall other public and animal health problems. Bonn, Germany Institut Pasteur de Dakar [email protected] Dakar, Senegal [email protected] Key words: A. Mirazimi Crimean Congo hemorrhagic fever, Rift Valley Swedish Institute for P. Almeida Infectious Disease Control Universidade Nova de Lisboa fever, West Nile fever, Arbovirus, haemorrhagic Solna Municipality, Sweden Lisbon, Portugal fever, encephalitis, mosquito, tick [email protected] [email protected] P. Calistri A. Brun Istituto Zooprofilattico Sperimentale Instituto Nacional de Investigación y dell’Abruzzo e del Molise ‘G. Caporale’ Tecnología Agraria y Alimentaria Teramo, Italy Madrid, Spain [email protected] [email protected]

T. Avsic-Zupanc A. Papa-Konidari University Ljubljana Aristotle University of Thessaloniki Institute of Microbiology and Immunology Thessaloniki, Greece Ljubljana, Slovenia [email protected] [email protected] F. M. Ruggeri J. Paweska Istituto Superiore di Sanità National Health Laboratory Services Rome, Italy Johannesburg, South Africa [email protected] [email protected] A. Estrada-Peña J. Medlock University of Zaragoza Health Protection Agency Zaragoza, Spain Porton Down, UK [email protected] Coordinator [email protected] Dr Michèle Bouloy R. M. Elliott Institut Pasteur H. Yin University Court of the University of St 25-28 rue du Dr Roux Lanzhou Veterinary Research Institute Andrews 75724 Paris, France Lanzhou, People’s Republic of China St Andrews, UK [email protected] [email protected] [email protected]

J. Ahmed C. Sadegh O. Ergonul Research Center Borstel of Iran Marmara University Borstel, Germany , Iran Istanbul, Turkey [email protected] [email protected] [email protected]

T. Fooks M. Niedrig Z. Vatansever Veterinary Laboratories Agency Robert Koch Institute Kafkas University Weybridge, UK Berlin, Germany Kars, Turkey [email protected] [email protected] [email protected]

Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics 81 Assessment of human health impacts from emerging microbial pathogens in drinking water by molecular and epidemiological studies

Summary: Advanced methodology for environmental combining molecular and classical detection, The development and validation of molecular detection of depends on activity assessment and epidemiological detection technologies is urgently needed several factors: (1) the type of ; understanding of emerging pathogens in a in order to support comprehensive safety (2) the level of taxonomic resolution; (3) the specific set of drinking water systems from concepts for European drinking water, and is detection limit; and (4) the price per analysed different European regions. a main focus of the HEALTHY-WATER project, sample. The universal approach currently in addition to the epidemiology of waterborne pursued is to analyse nucleic acids, extracted Results: diseases. Molecular methods for screening, directly out of drinking water, with a suite of For the detection of the targeted microbial detection and quantification of pathogens and molecular methods ranging from polymerase pathogens by molecular methods, the the assessment of the physiological state of chain reaction (PCR) and DNA array-based necessary primer pairs were designed, tested, drinking water bacteria are developed, validated techniques. Additionally, viruses in drinking validated and/or improved in silico. Using these and applied within the HEALTHY-WATER project. water can be detected and quantified by PCR validated primers, a first survey for the targeted An example, demonstrating the applicability of techniques, such as real-time PCR, without the pathogenic bacteria was performed on a subset the molecular technology for whole drinking need to grow them in host cells. of drinking water samples from France, Spain water supplies is given below. and Germany. The first molecular screening Aim: of these samples resulted in several positive Problem: The overall aim of the project is to advance hits for the detection of members of the genus Currently, hygienic quality and potential health our knowledge on pathogenesis of emergent Helicobacter in some samples of drinking water risk from the consumption of drinking water microbial pathogens in drinking water to supply systems. These samples were then is assessed by the cultivation of indicator understand their transmission to humans. subjected to high resolution electrophoresis bacteria (Directive 98/83/EC). This classical The project will focus on all major types of using single strand conformation polymorphism microbiological methodology relies on the pathogens, i.e. viruses, bacteria and , (SSCP) analysis followed by sequencing of the cultivation of specific bacteria, e.g. plate and will concentrate on a representative set of single major bands. Some of the bands were counts of coliforms, and has a variety of European drinking water supply systems and identified as belonging to the genus Helicobacter serious drawbacks, like no correlation to many source waters of specific sensitivity to human and even the species could be determined for microbial pathogens and no valid identification health. To reach the overall goal, the following these Helicobacter-positive samples. of the pathogens. Therefore, this methodology detailed objectives are approached: is completely inappropriate for the detection of 1. validation and application of detection A specific effort was made to quantify all the emerging pathogens in drinking water. For this technologies for emerging microbial patho- major targeted pathogens using real-time reason, state-of-the-art detection methodology gens based on nucleic acids; PCR. For this purpose the validated primers is a main focus of this project. 2. molecular survey and comparative de- were tested with reference nucleic acids (DNA/ tailed study of emerging pathogens in Eu- RNA) in the real-time PCR to confirm the Drinking water microflora in tap water after chlorination. ropean drinking water sources and supply performance in comparison to normal PCR. The picture was taken with an epifluorescence systems; Also, spiking experiments were conducted using microscope at a magnification of 1 000 X using live- dead stain (BacLight, Molecular probes). The picture 3. understanding the human health impact of the respective bacterial cells or viral particles shows dead bacteria with injured cell membranes in emerging pathogens by primary epidemio- to validate the concentration and extraction red and live bacteria with intact membranes in green. logical studies targeted at specific systems methodology developed. These spiking and pathogens; experiments resulted in the determination 4. determination of epidemiological correla- of detection limits and the validation of the tions with molecular and environmental laboratory procedures for all major targeted data and assessment of risk for water- pathogens, such as hepatitis A virus (HAV), borne microbial infections in Europe. Norovirus, Helicobacter spp., Campylobacter spp., Legionella spp., pathogenic Escherichia An integrated research approach will be coli, Cyrtosporidium spp. and Gardia spp. pursued to achieve these objectives by

82 Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics Acronym: HEALTHY-WATER Contract/Grant Agreement No: FOOD-CT-2006-036306 Project type: Specific Targeted Research Project EC contribution: € 2 400 000 Starting date: October 1, 2006 Duration: 36 months

In addition to the real-time PCR for the quantification of the targeted pathogens, a DNA-chip was also validated for the massive parallel molecular screening of most of the targeted pathogens in raw and drinking water samples using this type of spiking assays. Different staining methods giving insight into the physiological state of drinking water bacteria were also evaluated (see Figure 1). Prof. Paul R Hunter These results demonstrate that the developed University of East Anglia screening and detection technology is in place School of Medicine for the next round of molecular analysis, i.e. the Health Policy and Practice Norwich, UK broad-scale, in-depth, molecular survey of the [email protected] raw and drinking water samples. Dr Georg Kasimir International Association for Danube Potential applications: Research (IAD) HEALTHY-WATER will generate validated Societas Internationalis Limnologiae c/o Federal Agency of Water Management detection technologies for the targeted Vienna, Austria waterborne pathogens and reveal possible [email protected] routes of transmission to humans via drinking Prof. Maria-José Figueras water consumption. This new knowledge will Universitat Rovira Virgii I Unitat de Microbiologia provide guidance for improving the hygienic Dept. De Ciències Bàsiques quality of European drinking water supplies and Reus, Spain reduce the burden of waterborne infections for [email protected]

those living in Europe. Prof. Albert Bosch Universitat de Barcelona Departamento de Microbiologia Key words: Barcelona, Spain molecular detection, waterborne pathogens, [email protected] epidemiology of diarrhoea Dr Sophie Courtois SUEZ Environnement - CIRSEE Le Pecq, France [email protected]

Dr Andrea Török Tamásné National Center of Public Health National Institute of Environmental Health Budapest, Hungary [email protected]

Prof. Richard Christen UNSA - CNRS UMR 6543 & Université de Nice Sophia Antipolis Laboratoire de Biologie Virtuelle Centre de Biochimie Coordinator Nice, France Dr Manfred Höfle [email protected] Helmholtz Centre for Infection Research Microbiology Division Dr Antonio Martinez-Murcia Inhoffenstr. 7 Molecular Diagnostics Center (MDC) 38124 Braunschweig, Germany Orihuela, Spain [email protected] [email protected]

http://www.helmholtz-hzi.de/en/healthy_water Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics 83 Providing tools to prevent emergence of enteric viruses

Summary: A challenge is that the viruses involved evolve sequences present in animals and humans Gastroenteritis is one of the most common rapidly through mutation and recombination. that will serve as a reference database for diseases worldwide. The majority of episodes are This may have an effect on epidemiology but future surveillance activities. caused by pathogens, such as viruses, bacteria also on the ability to detect and link virus strains and parasites, of which the main transmission from different cases. Therefore, understanding Expected results: route is faecal-oral. This can result in person- the population structure and patterns of change Contributions to standards for detection to-person spread, but it is also spread via faecal of these RNA viruses is important, including the of enteric viruses contaminated surfaces, food or water. Although possible contribution of animal viruses to the Protocols were developed for detection food and water is monitored for bacterial population diversity of human pathogens. Food- and characterisation of a range of enteric contamination, a large proportion of outbreaks borne and waterborne outbreaks are excellent viruses. For Norovirus and hepatitis A viruses, of food-related illness are caused by viruses, opportunities for exposure of humans to animal established links exist with groups developing especially Norovirus and hepatitis A. There is and human viruses simultaneously and as such robust virus detection methods for shellfish, growing evidence that viruses slip through the may contribute to generating a more diverse which is supported by advice on primers. food quality control net. In the EVENT project, range of viruses through recombination. The lack Similarly, standardised protocols for detection the partners are developing methods and a of understanding of the transmission patterns of Noroviruses in routine outbreak surveillance database infrastructure to unravel modes of of viruses with this potential gives cause for were developed and made available to the transmission by understanding genetic diversity concern, and is addressed through EVENT. appropriate surveillance networks (i.e. DIVINE- and evolution of enteric viruses that are or may Net and others). The harmonisation effort be transmitted through the food chain. Overall objectives of EVENT: underlying central data collection is a major • to network expertise on enteric viruses from step towards developing standards for Europe: Problem: molecular virological, clinical, medical and without knowledge about how data can be Noroviruses are the major cause of outbreaks veterinary perspectives; compared, the collection becomes less valuable, of acute vomiting and diarrhoea, many of which • to bridge the gap between research and and this realisation has been a stimulus for the are reported particularly during winter. Although routine application of molecular virological project partners to work towards harmonisation. the main mode of transmission is from person tools in communicable disease surveillance; Finally, a globally accessible genotyping tool has to person, waterborne and particularly food- • to facilitate the development of the been made available via the Internet. borne spreads are common as well. Norovirus laboratory basis for a surveillance network can cause large international outbreaks, and for detection of common-source outbreaks An integrated outbreak surveillance international food-borne and waterborne of Noroviruses; system transmission may play an important role in the • to facilitate the development of the The network managed to develop a fully dissemination of new genetic variants, which laboratory basis for a surveillance network integrated collection and analysis of laboratory additionally spread in the population by person- for detection of common-source outbreaks and epidemiological data that was used in the to-person transmission. As such, Noroviruses of hepatitis A virus by providing scientific DIVINE project. Using the same basic principles, serve as model pathogens, illustrating where and methodological guidance to the basic databases were developed for collection of and how food-borne transmission may occur. laboratory network for detection and typing data on hepatitis A and hepatitis E. This data of food-borne viruses in Europe; is currently being analysed, and will be made More challenging are other viruses with a • to provide science-based testing algorithms accessible to a broader public in the last phase longer incubation time and lower rate of clinical for detection and typing of Noroviruses and of the project. infection, such as hepatitis A and E. These hepatitis A viruses; viruses may cause severe illness, but linking • to provide a resource network for advanced The partners also found that genotyping this to food-borne transmission is very difficult investigation of cases of unusual gastro- information can help dissect food-borne from without the use of molecular characterisation enteritis and hepatitis of suspected (enteric) person-to-person outbreaks, and systematic and linking of data. viral aetiology; implementation of this would increase the quality • to provide a basic database representing of data collected on food-borne outbreaks. the currently circulating enteric viral gene This is needed, because food-borne outbreaks

84 Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics Acronym: EVENT Contract/Grant Agreement No: SP22-CT-2004-502571 Project type: Specific Targeted Research Project EC contribution: € 2 437 941 Starting date: September 1, 2004 Duration: 48 months

were found to be common, including diffuse, international outbreaks for which no control system is in place. Also, the European Food Safety Authority (EFSA) has indicated the need for such an outbreak-based surveillance system. Potential applications: The understanding of the pattern of evolution of Pierre Pothier Through the EVENT collaboration it became Noroviruses of genotype II.4, the most prevalent CHU-Dijon University of Dijon clear that hepatitis E is a significant cause of genotype, in a manner similar to influenza has Laboratoire de Virologie, unexplained hepatitis that was not previously sparked discussions about the potential for a CHU du Bocage Dijon, France recognised in several of the countries. Molecular vaccine, as well as a global collaboration to study [email protected] characterisation revealed that similar viruses are this issue on a wider scale. For hepatitis E, data present in a high proportion of pigs and that found are essential for assessing the potential Albert Bosch University of Barcelona the human and animal viruses are interspersed, impact of the presence of this virus in pigs. Department of Microbiology suggesting a common mode of transmission. The School of Biology de Barcelona Coordinator Barcelona, Spain exact source(s) of infection of humans with these The expertise developed in building, collecting Prof. Dr M. Koopmans [email protected], [email protected] viruses, however, remains to be established, and analysing complex datasets including genetic (scientific coordination); although food-borne and waterborne infections data of a range of pathogens is valuable, because Dr. Erwin Duizer Javier Buesa (project management) University of Valencia have been described. Understanding this is the genome databases are ever expanding and National Institute for Public UVEG important, because hepatitis E may cause a the mining and meaningful sorting of pathogen Health and the Environment Departamento de Microbiologia/ Center for Infectious Diseases Facultad de Medicina highly lethal infection in pregnancy. genetic data is increasingly important. In EVENT, Antonie van Leeuwenhoeklaan 9 Valencia, Spain the partners managed to develop an open 3721MA Bilthoven, Netherlands [email protected] [email protected]; Full analysis of data on other possible zoonotic exchange of strain information, based on agreed [email protected] Gábor Reuter pathogens as causes of unexplained illness is confidentiality rules and publication rights. This is State Public Health Service (ANTSZ) still ongoing. a model for other diseases. David Brown Regional Laboratory of Virology Health Protection Agency (HPA) Pecs, Hungary London, UK [email protected] Contribution to policy developments Key words: [email protected] Katalin Krisztalovics Partners from the EVENT network have served norovirus, outbreak, food-borne virus, emerging Carl-Henrik von Bonsdorff, National Center for Epidemiology (OEK) as a resource for questions on a range of viruses Leena Maunula Department of Epidemiology pathogens that can be transmitted via the faecal- University of Helsinki Budapest, Hungary Faculty of Veterinary Medicine [email protected] oral route. Some of the participants, including Department of Food the coordinator, have directly been involved and Environmental Hygiene Mateja Poljsak-Prijatelj Helsinki, Finland University of Ljubljana with risk assessment of transmission of SARS- [email protected], Institute of Microbiology and causing coronavirus and Avian Influenza viruses [email protected]. Immunology via this route. Laboratory for Blenda Bottiger Electron Microscopy Statens Serum Institute (SSI) Ljubljana, Slovenia The coordinator advises the World Health Copenhagen, Denmark [email protected] [email protected] Organization (WHO) on the exchange of data Ada Hocevar on food-borne viruses and has co-organised Kjell-Olof Hedlund Institute of Public Health Swedish Institute for Infectious of the Republic of Slovenia (IPHS) and hosted a Joint FAO/WHO Expert Meeting on Disease Control (SMI) Ljubljana, Slovenia Viruses in Food (21 to 24 May 2007, Bilthoven, Solna Municipality, Sweden [email protected] the Netherlands), in which several partners of the [email protected] Franco Ruggeri FBVE (Food-borne viruses in Europe) network Lennart Svensson Istituto Superiore di Sanita (ISS) participated (M. Koopmans, E. Duizer, A. Bosch, University of Linköping Department of Food Safety Department of Molecular Virology and Veterinary Public Health F. LeGuyader, D. Brown, C-H. von Bonsdorf). Linköping, Sweden Rome, Italy [email protected] [email protected]

http://www.fbve.nl Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics 85 Prevention of emerging (food-borne) enteric viral infections: diagnoses, viability testing, networking and epidemiology

Summary: the model developed through this network in respond to new and emerging enteric viral Noroviruses cause gastroenteritis and are order to study the evolution of these viruses in diseases. notorious for their propensity to cause outbreaks an international context. of illness in healthcare settings, restaurants Specific and cruise ships, among others. The DIVINE Problem: • to identify Norovirus outbreaks of EU public project was developed to provide meaningful Noroviruses are increasingly recognised as a health importance associated with traded data about the surveillance of this increasingly health threat, due to the propensity of these foods and tourism; prevalent disease. While there is a great diversity viruses to cause outbreaks in healthcare • to use this information for short-term of noroviruses, both in humans and animals, settings, with occasionally severe impact. In control; little was known about the population structure contrast to other disease-specific surveillance • to use this information to inform longer of these viruses in Europe; this knowledge is networks, the EC cannot rely on data aggregation term policy for Norovirus outbreak control needed to understand sources and modes of of laboratory test reports from individual sick at local, national and EU levels, with regard transmission. Therefore, DIVINE was coupled patients at national level, because methods for to food harvesting and hygiene, as well as with the research project EVENT to allow more Norovirus detection are not routinely used in the tourism sector for water, sanitation and in-depth analysis of the data collected through many countries. environmental hygiene; routine surveillance activities. • to develop a sustained Norovirus outbreak While epidemiological criteria can be used to surveillance system within the EU and Truly integrated virological and epidemiological identify outbreaks of illness due to Noroviruses across Europe; data collection was successfully accomplished in (as piloted in the ‘Food Borne Viruses in Europe’ • to ensure the quality of this network by 10 of the 13 participating countries. Norovirus (FBVE) project), the lack of underpinning providing proficiency testing; GII.4 strains were found to be the dominant laboratory data would result in a surveillance • to provide an open networked virtual centre cause of outbreaks of vomiting and diarrhoea in activity of little value for early warning purposes. for integrated collection of epidemiological hospitals and other healthcare settings, whereas Timely strain characterisation is essential for and virological data; a broader diversity was seen in outbreaks in other detection of emerging novel viral strains and • to provide access to a network of experts settings and transmission routes. The real added for offering an early warning for the emergence covering a wide spectrum of faecal-orally value of the integrated reporting was the ability of more aggressive strains. transmitted viruses. to distinguish patterns of outbreaks based on the molecular information. The DIVINE-Net partners Therefore, DIVINE-Net set out to build on the Expected results: found that a substantial proportion of outbreaks collaboration achieved by the FBVE project The network managed to develop fully is related to food-borne transmission, including in which national expertise in virology and integrated collection and analysis of laboratory diffuse outbreaks resulting from consumption epidemiology were combined to strengthen and epidemiological data in 10 countries, of imported foods. This is of concern because competence in Norovirus outbreak detection and comparative analysis without this level of the currently used control mechanisms are and control, and to develop the necessary integration for the others. The databases have insufficient to detect and/or predict presence or laboratory tools and databases. been filled with data from over 10 000 outbreaks, absence of viruses in the food chain. and have been (and are being) analysed for Aim: follow-up questions. Molecular characterisation For the successful intervention in the case of Overall of outbreak strains was done to provide the basis diffuse international outbreaks, completeness • to develop sustained surveillance and for a meaningful grouping of circulating viruses, and timeliness of reporting would need to be early warning for outbreaks of illness which then was applied in the surveillance. improved and expanded to countries that are not due to Noroviruses, including food, and currently participating. Following the decision not waterborne outbreaks, and based on the By doing so, the partners have for the first time to continue surveillance of Norovirus outbreaks framework developed through the ‘Food in the world demonstrated the unusual dynamics by the European Centre for Disease Prevention borne viruses in Europe research network’ of the most common Norovirus strain (GII.4), and Control (ECDC), the scientific community (QLK1-CT-00594); which evolves very rapidly in a manner similar agreed to launch a global collaboration following • to enhance the capability of the EC to to influenza A. It also showed that genotyping

86 Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics Acronym: DIVINE-Net Contract/Grant Agreement No: 2003213 Project type: Public Health Programme/ Surveillance Network EC contribution: € 471 185,20 Starting date: June 1, 2004 Duration: 42 months

information can help dissect food-borne from person-to-person outbreaks, and systematic implementation of this would increase the quality of data collected on food-borne outbreaks.

After discussions concerning this decision in the Javier Buesa This is needed, because food-borne outbreaks international scientific community, it was decided University of Valencia (UVEG) were found to be common, including diffuse, to launch a global collaboration to retain some Departamento de Microbiologia/ Facultad de Medicina international outbreaks for which no control of the expertise and study the evolution of Valencia, Spain system is in place. Also, the European Food these viruses in a global context. They will [email protected]

Safety Authority (EFSA) has indicated the need use the network to disseminate knowledge to Albert Bosch for such an outbreak-based surveillance system. developing countries, and network laboratory University of Barcelona Finally, a globally accessible genotyping tool has information as a tool to alert each other about Department of Microbiology School of Biology de Barcelona been made available via the Internet. new strains or otherwise unusual events. Barcelona, Spain [email protected], [email protected]

Potential applications: Key words: Coordinator Alicia Sanchez Fauquier At the end of this project, the European Centre norovirus, outbreak, food-borne virus, emerg- Prof. Dr M. Koopmans Instituto de Salud Carlos III for Disease Prevention and Control (ECDC) ing viruses (scientific coordination); Centro Nacional de Epidemiologia Dr Erwin Duizer Madrid, Spain decided not to continue with norovirus outbreak (project management) [email protected] surveillance. National Institute of Public Health and the Environment Gábor Reuter Centre for Infectious Diseases State Public Health Service ANTSZ Antonie van Leeuwenhoeklaan 9 Regional Laboratory of Virology 3720BA Bilthoven, Netherlands Pécs, Hungary [email protected]; [email protected] [email protected] The graph shows the number of outbreaks per month Mateja Poljsak-Prijatelj due to norovirus. The colours represent the different David Brown University of Ljubljana genotypes and variants. It clearly shows that GII.4 Health Protection Agency Medical Faculty strains dominate the epidemics and that new GII.4 Enteric Virus Unit, Institute of Microbiology and strains emerge quickly, and are able to fully replace Enteric & Respiratory Virus Lab, Immunology, Laboratory former endemic strains. Virus Reference Laboratory, for Electron Microscopy Central Public Health Lab Ljubljana, Slovenia 180 London, UK [email protected] non II.4 genotypes and II.4 variants [email protected] Franco M. Ruggeri 160 Markku Kuusi Istituto Superiore di Sanitaire II.4 2006b National Public Health Institute Department of Food Safety 140 II.4 2006a Helsinki, Finland and Veterinary Public health [email protected] Rome, Italy II.4 2004 120 [email protected] II.4 2002 Blenda Bottiger II.4 no var Statens Serum Institute Eckart Schreier 100 Copenhagen, Denmark Robert Koch Institute non II.4 [email protected] Berlin, Germany 80 [email protected] Kjell-Olof Hedlund 60 Swedish Institute for Maureen Lynch Infectious Disease Control Mater Misericordiae Hospital Solna Municipality, Sweden Dublin 7, Ireland 40 [email protected] [email protected]

20 Pierre Pothier Kirsti Vainio University of Dijon (CHUD) Norwegian Institute of Public Health 0 Laboratoire de Virologie Division of Infectious Disease Control 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 Dijon, France Oslo, Norway [email protected] [email protected]

http://www.fbve.nl Chapter 5 - Zoonoses, Food- and Waterborne Emerging Epidemics 87 FUNDING PROGRAMMES

88 Funding Programmes FP6

EDEN (Sustainable development, global change and ecosystems), VIZIER (Life sciences, genomics and biotechnology for health), POLYMOD (Research for Policy Support), EUTRICOD (Research Infrastructures), RaSP (Research for Policy Support), DENCO (International Co-operation activities), DENFRAME (International Co- operation activities), VHF DIAGNOSTICS (International Co-operation activities), VHF/Variola-PCR (Research for Policy Support), SEPSDA (Research for Policy Support), DISSECT (Research for Policy Support), SARS-DTV (Research for Policy Support), SARSVAC (Research for Policy Support), SARSTRANS (Research for Policy Support), EPISARS FP7 (Research for Policy Support), SARSControl (Research for Policy Support), NEUROPRION (Food Quality and Safety), Prionscreen (Research for Policy Support), TSEUR (Life sciences, genomics and EMPERIE (Health), ARBO-ZOONET (Food, Agriculture biotechnology for health), ANTEPRION (Life sciences, genomics and and Fisheries, Biotechnology) biotechnology for health), NEUROPRION (Food Quality and Safety), IMMUNOPRION (Food Quality and Safety), STRAINBARRIER (Food Quality and Safety), GOATBSE (Food Quality and Safety), MED-VET- NET (Food Quality and Safety), HEALTHY WATER (Food Quality and Safety), EVENT (Research for Policy Support).

Programme of Community Action in the field of Public Health (SANCO)

EuroNHID, ENIVD, ENP4Lab, REACT, DIVINE-Net

Funding Programmes 89 Project Index

Chapter 1 Chapter 3 Chapter 5 Preparedness and SARS capacity building for Zoonoses, food- and emerging epidemics SEPSDA 44-45 waterborne emerging DISSECT 46-47 epidemics EMPERIE 12-13 SARS-DTV 48-49 EDEN 14-15 SARSVAC 50-51 Med-Vet-Net 78-79 VIZIER 16-17 SARSTRANS 52-53 ARBO-ZOONET 80-81 POLYMOD 18-19 EPISARS 54-55 HEALTHY-WATER 82-83 EuroNHID 20-21 SARSControl 56-57 EVENT 84-85 ENIVD 22-23 DIVINE-Net 86-87 EUTRICOD 24-25 ENP4LAB 26-27 Chapter 4 REACT 28-29 Transmissible RaSP 30-31 spongiform encephalopathies

Chapter 2 (N)EUROCJD 60-61 Denge and other Prionscreen 62-63 haemorrhagic fevers TSEUR 64-65 AntePrion 66-67 DENCO 34-35 NeuroPrion 68-69 DENFRAME 36-37 IMMUNOPRION 70-71 VHF Diagnostics 38-39 StrainBarrier 72-73 VHF/VARIOLA-PCR 40-41 GoatBSE 74-75

90 Indexes COORDINATORS Project Index Acronyms

Aguzzi, A. (TSEUR) 65 AntePrion 66-67 Anderson, Roy M. (SARSTRANS) 53 ARBO-ZOONET 80-81 Bossers, Alex (GoatBSE) 75 DENCO 34-35 Bouloy, Michèle (ARBO-ZOONET) 81 DENFRAME 36-37 Canard, Bruno (VIZIER 17 DISSECT 46-47 Deslys, Jean-Philippe (NeuroPrion) 69 DIVINE-Net 86-87 Donnelly, Christi A. (SARSTRANS) 53 EDEN 14-15 Duizer, Erwin (DIVINE-Net) 87 EMPERIE 12-13 Duizer, Erwin (EVENT) 85 ENIVD 22-23 Edmunds, John (POLYMOD) 19 ENP4LAB 26-27 Enjuanes, Luis (DISSECT) 47 EPISARS 54-55 Fleischer, Bernhard (EUTRICOD) 25 EuroNHID 20-21 Fontanet, Arnaud (EPISARS) 55 EUTRICOD 24-25 Fusco, Francesco Maria (EuroNHID) 21 EVENT 84-85 Günther, Stephan (VHF/VARIOLA-PCR) 41 GoatBSE 74-75 Hilgenfeld, Rolf (SEPSDA) 45 HEALTHY-WATER 82-83 Höfle, Manfred (HEALTHY-WATER) 83 IMMUNOPRION 70-71 Jaenisch, Thomas (DENCO) 35 Med-Vet-Net 78-79 Jestin, André (Med-Vet-Net) 79 (N)EUROCJD 60-61 Koopmans, M. (DIVINE-Net) 87 NeuroPrion 68-69 Koopmans, M. (EVENT) 85 POLYMOD 18-19 Lancelot, Renaud (EDEN) 15 Prionscreen 62-63 Lang, Ekkehardt (REACT) 29 RaSP 30-31 Marche, Patrice (IMMUNOPRION) 71 REACT 28-29 Niedrig, Matthias (ENIVD) 22 SARSControl 56-57 Nisii, Carla (ENP4Lab) 27 SARS-DTV 48-49 Osterhaus, Albert D. M. E. (EMPERIE) 13 SARSTRANS 52-53 Pardigon, Nathalie (DENFRAME) 37 SARSVAC 50-51 Peters, Peter J. (AntePrion) 67 SEPSDA 44-45 Pizza, Mariagrazia (SARSVAC) 51 StrainBarrier 72-73 Richardus, J. H. (SARSControl) 57 TSEUR 64-65 Snijder, Eric J. (SARS-DTV) 49 VHF Diagnostics 38-39 Spaan, Willy J. M. (SARS-DTV) 49 VHF/VARIOLA-PCR 40-41 Taraboulos, Albert (StrainBarrier) 73 VIZIER 16-17 Velten, Thomas (RaSP) 31 Weidmann, Manfred (VHF Diagnostics) 39 Will, Robert G. ((N)EUROCJD) 61 Zerr, Inga (Prionscreen) 63

Indexes Indexes 91

European Commission

EUR 23172 — EMERGING EPIDEMICS RESEARCH - EU FUNDED PROJECTS 2002-2008

Luxembourg: Office for Official Publications of the European Communities

2007 — 94 pp. — 21.0 x 29.7 cm

ISBN 978-92-79-09458-3

DOI 10.2777/8539

How to obtain EU publications

Our priced publications are available from EU Bookshop (http://bookshop.europa.eu/), where you can place an order with the sales agent of your choice. The Publications Office has a worldwide network of sales agents. You can obtain their contact details by sending a fax to (352) 29 29-42758. KI-81-08-342-EN-C Emerging and re-emerging infectious Following our recently published project synopsis of EU-funded influenza (a potentially pandemic infectious pandemic potentially (a influenza EU-funded of synopsis project published recently our Following other on projects 34 assembles catalogue present the projects, research concern) particular of disease emerging epidemics, funded between 2002 demonstrates It and Programmes. Health Public its 2008 through also but mostly Research, for Programmes Framework through the European Commission’s the scope and long-term track of record EU funding research in this field. The broad range of different the highlights support) policy and aspects environmental to health human and animal (from approaches collaboration in this area. importance of interdisciplinary diseases (EID) are of particular concern because they usually hit populations unprepared. Factors like climate change, increased long-distance travel and international animal trade, all contribute to a drugs, vaccines, tests, diagnostic Appropriate diseases. these of spread faster and pattern changing and proven containment and mitigation measures are frequently not available and the potential for anepidemic or pandemic exists. Research on EID is the only way to enhance preparedness, to react quickly in the case of a new epidemic and – to the extent to which that is possible – to for “prepare the unknown”. Infectious Diseases, once considered to be an issue of the past, remain firmly on the worldwide agenda agenda worldwide the on firmly remain past, the of issue an be to considered once Diseases, Infectious and are a major cause of mortality and years of life lost.