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Use of FMDV sequence data to trace outbreaks and monitor disease incursion risks to the UK - SE2944

Foot-and-mouth disease (FMD) is a highly infectious disease that affects cloven-hooved animals, including farmed livestock (e.g. cattle, pigs, goats and sheep) and wildlife (e.g. deer and wild boar). The United Kingdom (UK) is currently free of FMD. However, when outbreaks occur, as they did in 2001 and 2007, they have a substantial impact on the farming community and on the wider economy. The 2001 epidemic resulted in >2000 infected farms and the slaughter of over 6 million animals and is estimated to have cost the farming industry >£3 billion (the majority of which was borne by Government) and the wider economy >£5 billion, mainly through the impacts on tourism.

FMD is caused by foot-and-mouth disease virus (FMDV; genus Aphthovirus, family Picornaviridae) that exists as seven distinct serotypes (O, A, C, Asia 1, Southern African Territories [SAT] 1, 2, and 3). The virus has an RNA genome that 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. The focus of this project is to generate and analyse FMDV genomic sequence data to trace the origins of FMD outbreaks. At the broadest scale, these analyses 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. Sequence data can also be used to define the farm-to-farm relationship between closely related samples collected during FMD outbreaks as demonstrated for previous outbreaks in the UK (2007, 2001) and Europe (Bulgaria, 2011). Analysis of these complete genome sequences provides data at high-resolution, playing a central role in the event of a future FMD outbreak in the UK.

Key capabilities that will be provided to Defra by this project:
•Rapid response to characterise FMD viruses submitted to the FMD NRL at Pirbright associated with outbreaks in the UK;
•Analytical tools that can be used in real-time to support a more effective National control and eradication policy (in the event of an FMD incursion into the UK);
•Critical surveillance of FMD virus lineages that are circulating in different parts of the world;
•On-going assessment of FMD virus risks that pose greatest threats of disease incursions into the UK livestock sector.

This project will provide 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 will also develop and validate bespoke analytical and statistical pipelines that can be used to increase our confidence in local FMDV transmission pathways, particularly focusing on approaches that can be used in real-time during FMD outbreaks in the UK.

Objective 1: Development of analytical tools to reconstruct disease transmission networks at the farm-level
Objective 2: Monitoring and mapping the global distribution of FMDV strains to define risk to the UK
Time-Scale and Cost
From: 2019

To: 2022

Cost: £1,326,558
Contractor / Funded Organisations
IAH - Institute for Animal Health
Fields of Study
Animal Health