Development of magnetometer immunoassay technology to improve screening accuracy and user friendliness with sequencing and resistance information
Lead Research Organisation:
Earlham Institute
Department Name: Research Faculty
Abstract
This project will support the development of a novel, portable and cost effective system for the detection of animal diseases in pigs. These diseases have a significant impact on animal health and represent a financial burden to countries worldwide. This collaborative project will deliver a magnetic sensor-based device and surveillance system which would provide early detection of disease and enable quick action in order to reduce the risk of disease spread, with economic benefits to farmers and food producers and welfare benefits to farm animals.
Technical Summary
This project will support the development of a novel, portable and cost effective system for the detection of animal diseases in pigs. These diseases have a significant impact on animal health and represent a financial burden to countries worldwide. This collaborative project will deliver a magnetic sensor-based device and surveillance system which would provide early detection of disease and enable quick action in order to reduce the risk of disease spread, with economic benefits to farmers and food producers and welfare benefits to farm animals.
Planned Impact
The MagSal system will be a robust, cost-effective, flexible and portable platform for testing a range of animal diseases using oral saliva samples at the point of use. We foresee a range of economic impacts for the industrial biotechnology sector, specifically in animal health and medical diagnostics (through the lead industry partner, Clarity Biosolutions Ltd). Farmers and the broader agricultural industry will also stand to benefit in the longer term from potentially improved monitoring and rapid in-field testing for disease.
Effective communication within the broader scientific community will be achieved through publication of non-commercially confidential outcomes in top-tier conferences and journals in the areas of bio-sensing, instrumentation veterinary and public health. Specifically the partners will target the International Conference of Biosensing Technology. The lead partner will attend relevant trade shows e.g Medica.
Effective communication within the broader scientific community will be achieved through publication of non-commercially confidential outcomes in top-tier conferences and journals in the areas of bio-sensing, instrumentation veterinary and public health. Specifically the partners will target the International Conference of Biosensing Technology. The lead partner will attend relevant trade shows e.g Medica.
| Description | The project partners developed a fast and robust method for detecting the presence and genotype of Porcine reproductive and respiratory syndrome virus (PRRSV) in pig saliva samples. Our organisation's role was to sequence the genetically characterised positive samples. The project evolved to encompass new sequencing technology that was becoming available to develop the ability to sequence on location in the field using portable Nanopore technology. We also developed a pooling approach handling low sample volumes, barcoding and pooling (up-to a theoretical minimum of a 1000-fold efficiency) to reduce the otherwise prohibitive costs of a sequencing based test. |
| Exploitation Route | The methodology developed could be used in other labs both academic and non-academic. The project has enabled EI to advance our technology understanding for sequencing and data analysis, applied to a real-world need, which strengthens our provision of a National Capability in Genomics. We have shared our knowledge with the project partners bringing a new development to the table by applying nanopore sequencing and our efficiency saving for sample processing in low sample volumes, barcoding and pooling (up-to a theoretical minimum of a 1000-fold efficiency). The project partners are investigating the provision of commercial screening using the project outcomes to achieve farm-side testing and bring disease surveillance tools to the market. |
| Sectors | Agriculture, Food and Drink,Healthcare |
| Description | The project brought together three diverse elements (user-friendly farm testing, rapid identification & sequencing and national surveillance) to bring the power of big data to farmers and the meat industry. This project offers an opportunity for a UK technology company to make a significant contribution to this important global market. The added value the study can bring is i) helping reduce the overall heavy economic burden of PRRSV; ii) giving farmers a more comprehensive and regular herd health status; iii) providing meat producers such as TL with much more rapid alerts of outbreaks of new strains so that they can implement earlier control measures and stop wider spread; iv) offering regulatory bodies the possibility of a national surveillance and disease modeling system based on widespread screening and rapid sequencing. A sequence analysis pipeline has been created and fed into the EI Genomics National Capability knowledge base. Sequencing with Oxford Nanopore Technology could not be provided as a fee-paying service at the time of grant completion. EI's national capability will in the future be able to provide a service utilising these advancements. Two research assistants were trained in creating amplicons for sequencing, data analysis and project management. Both have since registered for PhDs and have continued to work with the EI lab utlisiing related technology. |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Other |
| Impact Types | Economic,Policy & public services |
| Title | PRRSV diagnostics - qPCR to sequencing pipeline |
| Description | Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-sense RNA virus which infects domestic pigs. The PRRS disease is now the most economically important disease for the global pig industry. PRRSV has a very high mutation rate, which makes efficient control and vaccination extremely difficult. Therefore, diagnostic assays to detect and monitor the genetic diversity of PRRSV are needed. Our laboratory based diagnostics pipeline allows us to detect and quantify low levels of PRRSV in pig saliva samples, then verify the result and identify the specific genotype by DNA sequencing. Saliva samples are preserved in RNA Shield™ upon collection, which inactivates the virus and stabilises the RNA for transport at ambient temperatures to the laboratory. RNA is extracted from the saliva, reverse transcribed into cDNA, and then analysed by quantitative PCR (qPCR). The resulting amplicons can be verified by sanger sequencing or a high throughput sequencing platform. Nanopore sequencing is ideal for this application as it can sequence amplicons of any length as a single read, which allows us to identify the specific PRRSV genotype with greater ease. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | This pipeline is a fast and robust method for detecting the presence and genotype of PRRSV in pig saliva samples, we aim to make this available via the Genomics NCG at Earlham. |
| Description | ClarityBio |
| Organisation | Clarity BioSolutions |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Our organisation's role was to sequence the genetically characterised positive samples which we have done. The project evolved to encompass new technology becoming available to develop the ability to sequence on location using Nanopore technology, in addition we have worked to reduce otherwise prohibitive costs of the test by pooling samples. |
| Collaborator Contribution | Development of magnetometer immunoassay (MIA) technology to improve screening accuracy and on-farm user friendliness together with sequencing and resistance |
| Impact | Development of portable screening magnetometer immunoassay (MIA) technology |
| Start Year | 2015 |
| Title | Assay Design and Library Analysis (ADLA) |
| Description | We have been developing software that will assist in the designing of novel Next Generation Sequencing (NGS) methods, especially new assays. The software currently comprises of two parts: 1) Assay setup and Design (AD) application. This enables the user to design primers for amplification. The user is able to choose from a drop down menu of NGS platform library adaptors or provide their own custom designs. Where the user has chosen to provide their own designs the application provides advice, and warnings with regards to the design structure of these adaptors. 2) Library Analysis (LA) application uses PacBio reads to confirm the adaptor structure within the libraries. Due to the short insert sizes of Illumina libraries, and the long PacBio reads most molecules will be sequenced as CCS reads to >95% accuracy. ADLA then uses the adaptor structure from the adaptor setup and design application to orientate reads and perform a series of QC analysis. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | The Adapter Design and Library Analysis (ADLA) package will be a solution for the development of adaptor sequences for novel applications using NGS platforms, especially Illumina. It also provides an analysis suite for the quality control of potentially problematic libraries using as little as a single SMRTcell of PacBio sequence data. |