For all the advances of modern medicine, SARS-CoV-2—the new coronavirus behind the pandemic—is alarmingly successful. It is stealthy, with symptoms that only show up a week or two later, if at all. It spares no one, from seemingly healthy children and young adults to elderly patients who often bear the brunt of the disease. Above all, it has already infected millions—and those are just the cases that we know about.
Without a vaccine, the ‘test, trace and isolate’ trifecta appears to be the most practical way to quell any potential community outbreak. But as Singapore looks to safely restart leisure travel, it needs to significantly expand COVID-19 testing. Accordingly, the Republic aims to conduct up to 40,000 tests per day in the latter half of 2020.
It is an ambitious goal, but not impossible. By streamlining and automating key steps in the current testing protocol, an integrated COVID-19 testing system developed by A*STAR and its collaborators is set to help the country achieve this milestone.
The need for speed
The most common COVID-19 testing method relies on a technique known as real-time reverse transcriptase polymerase chain reaction (RT-PCR). Though no single test is 100 percent accurate, RT-PCR hits close to the mark. Its sensitivity and specificity rates are over 90 percent, meaning that people who test positive truly have the disease and vice versa. For this reason, the technique is widely regarded as the gold standard for detecting and diagnosing viral infections.
RT-PCR derives its name from a key step in the process known as reverse transcription. While most people are familiar with DNA, SARS-CoV-2’s genetic material takes the form of RNA. Hence, before any subsequent analyses like PCR can occur, the coronavirus’ RNA must be converted to DNA by the reverse transcriptase enzyme. This process occurs after viral RNA has been successfully isolated from patient samples. If RNA isn’t extracted and purified, contaminants in the sample may interfere with the PCR reaction, leading to inaccurate results like false positives.
Once the purified viral RNA has been converted into DNA, the PCR reaction finally takes place. Upon the addition of matching DNA sequences called primers, a series of heating and cooling cycles prompts the Taq polymerase to repeatedly synthesize multiple copies of viral DNA until it reaches a detectable threshold.
RT-PCR, however, has its drawbacks. First of all, it is a time-consuming process. The A*STAR-developed Fortitude test kit currently takes at least 90 minutes to run. Factor in the time required to collect patient swabs and extract RNA, as well as testing backlogs, and COVID-19 test results may very well take a day or longer to be released. In resource-strapped settings, this excruciating wait could even take up to a week.
To make things even more complicated, global shortages in RNA extraction kits have also slowed down RT-PCR testing everywhere from the US to India. As speed is essential in containing the virus, scientists worldwide have been searching for ways to make the testing process more efficient, as well as resilient to shocks in the supply chain.
Minimum exposure, maximum efficiency
The RESOLUTE test kit jointly developed by the DSO National Laboratories and A*STAR’s Diagnostics Development (DxD) Hub is poised to halve testing time. The test achieves this through a breakthrough direct PCR method that skips the RNA extraction step entirely. Instead, the patient samples are placed in a universal transport medium, which can store viruses stably at room temperature. Samples are then placed in wells containing the pre-mixed RESOLUTE test kit reagents, after which RT-PCR commences as usual.
To further accelerate the process, A*STAR is automating the RESOLUTE test kit with the help of the robotics system RAVE, which stands for Rapid Automated Volume Enhancer. The automated laboratory system was co-developed by A*STAR’s Advanced Remanufacturing and Technology Centre (ARTC) and Singapore Institute of Manufacturing Technology (SIMTech) in around 3 months—a considerable achievement as such projects typically take at least a year to complete.
Their achievement is made even more impressive in light of the many setbacks the team encountered along the way. “There were tons of challenges in our journey from conceptualization to deployment,” shared Rick Chua, Senior Business Development Manager at ARTC. “There was no opportunity to test our system with live samples. We tried to simulate mucus [from the swab] with shampoo, detergent, ladies’ finger (okra), starch, glue and even grease.”
RAVE automates the manual steps required for processing samples during RT-PCR, including moving and uncapping tubes, pipetting reagents and even scanning the barcodes on the tubes that distinguish individual samples from one another. In doing so, the system significantly speeds up the testing process from start to finish. Combined, the RESOLUTE test kit and RAVE system can process 96 samples in under an hour, resulting in a record-shattering output of 4,000 samples processed per day.
Beyond speed, the integrated RESOLUTE test kit and RAVE system also delivers a host of other benefits. By eliminating the RNA extraction step, the RESOLUTE test kit simplifies sample processing and lessens the chance of human error. The test also removes the need to acquire RNA extraction kits, reducing costs and making the workflow less likely to be affected by supply chain shortages. Meanwhile, by automating various steps in the RT-PCR protocol, RAVE makes the technique more accessible even to entry-level technicians and minimizes the prolonged exposure of staff to the virus.
Racing to the finish line
The RESOLUTE test kit and RAVE system will be distributed by Advanced MedTech Holdings, which has also received provisional authorization from the Health Sciences Authority to manufacture RESOLUTE test kit. The joint solution is already being used at three hospitals in Singapore, but may soon be deployed overseas.
Neighboring countries like Indonesia and the Philippines as well as far-off nations like Kazakhstan, Saudi Arabia and the US have expressed interest in acquiring the combined system. Given this, the teams at ARTC and SIMTech are looking into equipping the RAVE system with the industrial Internet of Things (IIoT) capabilities. According to Mr Chua, IIoT could allow the team to remotely monitor the health of various RAVE systems that could soon be installed all over the world.
As scientists scramble to develop vaccines in highly compressed timelines and deploy artificial intelligence to speed up drug discovery, it’s clear that time is of the essence in the fight against the coronavirus. Testing is no exception. To safely navigate the world out of this crisis, widespread testing should immediately take place on a global scale. The joint RESOLUTE test kit and RAVE system could be a shot in the arm that COVID-19 testing urgently needs.