MRC Centre for Outbreak Analysis and Modelling

Lead Research Organisation: Imperial College London
Department Name: Infectious Disease Epidemiology

Abstract

The threat to human populations from new infectious diseases has been highlighted in recent years by the 2003 SARS epidemic, the highly pathogenic H5N1 bird flu strain and ongoing concerns about bioterrorism. Preparing for such eventualities is therefore a key priority for public health agencies and governments worldwide. In this context, computer modelling of epidemics coupled with scientifically rigorous data analysis have proven themselves as powerful tools for giving insight into the spread of disease outbreaks and how we can try and control the transmission of a new disease. The Centre for Outbreak Analysis and Modelling aims to undertaking research in epidemic modelling, and apply the tools developed to priority disease threats of concern. The Centre will provide a core infrastructure - the Outbreak Analysis Unit (OAU) - for establishing long-term collaborative relationships with key public health organisations (e.g. WHO, UN, HPA) and for translating the fundamental epidemiological research of Centre researchers into real improvements in outbreak planning and response. In addition, the Centre will develop the first truly global epidemic simulator. Staff of the Centre will also have a key role in providing training to public health professionals and policy makers.

Technical Summary

The threat to human populations from new and re-emerging pathogens has been highlighted in recent years by the 2003 SARS epidemic, the pandemic potential of the highly pathogenic H5N1 avian influenza strain and ongoing concerns about bioterrorism. Pandemic preparedness is therefore a key policy priority for public health agencies and governments worldwide. In this context, modern epidemiological modelling and analysis methods have proven themselves increasingly powerful tools for giving insight into the patterns of emergence of novel outbreaks and the options available for their control. The proposed Centre for Outbreak Analysis and Modelling aims to deepen and systemise the exploitation of epidemiological research on outbreaks by public health agencies and policy makers tasked with formulating and implementing response strategies to novel infectious disease threats. The eight Centre applicants are world-leaders in outbreak modelling and analysis. They have broad experience in responding to epidemics (e.g. BSE/vCJD , foot and mouth disease, SARS, H5N1 avian flu) and providing real-time epidemiological analysis which has directly influenced disease control policy. However, infrastructure to support this work has previously been lacking ? meaning ad hoc teams have had to be assembled to the detriment of longer term research, and that capacity is lacking to respond to many requests for specific policy-related work. Furthermore, relationships with the relevant clinical communities and government bodies have not always been able to be established and reinforced over the long-term timescale necessary for optimal communication. The proposed Centre would provide a core infrastructure - the Outbreak Analysis Unit (OAU) for establishing long-term collaborative relationships with key public health organisations (WHO, UN, HPA, ECDC) and for translating the fundamental epidemiological research of Centre researchers into real improvements in outbreak planning and response. Coupled to the OAU, a core (independently funded) research programme will develop the first global epidemic simulation and analysis platform, with the aim of providing next generation predictive modelling tools for epidemic planning and response. Six key thematically categorised satellite research clusters will be established, each addressing a key research priority in outbreak epidemiology via multiple individual research projects led by the applicants. The results generated by this research will be rapidly utilised by the core. Staff of the Outbreak analysis Unit will also have a key role in providing specialist skills transfer to public health partners, with all Centre researchers playing an active role in provision of innovative short training courses for public health professionals and policy makers.

Publications

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Campbell CN (2011) Hospitalization in two waves of pandemic influenza A(H1N1) in England. in Epidemiology and infection

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Cremin I (2012) Patterns of uptake of HIV testing in sub-Saharan Africa in the pre-treatment era. in Tropical medicine & international health : TM & IH

 
Description Recommendation for the long-term vaccination strategy for YF informing SAGE decisions
Geographic Reach Multiple continents/international 
Policy Influence Type Citation in other policy documents
 
Description MRC Centre Grant: Centre for Outbreak Analysis and Modelling
Amount £1,933,493 (GBP)
Funding ID G0600719/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 03/2008 
End 03/2013
 
Description MRC Supplement to MRC Centre Award: A continental-scale simulator for modelling malaria eradication strategies
Amount £280,558 (GBP)
Funding ID G0600719 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2009 
End 03/2013
 
Description Analysis of early H1N1 outbreak in UK 
Organisation Public Health England
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Public 
PI Contribution Collaborative analysis of early H1N1 case data from the UK
Collaborator Contribution Provision of early data on H1N1 pandemic in the UK
Impact The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom Azra C Ghani1*, Marc Baguelin2*, Jamie T Griffin1*, Stefan Flasche2,6*, Richard Pebody2*, Albert Jan Van Hoek2*, Simon Cauchemez1, Ian M Hall 3, Christl A Donnelly1, Chris Robertson4,6, Michael T White1, Iain Barrass3, Christophe Fraser1, Alison Bermingham2, James Truscott1, Joanna Ellis2, Helen E Jenkins1, George Kafatos2, Tini Garske1, Ross Harris2, Jim McMenamin4, Colin Hawkins2, Nick Phin2, André Charlett2, Maria Zambon2, W. John Edmunds2,5, Mike Catchpole2, Steve Leach3, Peter J White1,2, Neil M Ferguson1+, Ben S. Cooper2+. In Review and also available on PLoS Currents - Influenza
Start Year 2009
 
Description Estimation of HIV transmission dynamics using genomic sequences-2013 
Organisation Michigan State University
Department Department of Community Health
Country United States of America 
Sector Academic/University 
PI Contribution All analysis of data first author on PMID: 22761556
Collaborator Contribution provision of anonymised data set.
Impact PMID: 22761556
Start Year 2010
 
Description Ex Flu-2013 
Organisation Centers for Disease Control and Prevention (CDC)
Country United States of America 
Sector Public 
PI Contribution Sample design
Collaborator Contribution Alison Aiello: Principal Investigator Amanda Simanek: Study coordination, subject interaction Arnold Monto: Senior study coordinator
Impact none yet
Start Year 2011
 
Description MERS Coronovirus- Pasteur -2013 
Organisation Pasteur Institute, Paris
Country France, French Republic 
Sector Academic/University 
PI Contribution Assessing epidemic risk of MERS-CoV. Implications for health risk assessment and control.
Collaborator Contribution Assessing epidemic risk of MERS-CoV. Implications for health risk assessment and control.
Impact Corresponding publication. PMID 23787162
Start Year 2013
 
Description MERS Coronovirus- Saudi -2013 
Organisation Government of Saudi Arabia
Country Saudi Arabia, Kingdom of 
Sector Public 
PI Contribution Assessing epidemic risk of MERS-CoV. Implications for health risk assessment and control.
Collaborator Contribution Assessing epidemic risk of MERS-CoV. Implications for health risk assessment and control.
Impact Corresponding publication. PMID 23787162
Start Year 2013
 
Description Marisa Miraldo - 2016 
Organisation Imperial College London
Department Department of Physics
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Managed the collaboration
Collaborator Contribution Expertise in behavioral econ in designing and conducting flu vaccination study (PHE Porton Down)
Impact Data from final survey awaited. Likelihood check. Then apply for grant in the future to expand detail and scale of experiment (including lab experiments)
Start Year 2016
 
Description Molecular Epidemiology HIV group-2013 
Organisation Medical Research Council (MRC)
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Talk given. Attending research meetings
Collaborator Contribution The group meets every three months to share research information and data.
Impact none yet
Start Year 2013
 
Description Sara Machado 
Organisation London School of Economics and Political Science (University of London)
Department Department of Anthropology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Managing the collaboration
Collaborator Contribution expertise in experimental and behavioural economics
Impact Data from final survey awaited. Likelihood check. Then apply for grant in the future to expand detail and scale of experiment (including lab experiments)
Start Year 2016
 
Description The WHO Rapid Pandemic Assessment Collaboration 
Organisation World Health Organization (WHO)
Country Global 
Sector Public 
PI Contribution expertise in statistics, genetics, bioinformatics and mathematical modelling
Collaborator Contribution Local expertise on Mexican flu outbreaks, international expertise on policy needs
Impact 19433588
Start Year 2009
 
Title OutbreakTools (Epibase) - 2013 
Description epibase is the R package created during "Hackout", a hackathon for the analysis of disease outbreaks using R, which took place at the MRC Centre for Outbreak Analysis and Modeling at Imperial College, London, in January 2013. It implements essential tools for handling, visualizing, and analyzing disease outbreak data. 
Type Of Technology Software 
Year Produced 2013 
Impact The creation of epibase set up the basis of a new framework for disease outbreak analysis using free, open-source software. It gathered a community of worldwide experts in infectious disease modelling, statistics and bioinformatics working collectively on its development. It is also an essential piece of episerve, a new web-based platform for the collection and analysis of disease outbreaks, developed by Thibaut Jombart and David Aanensen, in collaboration with the Alert & Response Team at WHO. 
URL https://sites.google.com/site/therepiproject/r-pac/about
 
Title Outbreaker - 2013 
Description outbreaker is a new approach for reconstructing densely sampled epidemics and inferring transmission trees ('who infected whom') from pathogen genomic sequences. It is also the first approach of this kind of be widely available as a free and open-source software. 
Type Of Technology Software 
Year Produced 2013 
Impact While the method is still under evaluation, it has already received noticeable interest from the community, with two workshops having been dedicated to its presentation the "Genepi workshop", London, UK 2013 and the "pre-ESCAIDES workshop on molecular outbreak epidemiology", Stockholm, Sweden, 2013. 
URL https://sites.google.com/site/therepiproject/r-pac/outbreaker
 
Description Big Bang - CD - 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Schools
Results and Impact Over 1000 school children visited the MRC Centre for Outbreak Analysis and Modelling's stand, where children were 'infected' and 'vaccinated' to teach the basics of infectious disease epidemiology.

none recorded
Year(s) Of Engagement Activity 2013
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/medicine/newssummary/news_19-3-2013-13...
 
Description Big Bang - PW - 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Over 1000 school children visited the MRC Centre for Outbreak Analysis and Modelling's stand, where children were 'infected' and 'vaccinated' to teach the basics of infectious disease epidemiology.

unknown
Year(s) Of Engagement Activity 2013
 
Description Imperial Fringe - 2013 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Members of the public attended the event to learn about infectious disease outbreaks through intercative activities.

Not known
Year(s) Of Engagement Activity 2012
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_1-11-2012-13-44-43
 
Description Life Festival - SR - 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Over 1200 visitors attended the MRC centenary 'Life Festival' at the Science Museum. Through participation in our games and activities visitors learned about the concepts of infection, vaccination, and herd immunity.

97% of event visitors rated their experience as 'positive', with many visitors leaving specific positive feedback about our activities.
Year(s) Of Engagement Activity 2013
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/medicine/publichealth/mrscentreforoutb...
 
Description Life Festival - WH - 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Type Of Presentation Workshop Facilitator
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Over 1200 visitors attended the MRC centenary 'Life Festival' at the Science Museum. Through participation in our games and activities visitors learned about the concepts of infection, vaccination, and herd immunity.

97% of event visitors rated their experience as 'positive', with many visitors leaving specific positive feedback about our activities.
Year(s) Of Engagement Activity 2013
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/medicine/publichealth/mrscentreforoutb...
 
Description Summer Science NP - 2013 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Café Scientifique (Royal Society Summer Science Exhibition). Dr Nim Pathy gave a talk on the impact of increasing globalisation upon infectious disease risk. Around 75-100 people attended the event and took active part in discussions, raising several questions about pandemics and diseases.

Not known yet.
Year(s) Of Engagement Activity 2013
URL http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/medicine/publichealth/mrscentreforoutb...
 
Description Wellcome Trust Conference talk - 2013 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Infectious Disease Genomics & Global Health. 16-18 Oct 2013. Cambrige. Enhancing epidemiological surveillance of HIV with molecular data.

none yet
Year(s) Of Engagement Activity 2013
URL http://www.hinxton.wellcome.ac.uk/advancedcourses/IDG&GHprogramme.pdf