Roadmap for the research to underpin the development of control strategies for FMD

What are we trying to achieve and why? What is the problem we are trying to solve?

To understand the bases for functional genomic and predictive genomics for FMD

What are the scientific and technological challenges (knowledge gaps needing to be addressed)?

• Identify and deal with recombination in full genome sequencing, including phylogenetic models.
• Achieve holistic and unified understanding of functional genomics and deep sequence analysis of diversity.
• Develop methods allowing rapid FMDV strain typing.
• Apply NGS full genome to better understand the ecology and microenvironment of the virus.

What approaches could/should be taken to address the research question?

There is a range of FMD viruses’ strains which differ in terms of virulence and there are continuous changes in FMDV RNA sequences. Establishing the genomic differences of the various strains will assist in the identification of virulence mechanisms.
Continuous monitoring of FMD sequences will be necessary to ensure the diagnostic are adequate.

What else needs to be done before we can solve this need?

Existing knowledge including successes and failures

Next-generation sequencing technologies that allow sequencing of not only the predominant sequence but also
minority variants present within a single sample have emerged. This technology has been used to explore within host
virus evolution and selection in a way not previously possible, substantially advancing knowledge of FMDV dynamics within the host. A protocol, suitable for usage in a high-throughput laboratory, has been published for whole FMDV genome consensus sequencing.