Studentship: Inter-serotypic genetic evolution of Foot-and-Mouth Disease Virus

Lead Research Organisation: The Pirbright Institute
Department Name: UNLISTED

Abstract

Studentship: Foot-and-mouth disease virus (FMDV) is very genetically diverse and exists as a swarm of genetically related variants. This enables the virus to adapt rapidly to new environments and evade immune responses. The genetic variants seen at a herd and global level are a direct result of the virus diversity that is created through spontaneous mutation and recombination at the cell level. Processes such as genetic drift, migration and selection act upon the genetic variants to result in the genetic phenotypes characterised. Thus transmission events, and host immune responses shape the genetic diversity that is produced by the virus. FMDV exists in seven different serotypes which differ in their epidemiology (transmission, virulence, immunogenicity) and herd level genetic diversity. However, it is not known whether these differences are governed by environment and host, or whether the viruses have modified their own replication and diversity generation to achieve survival in a specific ecological niche.
Understanding how viruses generate diversity is crucial to studying the spread of virus and controlling disease. This PhD project addresses the question as to whether the variation between evolutionary phenotypes of the seven serotypes of FMDV at an epidemiological level, are due to inherent differences in the amount and structure of genetic diversity generated at a cellular level. The project evaluates the impact of varying replicative rates, protein diversity and genetic sequence flexibility on the generation and maintenance of genetic diversity within virus populations. The work embraces a cross disciplinary research approach incorporating molecular biology, next generation sequencing, and mathematical modelling of data.
 
Description Foot-and-mouth disease virus (FMDV) (Family: Picornaviridae, Genus: Aphthovirus) is a significant global pathogen with extensive economic impacts. It is an RNA virus that contains a low fidelity RNA-dependent RNA polymerase and lacks proof reading capability. This coupled with its relatively short generation time and large population sizes means that it exists in a swarm of genetically closely related variants. The reservoir of diversity contained within this mutant spectrum allows the virus to adapt rapidly to new environments. Much of the previous work looking at virus evolution has focused on the consensus level genetic sequence. The advent of next generation sequencing (NGS) technologies enables evolutionary studies of the entire viral swarm.

This PhD project used NGS technologies to interrogate the swarm structure by investigating factors affecting the viral swarm and the dynamics of variants within it. Furthermore, this work showed how analysis of the swarm can reveal fundamental information about the virus itself. Work was completed to establish a PCR-free NGS methodology to create deep sequencing data sets of all genomes present within an FMDV viral swarm. The elimination of the PCR step results in less errors being introduced in the sequencing process thereby improving the resolution and reliability of the identification of low level variants within the swarm. This optimised method was then used to define and compare the FMDV swarms of several wildtype isolates. This revealed differences in swarm structure from isolate to isolate and produced evidence of within swarm selection, different from selection at the consensus level. In some instances these difference were found to be due to the host from which a virus was sampled with African buffalo potentially able to maintain multiple infections. Subconsensus variants in these mixed samples had mutations at positions previously associated with immune escape. An experiment to observe how the swarm structure evolves was undertaken and results suggested two distinct populations structures with different distributions of variable nucleotide positions (when under adaptive pressure or not) but with comparative total levels of variation (as measured by Shannon's entropy). Finally this work considered how this understanding of the swarm can be used in fundamental virological studies using picornavirus packaging as an example. These experiments identified conserved novel stem loop structures that when mutated produced a virus which appeared to have a decreased packaging efficiency.
Exploitation Route This thesis includes novel analysis techniques for considering the viral swarm. It demonstrates how investigating the diversity in the swarm can help to understand how a virus will evolve and the limits on this. Understanding viral evolution at this scale has the capacity to improve our fundamental understanding of the evolution of FMDV which can in turn inform vaccine design and disease control strategies.
Sectors Agriculture, Food and Drink,Education,Environment,Pharmaceuticals and Medical Biotechnology

 
Title Deep sequencing to identify RNA packaging signals 
Description A novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in positive sense RNA viruses (e.g. the picornavirus foot-and-mouth disease virus [FMDV]). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA, we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem-loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Impact so far is fundamental knowledge but with several potential avenues for future impact in for example improved vaccines. 
 
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 U.S. Department of Agriculture USDA
Department Agricultural Research Service
Country United States 
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 Studentship Supervision 
Organisation University of Glasgow
Department Institute of Biodiversity, Animal Health and Comparative Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-supervision of PhD student
Collaborator Contribution Co-supervision of PhD student
Impact Multi-disciplinary collaboration to realize the outputs from NGS sequencing analyses of FMDV isolates
Start Year 2012
 
Description Diamond (TT) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Diamond Light Source Open Day - explaining to general public the importance of structural biology and microscopy for understanding viruses and designing improved vaccines.
Year(s) Of Engagement Activity 2019
 
Description EUROPIC 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at EUROPIC meeting: Logan G., King D. P., Haydon D. T. and Cottam E. M. Dissection of genetic diversity within virus populations: comparisons between the seven FMDV serotypes using a novel PCR-free NGS approach. 18th International Picornavirus meeting (EUROPIC), Blankenberge, Belgium, March 2014.
Year(s) Of Engagement Activity 2014
 
Description EUROPIC 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at EUROPIC: Lasecka-Dykes L., Tulloch F., Gold S., Luke G., Wright C. F., Knowles N. J., Logan G., Tuthill T. J., Jackson T. Simmonds P., Ryan M. and King D. P. Prediction of conserved RNA structures the within foot-and-mouth disease virus genome reveals functional cis-acting elements localised in the 3D coding region. 19th International Picornavirus Meeting, Les Diablerets, Switzerland, September 2016.
Year(s) Of Engagement Activity 2016
 
Description EUROPIC 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation provided at EUROPIC: Logan G., Newman J., Wright C. F., Lasecka L., King D. P., Haydon D. T., Cottam E. M. and Tuthill T. J. Virus quasispecies reveals RNA structures required for genome packaging. 19th International Picornavirus Meeting, Les Diablerets, Switzerland, September 2016.
Year(s) Of Engagement Activity 2016
 
Description Invited Keynote Presentation - EPIZONE meeting, Copenhagen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A keynote talk was presented to outline the use of new sequencing technologies to understand the epidemiology of FMDV

Title of talk:
Keynote: King D. P., Logan G., Valdazo-González B., Freimanis G. L., Wright C. F., King D. J., Knowles N. J., Wadsworth J., Bachanek-Bankowska K., Di Nardo A., Orton R., Haydon D. T. The consensus and beyond: developing new tools to reconstruct transmission pathways of foot-and-mouth disease virus. 8th Annual Meeting of the EPIZONE project, Copenhagen, September 2014.
Year(s) Of Engagement Activity 2014
URL http://www.epizone-eu.net/en/Home/show/8th-Annual-Meeting-Denmark-2014.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 Korean Vet Soc 
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., Logan G., Valdazo-González B., Freimanis G. L., Wright C. F., King D. J., Knowles N. J., Wadsworth J., Bachanek-Bankowska K., Di Nardo A., Orton R., Haydon D. T. The consensus and beyond: developing sequencing approaches for FMDV and other RNA viruses. Annual Meeting of the Korean Society of Veterinary Science, Jeju Island, Republic of Korea, October 2014.
Year(s) Of Engagement Activity 2014
 
Description SGM 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Presentation at SGM: Logan G., Kelly J. D., Lasecka L., Cottam E. M., King D. P., Tuthill T. J. and Haydon D. T. Adaptive evolution of foot-and-mouth disease virus: sub-consensus level genetic diversity influences viral phenotype. Society for General Microbiology Meeting, Birmingham, UK, April 2015.
Year(s) Of Engagement Activity 2015