Defra Biosecurity Chip

BioChip - an interagency collaboration developing micro-array screening methods for the detection of animal, fish and plant viruses.

DetectiV - a package for R, containing functions for the visualisation, normalisation and significance testing of pathogen detection microarray data.

Exotic, endemic and zoonotic viral diseases of livestock, companion animals, plants and fish pose a continual threat to the agricultural economy, animal welfare and natural environment of the UK. The 2001 outbreak of FMDV and current concerns over possible future outbreaks of avian influenza amply demonstrate this point. In addition, zoonotic viruses such as rabies, avian influenza and other potential new or emergent viruses pose a risk to human health. Accurate diagnosis and subsequent pathogen characterisation remains a cornerstone in the control of viral disease. In addition, the requirement for surveillance techniques to identify, in a rapid manner, new potential threats is viewed as a priority.

Developments in the application of diagnostic microarrays ("lab on a chip") indicate that they could soon become routine diagnostic tools in the identification and characterisation of infectious agents, particularly viruses. For example, the identification of the aetiological agent of severe acute respiratory syndrome (SARS) was achieved using a microarray, revealing a virus that was subsequently recognised to be a previously uncharacterized coronavirus (Wang et al., 2003).

The consortium will deliver a number of multiple target assays (Defra biosecurity chip) altogether covering 600+ known viruses of vertebrates, invertebrates, plants, including zoonotic viruses, which will be made available to government agencies as a usable tool. A validated probe database will also be available for use by other groups & agencies. The capacity of the chip will also allow identification of novel viruses and variants (by detecting distinctive viral features at the genus or family level) enabling surveillance for new and emerging diseases. In addition to identifying the agent(s), the tools will give sufficient resolution to genotype key viruses for pathogenicity, and probable geographical origin, including avian influenza, rabies virus and foot and mouth disease virus. The chip will also include probes specific to host species. Many disease syndromes have complex aetiologies which result from the interplay of multiple infectious agents, host factors and molecular triggers (eg post-weaning multisystemic wasting syndrome (PMWS)). Genotyping (or barcoding) a virus and its host will provide a paradigm-shift in the understanding of disease aetiology.