​Thomas Anthopoulos and his research group, in collaboration with Professor Arnab Pain, are developing solid-state, field-effect transistor based biosensors (Bio-FETs) for label-free, ultrasensitive, and real-time detection of SARS-CoV-2.

The Bio-FET technology combines a unique electrode geometry together with a few nanometers-thick conducting channel that provides extreme spatial proximity between the analyte and the sensing surface of the device. The sensor is able to transduce and simultaneously amplify the specific antibody-antigen interaction signal into electrical output reading.

Due to its high sensitivity the technology has the potential to enable SARS-CoV-2 detection from patients with COVID-19 symptoms using nasopharyngeal swab samples. The approach is simpler than established methods such as reverse transcription-polymerase chain reaction (RT-PCR) to detect SARS-CoV-2 and less time consuming.

Although the team is currently focusing on demonstrating discrete sensors, in the future a large number of these devices could be integrated into microarray chips for highly reliable biosensing applications. The Bio-FET technology offers potential for an inexpensive miniaturized sensing platform that could be applied in clinical diagnosis.

Vice President of Research Donal Bradley identified the reverse transcription loop-mediated isothermal amplification or RT-LAMP research activity of Professors Zhanfeng Cui and Wei Huang from the Department of Engineering Science at Oxford University as being an interesting collaboration opportunity for the KAUST R3T program and contacted his former colleague Professor Cui on March 21 to initiate a discussion.  

Professors Cui and Huang had started their RT-LAMP project in response to the COVID-19 situation in China where they both have research groups at the Oxford Suzhou Centre for Advanced Research (OSCAR) in Suzhou and had made good progress including specific detection of COVID-19 for patient samples in Shenzhen, China and Oxford, UK. The complementary bioscience skills of Professors Arnab Pain and Samir Hamdan at KAUST and our close collaborations with the local Ministry of Health (MoH) hospitals treating COVID-19 patients and the Saudi Center for Disease Control (Saudi-CDC) made the proposed collaboration attractive to both parties and a Memorandum of Understanding was signed on April 2, 2020.

RT-LAMP has the potential to be a much faster diagnostic test for COVID-19 (minutes rather than hours) and one that can be readily implemented in a hospital or other point-of-care environment. It uses a reverse transcription process as found in the standard RT-PCR test to convert the viral RNA into complementary DNA, but the subsequent DNA amplification step is performed at a single temperature unlike the polymerase chain reaction of RT-PCR, which requires thermal cycling. In addition, the results are easy to read through a simple solution color change rather than requiring measurement of a fluorescence marker using sophisticated analysis-lab-based instrumentation. 

The R3T teams of Professors Pain and Hamdan are working hard to validate and optimize the RT-LAMP test for sensitivity and reliability and on production of reagents at scale for use in this test. The test will need to be re-optimized for the reagents that are produced here, but success would, in principle, allow RT-LAMP test kits to be assembled in KSA for deployment within the local healthcare system. 

Other directions being studied at KAUST include implementation of the test using different detection methods, including alternative color change materials and fluorophores that could provide a back-up, second measurement option when the results may be ambiguous due to a low viral load or contamination concerns e.g. via swab-collected blood. Bradley has asked Professor Iain McCulloch and his team to look at this and they are synthesizing new chromophores and fluorophores to meet the challenge. Oxford are also working on making the test compatible with different swab solution media and on ways to remove the requirement for an RNA extraction step, to allow direct use of swab solutions, further simplifying the testing protocols.

KAUST received 30 RT-LAMP tests from Oxford on April 15 and these have very recently been used to test 30 individual patient samples at a Medina hospital facility. The patient samples had already been tested using RT-PCR in Medina and were subsequently re-tested at KAUST also using RT-PCR as a cross-check on RNA molecules extracted from nasal swab samples. Results are currently being analysed.

Wolfgang Fischle's research group, in collaboration with Professor Arnab Pain, aims to understand why a large proportion of individuals get infected by the SARS-CoV-2 virus but don't develop any recognizable disease, whereas some patients progress to life-threatening symptoms. Since the rate of patients developing severe COVID-19 is relatively high, it is unlikely that genetic variances are the sole cause for this phenomenon. The group is testing whether variations in the epigenome of individuals are key determinants of disease susceptibility.

While all cells in the body share the same genetic material in the form of DNA, differential expression of the genome in different cell types and in different individuals is directed by epigenetic mechanisms. Besides other aspects, these involve chemical modifications of DNA, such as methylation. 

To define signatures of COVID-19 susceptibility, the team is analyzing DNA methylation patterns of samples obtained from asymptomatic, mildly and severely affected COVID-19 patients. The data are bioinformatically integrated with disease severity, viral load, survival, time to recovery and a number of other parameters to derive diagnostic tools for identifying patients that will require special attention by healthcare systems, in terms of isolation or intensive care long before they develop life-threatening symptoms. This early intervention is targeted at improving disease outcome.

​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.

​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.

COVID-19 virus mutation tracker

Gojobori's team have developed an online resource providing interactive analysis of mutations and variants of the virus responsible for the COVID-19 pandemic (SARS-CoV-2) to enable mutation tracking in a time-spacio fashion. This is important for identifying pathogenic mutations and monitoring them time-wise in all the geographical regions around the world.

To date, the team has compared around 90,000 genomes of the SARS-CoV-2 virus available worldwide, including over 500 from Saudi Arabia, as of August 28, 2020. In practice, this mutation tracker allows scientists to explore isolates and virus variants globally, as well as for individual countries. The tracker also includes valuable information on source and infected location information; date of infection; virus clades; and mutation fingerprint of virus variants.

Keeping track of mutations is very important to understand local and global spread of prevalent variants; and to be considered in vaccine developments. This mutation tracker, now supported by a KACST grant, is being updated regularly to include more isolates of the SARS-CoV-2 virus.

The team are now sequencing around 2000+ additional isolates from Saudi Arabia to understand relationship of virus variants and disease severity considering patient age, gender and underlying conditions.

Learn more and experience the COVID-19 virus mutation tracker website: http://www.cbrc.kaust.edu.sa/covmt 

​Samir Hamdan's group is working on a local solution to develop a pipeline of reagents for use in biomedical and clinical lab applications. The COVID-19 pandemic has created a real challenge for the entire world to cope with the dire need for reagents and diagnostic kits. This unprecedented situation has pushed biotechnological companies to the limits in their capacity for sustaining their obligations toward the growing demand, thus threatening the continuity of the entire supply chain for various reagents required to produce the existing and new diagnostic kits. The majority of the kits require reverse transcriptases and DNA polymerases to amplify the viral genomic RNA to detectable levels by diverse techniques. It is unforeseen for how long the production lines of these enzymes and several other reagents in the diagnostic kits can sustain the growing demand for the entire world. Over several years, Hamdan's group has successfully established a robust production of DNA polymerases in their laboratory and has started working on producing reverse transcriptases. 

The aim is to scale up production to meet the needs of the Kingdom for these enzymes. The group also patented DNA polymerases produced from microorganisms in the Red Sea that can work under harsh conditions. They will be using these DNA polymerases to devise new detection assays. Hamdan's group will also utilize their resources and expertise in DNA replication and repair and in fluorescence-based detection of protein binding to nucleic acids to develop rapid fluorescence-based assays for the detection of COVID-19.

​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.

Robert Hoehndorf and his team have built a system that serves to create a repository of viral genomes sequenced in Saudi Arabia. Their work concerns the development of infrastructure to store and process COVID-19 associated data. In particular, the team seeks to develop sequencing data and metadata obtained from samples across the region. While there are several international data sharing efforts, it is important to collect regional information, develop standardized workflows, and generate sufficient metadata to exchange and combine datasets.

The viral genome database allows for the submission of unprocessed sequencing data. The database then executes a set of standardized workflows that automates large parts of bioinformatics processing and assembles the submitted sequences into a pangenome that can be queried and analyzed further. Importantly, the data is stored together with metadata, which ensures that any information in the sequence database can be exchanged and combined with other data worldwide.

​Peiying Hong's group in the Water Desalination and Reuse Center is collaborating with KAUST Health, Safety & Environment (HSE) and Facilities Management to detect the SARS-CoV-2 virus in untreated wastewater generated by the community.

World Health Organization data suggests that approximately 80 percent of COVID-19 infections are mild or asymptomatic. In particular, asymptomatic cases are concerning, as these individuals can unknowingly transmit the virus to others. 

There is therefore a strong need to detect not only the symptomatic patients but—more importantly—also the asymptomatic individuals who may be moving around in the community during and after the outbreak has subsided. Instead of testing every individual—which is not feasible because of the global lack of testing kits and the burden it imposes on the testing system—monitoring for SARS-CoV-2 directly in wastewater could be an alternate method for early outbreak detection.

Monitoring for SARS-CoV-2 in wastewater has already been demonstrated in the Netherlands and in the state of Massachusetts in the U.S. By initiating a similar program at KAUST, the group aims to detect SARS-CoV-2-infected community members who have gone previously undetected using the current quarantine and swab-testing system. The data obtained from wastewater monitoring could facilitate the HSE department to adopt appropriate intervention measures and to establish a plan to begin to return to business as usual.

Pending a successful pilot of the program, monitoring could be expanded beyond KAUST to meet the needs of the Kingdom. In collaboration with the Saudi Ministry of Health, wastewater sampling in Jeddah has commenced. By developing a continuous monitoring effort on wastewater for pathogenic viruses, a surveillance network that can potentially predict future outbreaks of other novel viruses could be established.

​Sahika Inal and Stefan Arold have joined forces to develop a programmable SARS-CoV-2 detection device that combines organic electrochemical transistor (OECT) technology (developed in the Inal lab) with a protein recognition layer (engineered by the Arold lab). OECTs transduce and amplify biomolecular interactions directly into electrical readouts. By using adapted biomolecular reporters as a recognition layer, the team turns OECTs into devices that can rapidly detect specific biomolecules (such as viral proteins or RNA) with ultra-high sensitivity. Sensor fabrication costs are modest, and the technology has the potential to surpass a wide range of diagnostic methods that are all depending on enzymatic amplification or reporter-based reactions (miniaturized PCR, isothermal amplification, ELISA and others).

For SARS-CoV-2 detection, the team will use their current prototype—which already has a picomolar sensitivity that surpasses complex optical instruments—and engineer it so that it specifically recognizes SARS-CoV-2 surface proteins.

​Mo Li’s lab is developing an ultra-sensitive and accurate method that is capable of being deployed in the field for rapid sequencing-based detection of SARS-CoV2. Multiple regions of the viral genome that harbor frequent mutations will be captured by molecular biology techniques and then sequenced on a pocket-sized sequencer called Oxford Nanopore minION. Thousands of samples can be sequenced in parallel in a matter of hours, with the data being analyzed using a bioinformatic pipeline developed in Li’s lab to detect the virus and report its sequences. The whole workflow can be carried out with equipment that fits inside a briefcase. 

Currently, clinical samples must be shipped to centralized laboratories for COVID-19 testing. This leads to longer turnaround time, limited access for rural areas and potential loss of samples integrity during shipping. This new method—once validated with clinical samples—could realize rapid and point-of-care diagnosis and significantly increase viral mutation data to facilitate epidemiological studies of COVID-19 and track the possible emergence of more virulent strains.

​Magdy Mahfouz is developing a simple, sensitive, accurate and point-of-care diagnostic test that will allow individuals to be quickly tested in any environment. The technology is based on the targeting of the SARS-Co-V2 virus RNA genome and converting a specific piece of the RNA genome into DNA molecules via reverse transcription. The DNA molecules are then amplified at a single temperature that does not require successive heating and cooling cycles, and this can be completed in just one hour using a portable simple machine. If the sample is positive, it would lead to a change of color that can be seen by the naked eye.

Such visual and colorimetric detection of the COVID-19 virus in patient samples will enable screening large populations in a short time. The group is also working on developing other versions of diagnostic platforms based on the same principle coupled with CRISPR enzymes, which can be used for home or point-of-care detection similar to pregnancy test strips and diabetes sensors. These efforts may contribute to overcoming the current challenge of COVID-19 detection at a large scale and in a short time for effective disease management and control.

​Magnus Rueping and his team are leveraging naturally occurring bacterial gas vesicles, first discovered in the high-salinity waters of the Red Sea and the Sabkha salt marshes, to develop a novel vaccination approach in collaboration with Tiba Biotech. These robust protein carriers can be engineered to display immunogenic fragments derived from the coronavirus to further boost recognition by the adaptive immune system.

Most COVID-19 vaccines in development today focus on the surface spike protein, the antigen that gives coronavirus its "crown" name. However, there is concern that these vaccines have limited duration of protection, particularly if the SARS-CoV-2 virus persists over several seasons or mutates over time.

Working in collaboration with Tiba Biotech, a Boston-based venture founded in 2017, Rueping and his team are developing a heterologous prime/boost vaccination regimen using complimentary nanoparticle delivery technologies developed at KAUST and at MIT. Tiba's fully synthetic mRNA vaccines target multiple coronavirus antigens, in addition to the spike protein.

After establishing an initial protective immune response with Tiba's mRNA vaccines as a prime dose, the KAUST all-protein booster vaccines are expected to enhance antibody production and longer-lasting immunity. The components of the vaccination protocol can be rapidly produced under halal-certified manufacturing conditions.

Valerio Orlando's lab is exploring the possibility of using novel generation antisense oligonucleotides as an adjuvant in therapeutic treatment of COVID-19 patients. The idea stems from recent cases reported from hospitals in Italy and China in which some patients treated with anti-inflammatory compounds against rheumatoid arthritis, in combination with conventional antiviral drugs, had important beneficial effects with complete remission of the disease.

Inflammation is a defense/protective mechanism initiated by signaling molecules (cytokines) that activate the production of endogenous factors that are activated when cells are challenged by pathogens.  

However, in certain acute conditions—like infections with aggressive retroviruses (SARs, MERs, coronavirus)—where, for example, alveolar epithelia are severely damaged by viral replication and bacterial infections, the high rate of inflammatory response may overtake the capacity of the immune system. In this situation, interferon response loses control, starting the production of uncontrolled levels of cytokines (a "cytokine storm") and provoking severe damage in the tissues. This contributes to the high rate of fatal prognosis in the case of COVID-19 patients.

Recent work from Orlando's lab identified new targets potentially involved in this process. The group has successfully used the activity of novel generation reagents against such targets in various disease model systems. Action that has been taken is aimed at collaboration with international and national laboratories and clinical centers potentially testing this idea, with the scope/hope to accelerate the identification of novel, effective, low toxicity adjuvant treatment against COVID-19.

Arnab Pain's group, in collaboration with the Saudi MoH and Saudi CDC (among others), has employed large-scale genome sequencing of COVID-19-positive individuals to analyze the genomes of SARS-CoV-2 viruses circulating in Saudi Arabia. The group then compares them in the global context by employing bioinformatic analysis of the datasets. The group has developed a genetic "barcode" of the global population of the SARS-CoV-2 viruses by systematically tracking mutations in their genetic material over time since the COVID-19 pandemic began. 

Genetic barcoding can offer a way of tracking how these viruses infect from one person to another; discovering whether there are imported cases; and also monitoring the effectiveness of the virus control or other containment measures taken by healthcare authorities. Combining the genome data with the clinical metadata may allow the identification of genetic features of the virus strains that make them more virulent or transmissible.

In collaboration with other colleagues in KAUST, Pain's team is also looking at:

1. Optimization of nucleic acid (genetic material)-based detection technologies for early detection of the virus in body fluids.
2. Benchmarking of currently available nucleic acid (genetic material)-based detection technologies.
3. Developing genomic visualization tools to understand the pandemic from a genetics perspective.
   

​Ivan Viola and his team have developed a new technique for rapid modeling and construction of scientifically accurate mesoscale biological models, which is being applied to the SARS-CoV-2 virus. The result is a 3D model based on 2D microscopy scans and the latest knowledge about the biological entity represented as a set of geometric relationships. This new technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise—techniques developed, in part, in collaboration with a team at The Scripps Research Institute for the purposes of better understanding the HIV virus. Collaborators at Nanographics GmbH created the video you see below.

From a few 2D microscopy scans, Viola's team is able to learn the statistical properties of various structural aspects, such as outer membrane shape, spatial properties and distribution characteristics of the macromolecular elements on the membrane. This information is utilized in 3D model construction. Once all imaging evidence is incorporated in the model, additional information can be incorporated by interactively defining rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, their distances and orientations to other structures. These rules are defined through an intuitive 3D interactive visualization and modeling feedback loop.

The team hopes that this 3D experience can help steer biological research to new promising directions in fighting the spread of the SARS-CoV-2 virus.

​With the COVID-19 pandemic, we are all in uncharted waters. There is an enormous sense of urgency to get out in front of the pandemic to understand where it is headed. More importantly, there is a barrage of information, and dashboards available are diluting key metrics. Governments, NGOs, caregivers and all of us as individuals need to respond to the pandemic quickly and effectively with smarter data.

To this end, KAUST teamed up with a global taskforce called The COVID Compass Taskforce. The taskforce consists of experts in data science, location intelligence, code, economics, journalism, public policy and media, and it is committed to quickly publishing relevant, relatable and actionable data around the COVID-19 pandemic.

With the global supply crisis in standard ventilator systems, there is an emerging need to provide more basic point of care assistance to those suffering from respiratory issues and requiring assisted ventilation. KAUST has joined the global effort to provide fast effective solutions to assist those on the front line of medical care. 

One such solution already underway is our work on the design and prototyping of mechanical actuators for AMBU bags, which will provide simple, easily deployable and effective breathing assistance to patients. 

​The design and fabrication of face shields for use by frontline hospital staff, including a partially 3D printed design from McLaren and a fully laser cut, clip-together design from our own Core Labs workshops has been executed.

Two face shield prototypes have been completed and have been sent to the National Guard Hospital for testing. KAUST will then share the design with Industrial Cluster so that they can be mass produced.