Project timeline: 07/05/2019 - 22/10/2019
Dr. Wasif Ali Khan
International Centre for Diarrhoeal Disease Research (icddr,b)
University of Notre Dame
Cholera is endemic in Bangladesh. The current method for testing samples requires three days and notification of results can take even longer. We hope to evaluate a device that could lessen that time required.
We hypothesize that there will be 90% accuracy of the device compared to the gold standard in terms of correct identification and we wish to test that.
In order to implement the device to identify dangerous water samples, the device must first be proven to be accurate at a satisfactory level. Therefore the hypothesis will be tested and conclusions drawn to determine the accuracy.
The accuracy of the device will be 90% compared to the gold standard.
Determine sensitivity and specificity of device in field. Discover and address any complications not found in lab that arise in field use. Draw conclusions about the validity of device
The OmniVis diagnosis process begins with a primer chip. The chip is a one-time-use disposable test kit that contains a freeze-dried biological assay specific for the ctxA gene of Vibrio cholerae. The assay includes six primers for the LAMP technique: F3, B3, FIP, BIP, LF, and LB. The shelf life of the chip with the freeze-dried primer is unknown; it has been proven viable for four months without the need for temperature or humidity regulation when stored with a desiccant. The transportation of the necessary equipment including these primers will be handled by OmniVis via shipment to Bangladesh or direct delivery by OmniVis staff. The chip has a reservoir that will fill when the chip is dipped into the water. The chip will be dipped into the water where it collects between 15 and 25 gl of water. The chip will be dried with a paper towel after which the app analysis will start. All waste products will be transported in biohazard bags and autoclaved before disposal.
Once the water sample is in the chip and the chip is dried, the app is started. The interface shows the user where to insert the chip into the heater. Once the chip is in, the heater works for thirty minutes while a flame moves up the screen to show the progress. During this phase, the LAMP technique is carried out in the housing. Samples containing the ctxA gene will undergo DNA polymerization resulting in the amplification of the strands. This process causes the toxic sample to have a higher viscosity from the saturation of DNA. Samples without the targeted gene will not undergo a significant change in viscosity as no DNA will amplify. The viscosity of the strands of non-amplified samples are significantly different from the polymerized strands — providing the basis for the in-app analytical algorithms measuring the Brownian motion. Once the heating portion is complete, the app prompts for the removal of the chip and the insertion into the camera slot where the microscope lens is used to analyze the sample. There the Brownian motion of the sample is measured via in-app algorithms using the iPhone camera and microscope lens in the apparatus. This analysis can take up to a few minutes after which the app displays the result showing either a cholera-contaminated sample or not. Our application will show us the diffusion coefficient measured by the camera in terms of m/s^2 so that analysis can be carried out on the data. GPS location will be recorded at the time of completion and the diffusion coefficient and location will be stored on the phone. The phone will transfer the data to a cloud server where the data can be accessed.
The previously established conventional sample enrichment technique or “gold standard” of cholera detection will be run in addition to the cellular diagnostic device. The gold standard for cholera detection is a time-intensive lab test to identify the presence of cholera in a sample. Alam’s 2015 study outlined the laboratory test. Water samples of 500 ml were collected from a site and incubated in 2X alk.
Cholera is endemic in Bangladesh. Community water sources contaminated with the bacteria place communities at risk of cholera infection and death.The current method for testing samples requires three days and notification of results can take even longer. We hope to evaluate a device that could lessen that time required.
The rationale behind studying the OmniVis device is the potential to reduce this test-time and reporting to communities. We hypothesize that it will take approximately 30 minutes to complete a water test and determine if the sample is contaminated with cholera. In order to implement the device to identify dangerous water samples contaminated with the cholera germs, the device must first be proven to be accurate at a satisfactory level. The objective of the project is to determine sensitivity and specificity of device in field; Discover and address any complications not found in lab that arise in field use; Draw conclusions about the validity of device.
The research project is designed to compare capability of the Omnivis Technologies rapid cholera detection device and conventional cholera detection method from water by comparing water sample analysis data of both. Based on the comparison, conclusions will be drawn to determine the accuracy.
This research project will generate evidence/data which will be used to improve the accuracy and efficacy of the OmniVis Technologies rapid cholera detection device. Potential use of the OmniVis device to detect dangerous water sample (contaminated with Vibrio cholerae) instantly from water body will lead to proper management, decision-making and control of the cholera epidemic at the initial stage by the government in future.
Sabeena Ahmed, icddr,b
Zahid Hayat Mahmud, icddr,b
University of Notre Dame (UND)