_To advance the novel CENOS medical device to the required Manufacturing Readiness Level to enable scaled production. CENOS enables the rapid, mobile detection of a range of significant animal and human diseases._

Project aim is to provide capability for early in-field direct testing of unprocessed biological samples e.g. swabs and blood for economically important veterinary pathogens, in this case screening swab samples taken from the beaks and cloaca of birds for detecting "bird flu". Initially we aim to support existing lab testing and ultimately explore the potential for moving tests into the field or farm. BG Research have developed a novel method and instrument for performing sensitive in-field molecular diagnostic tests for the detection of viruses without the requirement for expert scientists or shipping of samples to a test-lab and utilising the gold-standard PCR test methodology. Tests could be performed at ports of entry to prevent diseases being imported, on farms or at slaughterhouses to support surveillance/quarantine and emergency response. By performing rapid, sensitive, and cost-effective tests wherever required, the BGR technology could help protect the UK by preventing potential importation of infectious diseases at entry points and expedite outbreak response where incursions require rapid disease response activities. For example, the outbreaks of FMD in the UK cost the economy £10bn and COVID-19 is thought to have originated from wildlife. Such technology could assist Defra to more effectively monitor transboundary veterinary diseases and provide real-time data to contribute to the control of these diseases, reducing the socio-economic impacts of future outbreaks. We will develop the platform from a lab-based technology demonstrator into a late-stage prototype capable of being operated off-grid and moving the technology closer to the intended portable testing market. Test development assessment will be undertaken at the Animal and Plant Health Agency (APHA) where the necessary scientific expertise and facilities required to work with these pathogens are available. Bird flu has been in the news continually for the past few years and over 8.5 million UK birds have been lost/culled in that period, the impact of this has been seen by the consumer by the lack of eggs in the supermarket and turkeys for Christmas. A novel tool such as this could assist in future outbreak management -- reducing the economic burden and reducing the risk of bird flu becoming a human pathogen. The platform and associated validated tests would be made in the UK and marketed globally by BG, supporting growth and employment in UK Life Sciences and supply chains, while ensuring the UK is better prepared to respond to future epidemics of important human and animal pathogens.

Project objective is to provide capability for early in-field direct testing of swabs and blood for economically important veterinary pathogens in, supporting existing lab testing. BGR have developed a novel method and instrument for performing sensitive in-field molecular diagnostic tests for the detection of viruses without the requirement for expert scientists or shipping of samples to a lab. Tests could be performed at ports of entry to prevent diseases being imported, on farms or at slaughterhouses to support surveillance/quarantine and emergency response, and potentially support future vaccination efforts as a companion diagnostic. By performing rapid, sensitive, tests wherever required, the BGR technology could help protect the UK by flagging potential importation of infectious diseases at entry points and expedite outbreak response where incursions require disease response activities. For example, the outbreaks of FMD in the UK cost the economy £10bn and COVID-19 is thought to have originated from wildlife. Such technology could assist Defra to more effectively monitor transboundary veterinary diseases and provide real-time data to contribute to the control of these diseases, reducing the socio-economic impacts of future outbreaks. We will provide portable, low-cost molecular tests with the simplicity of the lateral flow tests, provided for COVID-19, yet with the sensitivity of gold standard PCR. _The CENOS platform (proprietary instrument and reagents) drives a technology led actionable strategy that we term 'At Patient Testing (APT)', representing a paradigm shift in molecular diagnostics. This novel approach provides testing whilst the patient waits, in a decentralised environment (no specialist lab facilities or infrastructure required) by users with minimal training. Patients rapidly diagnosed with sufficient sensitivity to enable early detection of subclinical, asymptomatic and non-symptomatic cases -- providing results in 'real time' to assist in triaging, treatment, and surveillance activities to help break onward disease transmission chains._ We will develop and validate tests for five important veterinary pathogens: Avian influenza virus (AIV), Newcastle disease virus (NDV), African swine fever virus (ASFV) and Foot-and-mouth disease virus (FMDV) and Seneca Valley Virus (SVV). Test assessment will be undertaken at TPI and APHA where the necessary scientific expertise and containment facilities required to work with these pathogens are available. The platform and associated validated tests would be made in the UK and marketed globally, supporting growth and employment in the UK Life Sciences and supply chains, while ensuring the UK is better prepared to respond to future epidemics of important human and animal pathogens.

BG Research have a simplified method for testing patients for infections caused by viruses, the QuRapID-XF technology. Developed in response to the Ebola outbreak, it enables portable testing directly from patient samples. This removes the need for a lab or expert users -- important as it was designed to be used in resource poor environments in rural Africa. This project will generate a direct from nasal swab test for COVID-19 infections that could be used anywhere, for example at ports of entry or via first responder. At-Point-Testing (APT) will be vital to effectively deal with COVID-19 in the UK. This approach is a highly sensitive, portable platform that ensures infected and those with no symptoms but infected(early stage) patients can be rapidly identified and isolated . . The portable molecular testing system can be used anywhere and gives results within 30 minutes while the patient waits . Hence facilitating immediate isolation and contact tracing. This COVID-19 test will work directly from nasal swabs, but the technology detects directly from saliva, blood, urine or other crude samples. QuRapID-XF assays are simple, so can be performed by non-expert personnel such as soldiers and nurses and large numbers of while-you-wait tests could be performed. Antigen tests based on molecular diagnostics are many times more sensitive than lateral flow tests, immunological tests, and can be used to differentiate between different viral diseases causing e.g. respiratory symptoms, such as the flu. This project will see the scaled release of this platform technology. PHE will be able to deploy their own assays onto the platform to rapidly respond to future outbreaks of blood borne and respiratory viral diseases. QuRapID-XF can also bring low cost testing to poorer developing nations. As the approach doesn't require nucleic acid extraction and uses our own reagent and instrument, there will be none of the supply chain issues seen relating to testing and so it will be possible to deliver large numbers of tests rapidly in response to any future outbreaks. The assay will go through a performance evaluation at multiple sites and countries, ensuring that the test will be highly sensitive. This technology allows the UK to respond to biosecurity threats, and outbreaks of human or veterinary viral diseases globally, reducing mortality and economic losses caused by disease.

BGR has developed a method for detecting viral pathogens directly from crude samples, removing the requirement for complex lab facilities or expert use. The technique was originally developed in the wake of the 2015 Ebola outbreak to establish if it is possible to perform laboratory standard molecular diagnostics in resource poor environments. The proposal here is to adapt the BGR technology from the detection of viral haemorrhagic fevers to diseases such as HIV that have lower viral loads but impact far higher numbers of individuals. In this project BGR will build a new reaction vessel for performing its in tube detection that enables the use of greater volumes of blood and hence increase the sensitivity. The reagents that BGR have developed are capable of detecting the viral RNA in the presence of high levels of blood, as much as 20% to date, and yet at these high percentages the optical data used to determine the presence of the targets are inhibited. The goal of this work is to create late stage prototype vessels that, in combination with evolved reagents, remove the blood from the optical light path and therefore increase the sensitivity of the approach and greatly increase the number of diseases the approach will be appropriate for. As an example, an Ebola patient may have a million viruses per millilitre of blood whereas a patient with hepatitis C will have fifty thousand and a HIV patient on drugs around ten thousand. The target is to increase the sensitivity to 3000/ml, the WHO has identified 5000/ml as being suited to low-cost diagnostics in resource poor regions for the detection of disease such as Hepatitis and HIV. The BGR approach takes less than fifty minutes, requires no laboratory facilities or training and is low cost simply because each test on consists of a plastic tube and a freeze-dried enzyme. Therefore, the improved reaction vessel, reagents and instrument would greatly increase the health impact of this innovation and the commercial opportunities for the company. The assays can then be used to assist in outbreak situations of blood borne diseases. It is also envisaged that the new vessel developed for this project could make possible the use of other sample types such as swabs for respiratory disease. BGR can then determine how sensitive the new assays are using a model virus and move towards commercialisation of appropriate tests.

BGR has developed a method for detecting viral pathogens directly from patients, removing the requirement for complex lab facilities or expert use. While human diagnostics has evolved, there has been little progress for testing animals for important pathogens. The UK foot and mouth disease outbreaks in 2001 cost the country over £3bn in losses to the agriculture sector alone and more rapid diagnostics would minimise the spread and impact of diseases. This proposal is to adapt the BGR technology from detecting pathogens like Ebola from human blood to being able to detect diseases like foot and mouth disease virus from blood or a simple swab from animals suspected of harbouring diseases. BGR have previously developed a test for dengue in humans that can simultaneously detect up to seven different viruses from 1 simple test. It should be possible to differentiate between different veterinary diseases that display similar symptoms using this approach. The tests take fifty minutes to complete and could be performed at pen-side, rapid diagnosis and response are key to preventing the spread of these dangerous pathogens. There are a number of diseases such as FMD, BTV and PPR that are OIE notifiable, they have to be reported if suspected or found, and these could be combined into a single test. These diseases are found endemically in particular locations or with a much higher frequency in areas in the world such as Africa and Asia and as such this technology would have global applications, driving UK manufacture and exports. In this project BGR will build a new reaction vessel for performing its in-tube detection that can take a wide range of sample types. This would mean being able to test for a range of diseases from blood sample, saliva or a nasal swab sample, as different diseases are detected in differing body fluids. The second stage will be for a vet to take samples (blood and swabs) from healthy cows, pigs, goats and sheep at RVC and then test these in the lab by spiking in known amounts of a harmless virus, to determine the suitability of each sample type. Lastly, the test will be applied to archived blood and swab samples at the Pirbright institute for testing on real world samples infected with a dangerous pathogen to determine the sensitivity and specificity of each sample type and then BGR will move towards commercialisation of appropriate tests.

The project investigates the feasibility of detecting bacterial infections, causing sepsis, directly from whole human blood. The process involves lysing the bacterial cells by rapid cyclical freezing and boiling followed by detection of the released nucleic acid by real-time PCR. This novel approach will enable detection of bacterial infection in the critical ,1hr period after sepsis is suspected, leading to more targeted and appropriate use of antibiotics in contrast to the broad-spectrum antibiotic treatment used currently. If the clinician has data outlining which bacteria are present and importantly which antibiotics are likely to be most suitable, then the outcome for the more than 150k annual UK cases of bacterial sepsis will be greatly improved and reduce the 40k annual mortalities attributable to this condition. BGR has demonstrated that the technique and it's instrumentation, the QuRapID, is able to detect blood borne diseases such as Ebola, Zika and Malaria. This project will test infected blood in order to find out if the benefits of the technique can be applied to sepsis, where the number of bacterial cells is much lower than in viral disease. BGR will have access to blood from infected patients to compare on a small scale to existing gold standard methods in use by an NHS hospital.

This project centres on the proof of concept of a simple, rapid diagnostic platform for the differentiation of viral haemorrhagic fevers in resource poor environments. The benefits of this approach; 1. Simplicity, requiring only a fingerprick of blood. 2. Reduced time to detection, from blood to result in around 30 mins. 3. Suited to resource poor environments, removes the requirement for lab facilities or cold-chain.Portable and as such can be used in remote areas. 4. A molecular diagnostic assay, the system can differentiate and quantify a large number of viral targets and be sensitive enough to detect down to the 1000 viruses per ml level. 5. Reduced costs per test, removing the requirement for a lab while allowing high level multiplexing make the approach compare well with multiple immunological based tests while providing viral load information. 6. Reduced hazard risk in testing to the medical professional; assay process is easy to use even with users deploying bio-hazard ptotection and the assay is closed tube. During the recent Ebola outbreak BG Research (BGR) was tasked with adapting its technology for the direct detection of sepsis causing organisms to the rapid, closed tube detection of Ebola in remote areas. The approach migrated the proven CDC assay onto a novel instrument capable of detecting down to as low as 20,000 viruses per ml of blood - the same sensitivity as the laboratory based approach. That project adapted existing BGR instrumentation into a new technology demonstrator and the goals of this project are to develop a new prototype featuring a larger reaction volume such that the sensitivity can be improved by over 20 times - enough to potentially detect infection in convalescent patients and to monitor close contacts of infected patients not yet displaying symptoms. The main goals of the project are firstly to demonstrate a novel first step that concurrently renders the virus non-infectious while releasing the viral RNA - this involves rapidly freezing and thawing the blood sample in a buffer containing an RNA stabilising biocide. The whole process takes place in a single tube and during this project a large reaction vessel, capable of analysing 5 times more blood than the Ebola technology demonstrator is the 2nd goal. A prototype instrument, capable of in-field use and able to process multiple samples concurrently in a random access manner will be designed. Lastly, assays will be developed to demonstrate the system’s capability to differentiate large numbers of different viral targets concurrently in a multiplexed assay. This is a platform technology, but the final assay chosen here will be an RT-QPCR molecular differential assay for Ebola, Lassa, Marburg, Crimean-Congo fever and Rift valley fever to be tested on live virus at PHE Porton. The platform technology can be adapted to other blood-borne diseases such as Zika, Dengue, Chikungunya and Malaria dependent on regional requirements.

This project will generate an optical detection system and associated software for true realtime determination of fluorescence levels generated during real-time PCR. BioGene (BG) has a technology platform capable of completing the real-time PCR process in 10 minutes and this speed combined with independent reaction control lends itself to a number of novel applications that could revolutionise the diagnostic field. “True real-time” PCR is a step change in this sector - the ability to perform reactions whereby the instrumentation can keep up with the chemistry and hence observe and collect data missed by the current one reading per cycle approach. The ability to monitor all visible wavelengths on a milliseconds timescale when combined with Ultra-Rapid PCR facilitates new assays centred on a machine learning approach. Principally, the system can learn the ideal amplification characteristics of any reaction, allowing processes such as factorial optimisation - the ability to optimise any new assay in a single run - by altering factors such as hold times and concentrations across a plate. This approach can be branded “intelligent PCR” (iPCR) as the system can monitor in cycle fluorescence as opposed to the whole reaction efficiency and so could automatically minimise reaction time, by detecting annealing, completion of extension and melting, and optimise each reaction individually by altering hold times and temperatures in run. Benefits include making calls within 5 minutes and in cycle differential annealing and melt analyses. The major commercial benefit is the speed and facilitation of the machine learning approach, for diagnostic users the ability to optimise any new assay in a single run is a very powerful tool and additionally makes much faster subsequent downstream diagnostic calls. Such a system will allow the use of novel assay types, supporting the medical community and generating growth globally from UK government funded research.

This project will produce and evaluate protype consumables suitable for the diagnostic separation and detection of DNA targets differing by only a single base pair in length. A large number of genetic tests rely on polymorphisms between DNA molecules, including DNA fingerprinting. The standard kits available on the marketplace involve the use of expert operators and expensive laboratory equipment. BioGene has previously demonstrated and applied for patent protection in the field of massive multiplexed detection, via novel chemistries and apparatus. The proposed research will investigate means of improving the resolution of this approach to the point where a lower cost, simplified consumable could be used in both the laboratory but also the field in markets such as forensics, human genomics and bacterial pathogen typing. BioGene(BG),BG Research(BGR)

BioGene, BG Research, and the University of Hull are working together to bring rapid, accurate testing for sepsis to the point of care. The system will identify not only the pathogen but also provide information on its antibitiotic sensitivity and in less than 1 hour, allowing the clinical team to correctly and rapidly treat the infection, saving both lives and costs to the NHS. Building on over 10 years of experience and research this innovation should reduce the impact of this life threatening condition and keep the UK at the forefront of medical diagnostics.

Recent increases in genomic information has led to an exponential increase in the numbers of genetic diseases characterised. This and a greater understanding of the infection process, generates the need to detect larger numbers of targets such as pathogens and disease causing genetic variants as rapidly as possible and in a single test. One such approach commonly in use is real-time PCR and yet the application of this for multiplex testing has been limited by inherent flaws in existing detection systems, cost of the technology, and the time taken to generate results. The design and manufacture of a rapid and low cost optical system capable of concurrently analysing a large number of targets is the goal of this study. Such an approach would reduce the cost of such testing, by allowing more targets to be screened in a single test and would reduce the cost for uptake of the technology, as well as reducing the time to result to the point it could be performed "while you wait", for example at a doctors surgery. Similarly this would allow novel PCR based techniques, previously impossible by conventional real-time PCR. Examples could include forensics, by virtue of being able to analyse more targets in a single run. This could also be applied to complex medical diagnostics such as mixed infections. The system would inherently also be many times faster than existing approaches, since it could detect and deconvolute all visible wavelengths of light in a single reading as opposed to having to switch between a series of filters which greatly increases the analysis time on current instrumentation as well as reducing the number of analytes that can concurrently be tested for. In essence this proof of concept will use expertise in the field of satellite imaging and mathematical modelling in conjunction with our Ultra-Rapid thermal cycling IP to solve the problem of multiplex detection of labelled PCR targets and hence allow unique targeting of a growing market niche.

The end goal of the project is the proof of concept demonstrator for rapid extraction of high quality DNA that could be performed in the field. Existing techniques either require significant expertise and manpower, large automation systems or are simply too time consuming to be performed in a ‘while you wait' situation. The ability to perform low cost and rapid DNA extractions out of the laboratory environment would be of great benefit in markets such as forensics, human medicine and pen side animal testing. The core technology could also be incorporated into larger laboratory based systems to further broaden the market for the technology. The core technology being explored in the proposal would be suitable for incorporation into a wide range of other instrumentation as well as being able to be marketed as either a stand alone laboratory system or field based and handheld unit. Currently there is only a single system available in the marketplace that incorporates this step and it is considerably more time consuming and expensive than the approach being considered in this proposal.It isd also not portable so would miss a key niche:the Point of Care(POC) one. The key benefit in the marketplace would be the time taken for extraction and the minimal number of steps required. Traditional approaches requiring multiple steps and additional reagents or equipment such as magnetic beads and centrifuges. The proposed proof of concept is to rapidly lyse the cells containing the DNA by optimised ‘Ultra-rapid’freeze thawing cycles in a suitable buffer medium. This would reduce the time taken to extract the DNA to less than 5 minutes. This could then be incorporated into downstream processes provided by many other companies, hence bringing in licensing revenue, but also combined with BioGene's rapid PCR technology and therefore making a UK built portable DNA testing system that is low cost,'world's fastest' and portable..all unique user benefits. Whilst the POC market is a key one,the low cost of ownership and compact size would allow penetration of the lab market. BioGene manufacture their own instrumentation and have a dedicated team of scientists and engineers and as as a result are well placed to realise the aims of thee project within the proscribed timescales.