Defra - Department for Environment, Food and Rural Affairs.

Science Search

Science and Research Projects

Return to Science Search homepage   Return to Project List

Molecular epidemiology of foot-and-mouth disease virus - SE2940

Foot-and-mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed livestock (cattle, sheep, pigs and goats). The causative agent is a virus (FMDV: genus Aphthovirus, family Picornaviridae) which exists as seven antigenically distinct serotypes. The virus is easily transmitted by movement of infected livestock or animal products, contaminated persons, objects, and aerosols. FMD is endemically or sporadically present in more than 60% of the countries around the world including sub-Saharan Africa, much of south Asia (Middle East, Indian sub-continent and Southeast Asia) and parts of South America. Outbreaks of FMD in these endemic regions continuously threaten livestock industries in countries that are free of FMD (with, or without vaccination). Such incursions can have dramatic impacts upon the agricultural industry and wider economy of an affected country as was shown during the 2001 outbreak in the UK.

The genome of FMDV is highly plastic and evolves rapidly as a consequence of errors that are introduced and inherited during replication. These characteristics allow nucleotide sequence data to be used to reliably reconstruct the relationship between viruses recovered from different locations, or at different times. At the broadest scale, analyses of sequences encoding a capsid protein (VP1/1D) are used to categorise field strains into discrete variants (or topotypes) which frequently show geographical clustering based on the historical distribution of FMDV. The pattern of serotypes and variants around the world is not static and sequencing of these viruses allows us to precisely characterise new isolates of FMDV and trace their origin and movements across international boundaries. More recently, complete genomes sequences have been used to define the relationship between closely related samples collected during FMD outbreaks in the UK (2001 and 2007) and Bulgaria (2011). Analysis of these complete genome sequences provides data at unprecedented resolution allowing transmission events at the farm-to-farm level to be reconstructed. Such data have the potential to play a central role in the event of a future FMD outbreak in the UK, and the development of bespoke analytical and statistical pipelines are now required to improve our confidence in the interpretation of these data.

The aim of this project is to continue with work that has been previously undertaken during SE2938 and SE2939, to generate real-time molecular epidemiology reports describing field strains of FMDV that are currently circulating, as well as to apply the latest tools to analyze (and display) these data. We plan to exploit next-generation sequencing approaches to increase our capacity to process the large number of samples that might be received for analysis during a future FMD outbreak in the UK, as well as to routinely generate capsid sequences to support the vaccine matching work undertaken at Pirbright. In addition to providing vital information to Defra regarding the emergence and circulation of new FMDV lineages that pose a threat to the livestock industries in the UK (and Europe), this project will also develop and validate tools that can be used to increase our confidence in local FMDV transmission pathways (such as those that occur between farms).
The project objectives are arranged into 5 themes that are outlined below:
1. Monitoring the global distribution of FMDV strains and use of phylogeographical approaches to map virus movements.
2. Development of statistical methods to reconstruct FMD outbreaks at high resolution and in real-time.
3. Application of next-generation sequencing tools for routine characterisation of FMD viruses.
4. Characterisation of FMDV capsid sequences and link to serological vaccine matching data from WRLFMD.
5. Development of improved web-based tools to display FMDV molecular epidemiological data.
Time-Scale and Cost
From: 2013

To: 2016

Cost: £1,260,318
Contractor / Funded Organisations
IAH - Institute for Animal Health
Disease Control              
Fields of Study
Animal Health