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Defra Biosecurity Chip - SD0443

The Defra funded bio-security chip (BioChip) is a pan-viral microarray which enables the detection of 1132 different viruses from 40 viral families in a single test. The array itself is based around a set of 8729 capture probes designed to specific sequences for each virus as well as a full suite of protocols and bio-informatic analysis tools developed by the project consortium. The array is suited to the detection of viruses in a range of animal, bird, human, plant and honey bee hosts.

This large pan-viral array is predominantly focused on virus discovery, investigation of syndromes/disease complexes and detection of unknown or unexpected pathogens. In addition to the large pan-viral BioChip, validated capture probes have been transferred to smaller, host or disease focused arrays which are more suited to high-throughput screening applications. The use of the BioChip for either virus discovery or high-throughput screening enables considerable improvements in both the speed and cost of virus analysis when compared to conventional techniques. For example a typical analysis of a sample for 41 targets is estimated to cost 24% less in consumables and take one quarter of the instrument time for performing the equivalent analysis performed using real-time PCR. The consequences of the improvements in speed to result when dealing with incursions of exotic pathogens may be significant, slowing down spread and making subsequent containment and eradication easier.

During the course of the project the BioChip has been used to help resolve the causal agent of disease in a number of ‘real’ samples, in most cases where application of traditional techniques failed to identify the suspect virus. One example is that of an outbreak of equine encephalosis virus (EEV) in horses in Israel. The disease has never been previously diagnosed in Israel or in other locations outside southern Africa, but in late 2008, early 2009 a horse disease was identified at more than 60 locations. Initial testing using virus isolation, serological, and polymerase chain reaction (PCR) methods for 15 of the most likely causes of the disease, based on clinical signs and suspect diagnosis in two laboratories failed to identify a candidate virus. In contrast the BioChip was used to test samples and indicated the presence of EEV, which was then confirmed using PCR and DNA sequencing.

The next steps involve making the array high throughput, more widely available and in some cases, broadening the applicability of the approach. An example of this is the further development of the honey bee virus array; detection of viruses in honey bees only scratches the surface of the complex of pests, pathogens and other microbes interacting in healthy and diseased bee colonies. As a result a high-throughput screening array based on the BioChip is in the latter stages of validation which will enable simultaneous testing of 41 pathogens, pests and other microbes that should be of great use in studies focusing on protecting the honey bee from diseases and pests.
Project Documents
• FRP - Final Report : Defra Biosecurity Chip   (1547k)
Time-Scale and Cost
From: 2006

To: 2009

Cost: £1,564,449
Contractor / Funded Organisations
Central Science Laboratory
Animal Diseases              
Avian Diseases              
Bee Diseases              
Biotech-non GM              
Fish Disease              
Method Development              
Molecular Biology              
Plant diseases