Following a call by President Tony Chan for KAUST PIs to contribute through their research capabilities to alleviate the COVID-19 pandemic, efforts coordinated by Donal Bradley, KAUST vice president for research, and Pierre Magistretti, KAUST dean of the Biological and Environmental Science and Engineering division, mobilized a group of faculty to form the Rapid Research Response Team (R3T). The focus of R3T is to collaborate with and strongly support the Kingdom's healthcare stakeholders to help combat the spread of COVID-19.
Efforts are focusing on the development of rapid diagnostic platforms, genomic analysis of the virus and bioinformatic tools to help track the spread and evolution of the disease. These efforts are based on research projects and competencies established over the years at KAUST. They are also part of the Smart Health Initiative recently established at KAUST to implement joint research projects with medical centers in the Kingdom.
R3T's group of faculty has been in close contact with the Saudi Centers for Disease Control (CDC) and the Ministry of Health (MoH) to coordinate efforts that will synergize to ensure fast and reliable diagnostic tests, as the demand in the Kingdom and internationally for the tests will increase. Initial efforts are aimed at optimizing existing tests to decrease the amount of reagents used without compromising reliability.
The group is also monitoring developments in other academic and biotechnology laboratories. In particular, R3T initiated a collaboration with the University of Oxford to implement a novel test that would greatly simplify the virus detection process.
Recently launched Rapid Research Response Team projects
CT-based detection, segmentation and classification system for COVID-19
Xin Gao's group has been developing an AI-based computer-aided diagnosis (CAD) system for detection of COVID-19 patients (especially the early stage); classification of the disease phase; segmentation of the infection; and quantification of the infection regions. The experience from clinicians battling COVID-19 all over the world has shown that purely relying on pathogen nucleic acid or antibody detection is not fully reliable and can result in missed detections, which has become a big threat to the global community. Therefore, CT-imaging, as a sensitive and readily accessible biomedical imaging technology, has been routinely used as one of the main diagnostic standards, in addition to nucleic acid detection.
The CT images from different stages of patients' illnesses have very different patterns. Patients at the middle and advanced phases often have symptoms already, and their CT images are easily identified by radiologists. However, the early phase very often requires a high level of expert knowledge and experience to differentiate. In fact, CT images of the early phase of COVID-19 patients can look very similar to those of other lung infection patients, such as RSV pneumonia and carbon monoxide poisoning. Furthermore, quantifying the area for infection from the CT images has been shown to be very important for patient prognosis and treatment. Gao's goal is to help Saudi clinicians and physicians to more efficiently analyze and diagnose the patients and provide them guidelines to proper treatment.
Immunodiagnostics to detect the COVID-19 virus
Charlotte Hauser is developing reliable, robust, simple and cost-effective detection tests for COVID-19. Immunodiagnostic tests are useful measures for the detection, management and control of the increasing spread of the SARS-CoV-2 virus. They utilize a technology called ELISA, which is based on serological testing to recognize antibodies induced by the SARS-CoV-2 virus or to detect the SARS-CoV-2 virus itself. The test will utilize small blood droplets to test for existing antibodies within individuals to monitor if the person is—or already has been—infected. Such tests can also help the community to identify people that carry antibodies against the SARS-Cov-2 virus and who may now be immune against COVID-19.
The test will support monitoring the spread of the virus, tracing super spreaders and people at risk. Identifying immune patients who are willing to donate their blood serum could enable doctors to have immunization treatments for SARS-CoV-2 virus-infected people at hand. The test can also be used to immunize the most at-risk medical personnel against possible future viral infections. Simple finger-prick tests, dipsticks or lateral flow devices similar to the ones used for monitoring diabetes or the onset of pregnancies are planned to be used, since fast, inexpensive and easy-to-use diagnostic kits will be beneficial for rapid field testing and for areas where infrastructure, resources and expertise are restricted.
Utilization of computational tools and big data for COVID-19 drug development and viral surveillance
Takashi Gojobori and the faculty at the KAUST Computational Bioscience Research Center (CBRC) are working on genomic analyses of SARS-CoV2 to identify potential drugs (new molecules and repurposed) and therapeutic targets to be used against the virus. In close collaboration with in-Kingdom healthcare stakeholders (including the MoH and the Saudi CDC), they are developing computational solutions to provide monitoring for the spread and mutation rate of the virus. The CBRC is also assisting with capacity building and training of research staff at other in-Kingdom institutions to support their efforts in diagnostics and genome sequencing.
Article by Takashi Gojoburi, et al. - https://www.biorxiv.org/content/10.1101/2020.02.17.952895v2