A New SARS-CoV-2 Descriptive Diagnostic Test – What Makes This Assay Different to Others?

Clear Labs is a company focused on the latest technologies in molecular testing, machine learning, automation and bioinformatics – it develops fully automated next-generation sequencing and in vitro diagnostics solutions. Clear Labs recently created a novel descriptive diagnostic for SARS-CoV-2, that has now been granted Emergency Use Authorization by the US Food and Drug Administration (FDA).

Technology Networks had the pleasure of speaking with ClearLabs’ CEO Sasan Amini, to learn more about the company’s NGS-based COVID test, Clear Dx™.

Candice Tolton (CT): For readers that are not familiar with Clear Labs, could you explain the history and the concept behind the company?

Sasan Amini (SA): Absolutely. Clear Labs started in 2014 with a goal to democratize DNA sequencing for the food safety and quality industry. We are currently working with many household brands in food manufacturing to provide pathogen screening diagnostics within their labs. That has been our core business since we started and it’s the demands of the food safety industry that really pushed us to develop an effective and efficient platform.

The reality of the food safety market puts very specific constraints on a DNA-based testing platform. For instance, food safety testing is time sensitive because the product is perishable, so the test had to be faster than what could be accomplished with next-generation sequencing at the time. Additionally, food is also price sensitive because the volume of testing is high and the manufacturer's margins are low – no one will play $100/per test.

It’s also worth noting that the operators of food safety technologies are also not necessarily specialized in running complex lab processes and the churn could be high, so our system needed to be completely automated and easy to use. Finally, because food manufacturers use our platform every single day, it needs to be robust and able to run without intervention around the clock.

These four factors led us to create the first fully automated library preparation and DNA sequencing platform for food safety.

With the emergence of COVID-19, we realized that the solution we had created for food safety had given users a platform that is easy to use, fast, cost-effective and leverages DNA sequencing, making the existing “standard” method (PCR) obsolete. It could just as easily be extended into the clinical market, and COVID-19 was the perfect opportunity to accelerate our focus within this space.

CT: Could you explain the mechanism behind the novel SARS-CoV-2 descriptive diagnostic?

SA: In short, our fully automated platform combines hardware, consumables and cloud-based bioinformatics without the need for on-staff specialized operators. However, let me break down how each of these different components work, as well as integrate, to create a holistic platform.

Let’s start with the hardware. Our hardware is an integrated system that takes care of sample preparation, library preparation and sequencing, managing all liquid handling in the process. This eliminates any manual intervention needed by lab operators (improving reproducibility, reducing cost and dramatically decreasing error rate, adding flexibility around lab shift schedule) and upfront work is as simple as, if not simpler than, existing workflows.

The consumables are the kitted reagents our customers would use to perform the test. The cloud-based bioinformatics seamlessly enables labs to make sense of all the data (the platform is generating millions of data points per run) and report back the results without need for interpretation or any hardware infrastructure.

The assay itself is a novel descriptive diagnostic targeting most of the viral genome. That allows for very high specificity while at the same time covering informative regions of the virus’ RNA. This means the results are not binary. We’re not just looking for presence or absence, but can take advantage of the sequencing information being generated to examine the evolution of the viral genome, identify new variants, monitor mutations that can potentially confer drug resistance, investigate virulence factors and flag mutations that cause loss of diagnostic targets for qPCR.

As far as we know, this is the first time anyone has combined a diagnostic test with genomic surveillance functionality while offering a fully automated seamless workflow. Usually this is done separately – you are either looking for presence and absence or you are starting with a positive sample and perform deeper characterizations (e.g. mutation mapping etc.). Our assay can do both at the same time.

CT: Could this technology lessen the workload of those working within hospitals/laboratories where COVID-19 testing is busiest?

SA: That is certainly our goal. Take the fact that we are about to enter flu season. Particularly given the current COVID-19 numbers in the US, there’s a real concern that once we enter the thick of flu season, physicians and hospital workers will be overwhelmed with patients that have symptoms that correspond to either illness – your typical flu or COVID-19. With other testing solutions, these hospital workers would have to administer two separate tests to diagnose the patient, requiring additional resources as well as more hospital staff time. Clear Dx, with its ability to identify virus differentiation, can potentially eliminate this need for multiple tests and in turn streamlines physician workflows.

Beyond flu scenarios, there are a variety of different situations in which Clear Dx can lessen hospital workloads. For example, our platform is fully automated, reducing labor and error potential by offering a hands-free workflow, maintaining highest level of reproducibility. By minimizing false positive and negative results, we can also ensure hospital staff are not caught up in unnecessary additional tests or diagnostic procedures.

Credit: ClearLabs

Laura Lansdowne (LL): What are the implications of a false-positive test result and how does the Clear Dx test minimize false positives?

SA: False-positive test results are a drain on our already strained supply of resources. Receiving a positive diagnosis on a COVID-19 test means self-isolating, contact tracing and further medical care – including taking more tests. Being given a false-positive test means missing out on money and quality time with others and puts unnecessary stress on the patient and their family.

The Clear Dx test minimizes false positives by providing more than a “yes” or “no” answer to a diagnostic test. Because the Clear Dx test covers a large fraction of the viral genome, its sensitivity and accuracy is much higher, making it incredibly unlikely the genetic sequencing of the virus will be misdiagnosed.

LL: Can you elaborate on how the test monitors for mutations and strain variance that may confer drug resistance?

SA: Because the assay generates genomic data, Clear Dx can be used to monitor viral mutations. Usually, drugs or other therapeutic interventions target essential machinery of the virus like the spike protein or RNA polymerase (which is required for the replication of the virus). Sequencing the viral genome allows physicians to look for mutations within these targets and flag resistance patterns and begin to stratify patients based on how likely they are to respond to a given treatment. In addition, we can subtype the virus based on those differing regions of the genome, giving additional insight into correlations between virus strain and medication efficacy.

Sasan Amini was speaking to Candice Tolton, Editorial Assistant and Laura Lansdowne, Senior Science Writer for Technology Networks.