Epi-SEQ - Molecular epidemiology of epizootic diseases using next generation sequencing technology

Lead Research Organisation: University of Glasgow
Department Name: College of Medical, Veterinary &Life Sci

Abstract

Next-generation sequencing (NGS) techniques offer an unprecedented step-change increase in the amount of sequence data that can be generated from a sample. NGS technologies can determine complete viral genomes with a resolution allowing the quantification of RNA quasispecies variation within samples and can economize the sequencing of large numbers of samples or larger DNA virus genomes. Focusing on important epizootic viral diseases that threaten livestock industries in Europe, the aim of this project is to exploit NGS to generate improved tools that can be used in real-time during epidemics. This work will be undertaken by a multidisciplinary team of scientists from Belgium, Germany, Italy, Sweden, and the United Kingdom with expertise in molecular virology, bioinformatics, mathematical modeling, and evolutionary biology. RNA viruses evolve rapidly and quickly adapt to different environmental pressures escaping host immune defenses, altering their pathogenicity and host range, and evading diagnostic tests. Current methodologies limit the resolution at which we can study the evolutionary dynamics of the complex genomic mixtures (quasispecies) that are typical for these viruses. Archived sample collections representing epizootic outbreaks of pathogens such as foot-and-mouth disease virus (FMDV), avian influenza virus (AIV), Newcastle Disease Virus (NDV) and classical swine fever virus (CSFV) will be used to monitor the evolution during field outbreaks of disease. Spatiotemporal data collected in the field will be integrated with this genetic data to produce robust models that can be used to reconstruct transmission trees during viral epidemics. Furthermore, in vitro experiments will be performed using FMDV (ss+RNA genome) and AIV (ss segmented-RNA genome) under strong selection pressures. Modeling of the resulting NGS data will provide a framework to describe the wider scale evolutionary patterns that are measured during these field outbreaks. Linking genetic data to viral phenotype will be undertaken by studying DNA viruses with large genomes (ASFV and poxviruses). Although the viruses have relatively stable genomes, their large size poses challenges for sequencing using traditional Sanger approaches. Specific work packages will focus on the improvement and dissemination of technical protocols and on data analysis and dissemination of bioinformatics and modeling tools. Insights from this project will result in: a) Novel information on viral evolution and (sub)populations; b) comparative evolutionary data between viruses with different genome organisation (+ vs. - sense RNA, segmented RNA, c) Improved diagnostic assays, based on an improved recognition of suitable sequence motifs; d) Powerful tools for molecular epidemiology; e) Enhanced capacity to optimize the strain composition of vaccines, and match to emerging virus variants; f) More effective tools to control epidemic and endemic infectious diseases.

Technical Summary

Next-generation sequencing (NGS) techniques offer an unprecedented step-change increase in the amount of sequence data that can be generated from a sample. NGS technologies can determine complete viral genomes with a resolution allowing the quantification of RNA quasispecies variation within samples and can economize the sequencing of large numbers of samples or larger DNA virus genomes. Focusing on important epizootic viral diseases that threaten livestock industries in Europe, the aim of this project is to exploit NGS to generate improved tools that can be used in real-time during epidemics. This work will be undertaken by a multidisciplinary team of scientists from Belgium, Germany, Italy, Sweden, and the United Kingdom with expertise in molecular virology, bioinformatics, mathematical modeling, and evolutionary biology. RNA viruses evolve rapidly and quickly adapt to different environmental pressures escaping host immune defenses, altering their pathogenicity and host range, and evading diagnostic tests. Current methodologies limit the resolution at which we can study the evolutionary dynamics of so-called 'quasispecies' that are typical for these viruses. Archived sample collections representing epizootic outbreaks of viral pathogens will be used to monitor the evolution during field outbreaks of disease. Spatiotemporal data collected in the field will be integrated with these genetic data to produce robust models that can be used to reconstruct transmission trees during viral epidemics. Specific work packages will focus on the improvement and dissemination of technical protocols and on data analysis and dissemination of bioinformatics and modeling tools. Insights from this project will result in: a) Novel information on viral evolution and (sub)populations, more powerful tools for molecular epidemiology, and more effective tools to control epidemic and endemic infectious diseases.

Planned Impact

Epi-SEQ brings together a multidisciplinary team of scientists with expertise in molecular virology, bioinformatics, mathematical modeling, and evolutionary biology. The power of the consortium lies in the complementary expertise ranging over virology, next generation sequencing, bioinformatics, mathematical modeling and data analysis, and in the synergy that will be generated as a result of complementarity between methodological and analytic expertise and the unparalleled access to sample collections available in partner labs from past epidemics and experiments. Focusing on important epizootic viral diseases that threaten livestock industries in Europe, the project will generate improved tools that can be used in real-time during epidemics. Archived sample collections representing epizootic outbreaks of pathogens such as foot-and-mouth disease virus (FMDV), avian influenza virus (AIV), Newcastle Disease Virus (NDV) and classical swine fever virus (CSFV) will be used to monitor the evolution during field outbreaks of disease. Spatiotemporal data collected in the field will be integrated with these genetic data to produce robust models that can be used to reconstruct transmission trees during viral epidemics.

The University of Glasgow component of the project will focus specifically on FMDV. FMDV is highly contagious and disease outbreaks are difficult to control. The exact mode of transmission between farms remains poorly understood and during the UK outbreak in 2001 the viral origin for many infected premises was attributed simply to "local spread". Working in close partnership with IAH-Pirbright, and in collaboration with other members of this consortium we will address the important problem of how to use viral sequence data to infer the movement of virus between farms. Full-length viral genomes from all farms from which virus was recovered during the UK 2001 outbreak will be generated and methods developed to infer the epidemiological transmission trees that relate how precisely the infection spread between farms. FMDV in the UK is an ideal system for this since the outbreak is likely to have been sampled close to exhaustively at the level of the 'premise'. Such a data set would become an absolute classic of its type, and hugely useful for testing ideas about the microevolution and transmission of RNA viruses generally. In order to maximize the robustness and confidence that can be placed in these inferences it is necessary to develop a more refined understanding of how the genetic signal in the data is generated, and transmitted between individuals from different herds. At the end of this project we will have developed new and improved viral tracing tools that can be used in real-time to support the FMD control and eradication programmes. Methods and results generated through this project will increase our confidence in the use of this type of sequence data to support epidemiological investigations realising the potential of full-genome sequencing for analysis of future epidemics of FMD.

Our ability to generate sequence data is undergoing sequential step-changes, leaving methods for analyzing these data trailing behind. However, the incredible uplift in the affordability of sequencing can potentially transform our understanding of how infectious diseases are transmitted between hosts (or closely related groups of hosts) - a process for which the fine-scale detail has to-date remained largely concealed from us. The capacity to reconstruct such a high resolution estimate of the transmission process would have a huge impact on our ability to focus efforts of control infectious disease, maximizing their effectiveness and efficiency.

Publications

10 25 50
 
Description This project currently only at the mid point.

The work so far has focussed on developing the methods and software pipelines that we will need to analyse the large volumes of sequence data that we expect from collaborators on this project - in particular the 2001 foot-and-mouth-disease epidemic. Therefore, the discoveries are currently limited but we fully expect this to change as the project progresses and data becomes available for analysis.
Exploitation Route We believe that the methods and tools developed on this project will be widely used by the scientific community in the analysis of similar data sets.

Furthermore, we believe that the large 2001 foot-and-mouth disease sequence data and associated analysis will be a key resource for the community and used as both an exemplar data in epidemic analyses and for methodological development.
Sectors Agriculture, Food and Drink,Healthcare

URL http://www.episeq.eu/
 
Description This project is currently at the mid point, rather than the end. Therefore the findings are currently limited as we have focussed on the methodological development that will enable us to effectively analyse the large volume of sequence data that we expect in the near future from collaborators on the project - in particular the 2001 foot-and-mouth disease epidemic data set. We have now completed the sequencing of all the FMDV isolates from the 2001 outbreak for which useable amounts of RNA were available. We have NGS whole genomes for 684 IPs and are planning what he hope will be a substantial publication that will analyse these data in the very near future.
First Year Of Impact 2013
Sector Environment
Impact Types Policy & public services

 
Description OIE working Group - FMD in North Africa
Geographic Reach Africa 
Policy Influence Type Participation in a advisory committee
Impact Participated in an an OIE (World Organisation for Animal Health) committee to review the emergence of foot-and-mouth disease in North African countries (Libya, Tunisia, Algeria and Morocco), and to provide advice about measures that should be adopted to control these outbreaks.
 
Description ISSF Catalyst Award
Amount £10,656 (GBP)
Organisation Wellcome Trust 
Department Wellcome Trust Institutional Strategic Support Fund
Sector Charity/Non Profit
Country United Kingdom
Start 09/2014 
End 09/2015
 
Description OIE Twinning project with the National Animal Health Investigation Centre (NAHDIC) - Ethiopia
Amount € 146,760 (EUR)
Organisation World Organisation for Animal Health 
Sector Public
Country France
Start 11/2015 
End 10/2018
 
Title Universal method to sequence RNA virus genomes 
Description Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We have developed a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using FMDV positive clinical samples, as well as samples that had been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment. 
Type Of Material Technology assay or reagent 
Year Produced 2013 
Provided To Others? Yes  
Impact This protocol is now being routinely applied to samples received into FMD Reference Laboratories. 
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247156/pdf/12864_2014_Article_6688.pdf
 
Title NGS error detection model 
Description This model simulates the errors introduced into a NGS data set from RT-PCR and machine error, and predicts the most likely number of true biological mutations that are present across the viral genome in the NGS dataset. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact The model will be made publicly available on publication, and we have already submitted a paper describing the model entitled "Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data". 
 
Title Viral fitness landscape model 
Description This model utilise NGS data and the underlying mutations observed across the viral genome to predict the fitness landscape of the virus by considering the viral mutation matrix and replication cycle. Mutliple NGS data sets, for example from a time course or transmission/passage chain, can then be used to examine how the fitness landscape evolves over time. 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact We aim to publish the model in the near future 
 
Description Classical Swine Fever transmission 
Organisation Technical University of Denmark
Country Denmark 
Sector Academic/University 
PI Contribution Collaborative project with Thomas Bruun Rasmussen and Ulrik Fahnøe (DTU National Veterinary Institute). DTU had a large amount of NGS data on various classical swine fever projects ranging from clonal controls, to vaccine and transmission experiments in pigs. We collaborated on the analysis of the NGS data, error correction and variant detection, and haplotype reconstruction.
Collaborator Contribution DTU provided all the biological samples and NGS data sets, and collaborated on the analysis of the NGS data, error correction and variant detection, and haplotype reconstruction.
Impact A paper provisionally entitled "Analyzing the fitness of a viral population: Only a minority of circulating virus haplotypes are viable"
Start Year 2014
 
Description Collaboration with the Southern Africa Centre for Infectious Disease Surveillance (SACIDS) 
Organisation Sokoine University of Agriculture
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution TPI staff have mentored research scientists at SUA, participated in visits to Tanzania and hosted visiting African scientists in the UK.
Collaborator Contribution These activities are designed to develop enhanced research capacity at SUA (Tanzania) and the other affiliated research organisations in Southern Africa. As an example, during August 2016, two TPI researchers travelled to SAU to provide training and technical expertise in methods that can be applied to sequence viral genomes.
Impact This collaboration has generated a number of joint publications/presentations and has led to the preparation of joint proposals to understand the circulation of transboundary diseases in endemic settings.
Start Year 2010
 
Description Error detection in NGS data 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution Collaborative work with Samuel Soubeyrand (INRA) on the development of statistical models to effectively detect errors in next generation sequencing data.
Collaborator Contribution Collaborative work with Samuel Soubeyrand (INRA) on the development of statistical models to effectively detect errors in next generation sequencing data.
Impact A paper provisionally entitled "Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data" has been submitted.
Start Year 2013
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Botswana Vaccine Institute
Country Botswana 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Department of Livestock Development
Country Thailand 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation FGBI Federal Centre for Animal Health
Country Russian Federation 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation French Agency for Food, Environmental and Occupational Health & Safety (ANSES)
Country France 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Lanzhou Veterinary Research Institute
Country China 
Sector Learned Society 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Lombardy and Emilia Romagna Experimental Zootechnic Institute (IZSLER)
Country Italy 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation National Agri-Food Quality and Health Service (SENASA)
Country Argentina 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation National Centre for Foreign Animal Diseases (NCFAD)
Country Canada 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Onderstepoort Veterinary Institute
Country South Africa 
Sector Academic/University 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Pan American Foot-and-Mouth Disease Center (Panaftosa)
Country Brazil 
Sector Charity/Non Profit 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Project Directorate on Foot and Mouth Disease
Country India 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description OIE/FAO Laboratory Network for FMD 
Organisation Veterinary and Agrochemical Research Centre
Country Belgium 
Sector Public 
PI Contribution The Pirbright Institute currently coordinates a global network of fourteen International Reference Laboratories for FMD.
Collaborator Contribution The Network of OIE/FAO FMD Reference Laboratories has been established with two principal goals: 1) To understand global virus distribution patterns and use these data to inform vaccine recommendations and 2) To harmonise and improve the quality of laboratory testing carried out by international and national reference laboratories. These activities require sharing and joint evaluation of surveillance information from laboratory diagnosis, serotyping, genetic characterisation and vaccine matching tests and harmonisation of standards for diagnostic procedures.
Impact Outputs from the network provide vital information to international organisations involved in the control of FMD (such as OIE and FAO), as well as specific regional and national programmes to control FMD
Start Year 2006
 
Description Viral fitness landscapes 
Organisation University of Glasgow
Department MRC - University of Glasgow Centre for Virus Research
Country United Kingdom 
Sector Academic/University 
PI Contribution We are developing mathematical models to predict the fitness landscapes of viruses - to identify genomic sites/regions that are (or are not) under selective pressure - utilising next generation sequence data and operating at a number of scales - from the cell to the animal depending on the data set. The model is generic and can be applied to any virus.
Collaborator Contribution Sam Wilson and Suzannah Rihn (MRC Centre for Virus Research) will be supplying viral samples for sequencing from a large cell passage experiment that monitors the micro-evolution of HIV-1 utilising novel methods to limit the amount of sample processing error and viral hitchhiking.
Impact This collaboration has already led to a ISSF Catalyst grant (Wellcome Trust) of £10,656 to sequence the samples that be used to effectively parameterise the model.
Start Year 2014
 
Title DiversiTools 
Description DiversiTools is a software tool to analyse the diversity in viral NGS datasets (coverage, entropy, dNdS, variants etc). DiversiTools includes a GUI frontend enabling users to graphically explore the data. 
Type Of Technology Software 
Year Produced 2014 
Impact A paper describing this software is currently being written and the software will be made publicly available. 
 
Description CEEZAD BSL-3 Training/Transboundary Animal Disease Summer Program - Manhattan, Kansas, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact CEEZAD BSL-3 Training/Transboundary Animal Disease Summer Program Provides a Unique Opportunity for Future Veterinary Professionals

Ten future veterinary professionals with an interest in transboundary disease research took part in a two-week training program conducted by the Center of Excellence for Emerging Zoonotic and Animal Diseases (CEEZAD) at Kansas State University in coordination with the Kansas State University Biosecurity Research Institute (BRI).

The program involved one week of exposure to operations, safety techniques and lab principles of high-containment BSL-3 work at the Biosecurity Research Institute at Kansas State University followed by a second week of visits to institutions involved in the animal health industry and lectures. Students, representing 10 universities from around the USA, heard from prominent professionals in the area of zoonotic and transboundary disease research. The participants include students in veterinary medicine, doctoral students and post-DVM residents
Year(s) Of Engagement Activity 2016
URL http://ceezad.org/news_events/
 
Description Invited Seminar - Transboundary Seminar Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Contributed a talk to the transboundary seminar series hosted by the Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD) at Kansas State University, USA. The title of the talk was "Who infected who? - the use of sequence data to reconstruct transmission pathways in FMD outbreaks" - and described insights from our work on the evolutionary biology of FMD.
Year(s) Of Engagement Activity 2016
 
Description Invited Talk - 17th International Symposium of the World Association of Veterinary Laboratory Diagnosticians, Saskatoon, Canada, June 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Talk: King D. P., Valdazo-González B., Freimanis G., King D. J., Wright C. F., Di Nardo A., Wadsworth J., Soubeyrand S., Knowles N. J., Kim J. and Haydon D. T. The challenges of linking genetic and epidemiological datasets to reconstruct transmission trees for livestock viral diseases. OIE Symposium at the 17th International Symposium of the World Association of Veterinary Laboratory Diagnosticians, Saskatoon, Canada, June 2015.
Year(s) Of Engagement Activity 2015
 
Description Keynote presentation - 3rd Global Conference of OIE Reference Laboratories. Incheon (Seoul), Republic of Korea, October 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented an Invited-Keynote talk at the 3rd Global Conference of OIE Reference Laboratories. Incheon (Seoul), Republic of Korea, October 2014. This session considered the practical applications of new genomic sequencing methods to understand the epidemiology of pathogens that infect livestock.

Talk title:
King D. P. Use of next-generation sequencing to investigate foot-and-mouth disease virus transmission.
Year(s) Of Engagement Activity 2014
URL http://www.oie.int/eng/refcentre2014/presentations.htm
 
Description Keynote presentation - 7th International Symposium on Emerging and re-emerging Pig Diseases, Kyoto, Japan 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk outlining our research findings - entitled: "King D.P., Logan G., Freimanis G. L., Wright C. F., King D. J., Knowles N. J., Wadsworth J., Lasecka L., Bachanek-Bankowska K., Di Nardo A., Orton R. and Haydon D. T. Using sequence data to understand the epidemiology of foot-and-mouth disease" at the 7th International Symposium on Emerging and re-emerging Pig Diseases, Kyoto, Japan, June 2015.
Year(s) Of Engagement Activity 2015
URL http://emerging2015.com
 
Description Keynote presentation - European Association of Veterinary Laboratory Diagnosticians 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited to present a Keynote Presentation at the EAVLD meeting in Prague, Czech Republic in November 2016
Year(s) Of Engagement Activity 2016
URL http://www.eavld2016.org
 
Description Keynote presentation - GFRA Workshop, Hanoi, Vienam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited to present the opening keynote talk at the Global Foot-and-mouth disease Research Alliance meeting in Hanoi, Vietnam. Presented talk entitled " Global foot-and-mouth disease update: new tools to monitor outbreaks and predict threats" describing our research findings and their impact upon the global control of FMDV
Year(s) Of Engagement Activity 2015
URL https://www.ars.usda.gov/GFRA/2015workshop-presentations.htm
 
Description Workshop - Next Generation sequencing 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Taught in a training workshop for next generation sequencing methods. Participants included post-doctoral level scientists from European research institutions.
Year(s) Of Engagement Activity 2016