Roadmap for the development of diagnostic tests 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.

To develop portable, rapid, low-cost methods and tools for early field characterisation of FMDV.

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

• Development of methods allowing rapid FMDV strain typing
• 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
• Validate rapid sequencing tools to be used in the field

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. 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?

• FMDV genome sequencing.
• FMDV detection tools.

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.