Periodic Reporting for period 3 - SWINOSTICS (Swine diseases field diagnostics toolbox)
Période du rapport: 2020-05-01 au 2021-10-31
The time between initial disease outbreak, sample transportation and laboratory confirmation of the etiologic infectious agent can be up to weeks or months, recognizing the need for the development of mobile diagnostic units.Traditionally,virus detection in a lab relies on cell culture or detection of circulatory antibodies.The former can be extremely time consuming.The later though fast,simple and often informative,does not coincide with time of infection or correlate to clinical disease.Rapid diagnostic systems are designed to detect the nucleic acid(NA) or protein of the infectious agent.Most of these rely on NA extraction&purification or PCR-based amplification&detection.Methods enabling rapid&simple NA extraction under resource-limited settings are still scarce.Also,PCR amplification methods are so sensitive that often produce false positives. Detection of microbial antigen is viewed as more reliable than NA detection, but development of such diagnostic technology was hindered by lack of sensitivity, increased cost and lack of portability.Lately,silicon based Photonic Integrated Circuits (PIC) demonstrated as a powerful platform for biosensing systems and in combination with integrated antibodies on the device,they can provide portable multiplex detection of proteins with sensitivity and specificity previously not realized.SWINOSTICS addressed these challenges/needs with a novel field diagnostic device based on advanced, proven,bio-sensing technologies to tackle emerging&endemic viruses causing epidemics in swine farms in Europe.The device allows immediate threat assessment at farm level with the analytical quality of commercial laboratories.
The project’s main outcome is the delivery of the SWINOSTICS device able to detect 6 diseases at the same time.It is easily transportable and its modular construction allows for future upgrades if necessary(more samples analysed parallelly).The heart of the device is the PIC biosensor that consists of eight ring resonators (RRs).The whole PIC is covered by a SiO2 layer (1000nm,width) to optimize the performance of the grating couplers and act as a protective layer.Regarding the SWINOSTICS device,a prototype was created, optimized and integrated.Small-scale manufacturing of the device and the sensors followed with the production of 4 devices and ~100 sensors used during the field trials.
To support the device, a cloud platform and a mobile app were developed.The platform collects data from all the devices at the 4 pilots.It provides simple and well-organized results visualization and allows downloading of the analysis results in raw format for analysis,validation and possible certification.The app is used as the device’s user interface and plays part in the secure transfer of data to the cloud platform.
SWINOSTICS fulfills the proposed ‘toolbox’vision with the delivered device able to minimize the time required by traditional methods of viral detections and also created a solution that can be used by almost anyone, not just trained personnel.The device is transportable and relatively inexpensive compared to traditional methods.
There are several lessons learnt from SWINOSTICS to consider in future work.First attention must be given on the manufacturing of the PICs due to their sensitive nature.Low performing PICs may significantly affect sensitivity and specificity values, essential for a detection device.They were seen as measurements for accurate detection however,sensitivity outperformed specificity.The viruses selected can cause serious illness,spread rapidly among swine populations, negatively affecting animal health and the economy.Hence,the objective for a device that can rapidly detect viruses is aligned with the notion that rapid and sensitive detection of these viruses can help prevent the spread of the diseases even by sacrificing specificity or having false positives.Moreover,the performance of the device based on sensitivity and specificity is already very good for a point of care device and can be further optimized.
The project’s main outcome is the delivery of the SWINOSTICS device able to detect 6 diseases at the same time.It is easily transportable and its modular construction allows for future upgrades if necessary(more samples analysed parallelly).The heart of the device is the PIC biosensor that consists of eight ring resonators (RRs).The whole PIC is covered by a SiO2 layer (1000nm,width) to optimize the performance of the grating couplers and act as a protective layer.Regarding the SWINOSTICS device,a prototype was created, optimized and integrated.Small-scale manufacturing of the device and the sensors followed with the production of 4 devices and ~100 sensors used during the field trials.
To support the device, a cloud platform and a mobile app were developed.The platform collects data from all the devices at the 4 pilots.It provides simple and well-organized results visualization and allows downloading of the analysis results in raw format for analysis,validation and possible certification.The app is used as the device’s user interface and plays part in the secure transfer of data to the cloud platform.
SWINOSTICS fulfills the proposed ‘toolbox’vision with the delivered device able to minimize the time required by traditional methods of viral detections and also created a solution that can be used by almost anyone, not just trained personnel.The device is transportable and relatively inexpensive compared to traditional methods.
There are several lessons learnt from SWINOSTICS to consider in future work.First attention must be given on the manufacturing of the PICs due to their sensitive nature.Low performing PICs may significantly affect sensitivity and specificity values, essential for a detection device.They were seen as measurements for accurate detection however,sensitivity outperformed specificity.The viruses selected can cause serious illness,spread rapidly among swine populations, negatively affecting animal health and the economy.Hence,the objective for a device that can rapidly detect viruses is aligned with the notion that rapid and sensitive detection of these viruses can help prevent the spread of the diseases even by sacrificing specificity or having false positives.Moreover,the performance of the device based on sensitivity and specificity is already very good for a point of care device and can be further optimized.
For the final period,focus was on device and sensors’ optimization through extended lab testing and field validation.Initially the preliminary lab testing(initiated in the previous period) was concluded, allowing device and sensors upgrades through highly valuable feedback.This led to the development of the final device design produced in 4 replicas & shipped to the 4 pilot sites.The devices were used by the end-users for extended lab validations with spiked and clinical samples.Results allowed an evaluation of the SWINOSTICS system performance.Then,field testing and tests in the lab using field-collected samples took place, in the 4 pilot sites.All test results were used to validate&assess the performance of the complete system.Results are highly promising.
The final version of the dissemination plan was prepared, website and social media accounts regularly updated.Two additional peer reviewed publications were published and event presentations took place.A final workshop was organized online,due to COVID-19 restrictions.An updated data management plan was delivered at project end showing the actual handling of data produced within the project lifetime, and how data was shared.Also,the SWINOSTICS community in Zenodo.org for openly sharing project data was updated.The business and exploitation plan was finalized during this period and a patentability analysis took place.Target markets and end users revealed urgent needs for a system like SWINOSTICS.
The final version of the dissemination plan was prepared, website and social media accounts regularly updated.Two additional peer reviewed publications were published and event presentations took place.A final workshop was organized online,due to COVID-19 restrictions.An updated data management plan was delivered at project end showing the actual handling of data produced within the project lifetime, and how data was shared.Also,the SWINOSTICS community in Zenodo.org for openly sharing project data was updated.The business and exploitation plan was finalized during this period and a patentability analysis took place.Target markets and end users revealed urgent needs for a system like SWINOSTICS.
For progress beyond the state of the art: a)the device is the only field-use device capable of detecting 6 important swine viruses b)samples are oral fluids simplifying sample collection & reducing the test time though has compatibility with other sample types, c)sample analysis time reduced to <60 minutes d)4 PIC sensors working in parallel &simultaneously process up to 4 samples d)the PIC sensors do not require use of a fluorescent label for the detection e)the device integrates a biosensor regeneration mechanism making each PIC reusable for at least up to 10 times.
The main project results include a) the device,App and cloud software, b)the validation results, after testing the device both with laboratory(spiked) samples as well as with real samples from the field.SWINOSTICS delivered a mobile diagnostic device and complete system,providing reliable and simple diagnostic testing directly on site enabling rapid local decision making, crucial for prevention of disease spreading,animal & food safety and human health.It has a direct positive economic impact on swine farms & the agri-food sector and since it is a modular approach,could be used for monitoring other swine or other animals’ diseases through appropriate adaptation of the biosensors.
Swine industry operators have confirmed that the SWINOSTICS toolbox can constitute a valuable solution for animal health monitoring at farm level.Based on the results from research and the survey responses, the device can add value to the operations and also to the breeders’ management aspects of the sector.The SWINOSTICS device presented in the project is a prototype that would act as a baseline for future iterations.Future versions would reduce the size and weight of the device allowing easier and frequent use at farm level and deliver robust sensors that follow standardization protocols for production/calibration,significantly improving field operability and market acceptability.
The main project results include a) the device,App and cloud software, b)the validation results, after testing the device both with laboratory(spiked) samples as well as with real samples from the field.SWINOSTICS delivered a mobile diagnostic device and complete system,providing reliable and simple diagnostic testing directly on site enabling rapid local decision making, crucial for prevention of disease spreading,animal & food safety and human health.It has a direct positive economic impact on swine farms & the agri-food sector and since it is a modular approach,could be used for monitoring other swine or other animals’ diseases through appropriate adaptation of the biosensors.
Swine industry operators have confirmed that the SWINOSTICS toolbox can constitute a valuable solution for animal health monitoring at farm level.Based on the results from research and the survey responses, the device can add value to the operations and also to the breeders’ management aspects of the sector.The SWINOSTICS device presented in the project is a prototype that would act as a baseline for future iterations.Future versions would reduce the size and weight of the device allowing easier and frequent use at farm level and deliver robust sensors that follow standardization protocols for production/calibration,significantly improving field operability and market acceptability.