NEW YORK – The ongoing COVID-19 pandemic has brought companies with little diagnostic experience firmly into the space in attempts to offer a variety of assays for SARS-CoV-2 detection.
Add Takara Bio USA to the growing list of firms trying to make that transition.
The company announced earlier this month the development of a new method for detecting SARS-CoV-2 RNA using its SmartChip real-time PCR instrument in partnership with BioSyntagma, which is seeking Emergency Use Authorization from the US Food and Drug Administration for the test. Takara developed the assay, and BioSyntagma served as the validation partner.
An infectious disease diagnostic application is new ground for the SmartChip. After acquiring the technology in 2017 as part of its purchase of WaferGen Biosystems in 2017, Takara had focused the SmartChip on gene expression studies and research. The system consists of a high-throughput liquid dispenser, an aluminum chip with 5,184 wells, and a real-time PCR instrument. The platform dispenses in 100 nanoliter volumes, which Takara Chief Scientific Officer and Head of R&D Andrew Farmer noted isn't especially high, but because it can run a high number of samples, it cuts down on the cost of reagents and other supplies.
The 5,184-well chip is another major selling point, especially as testing capacity across the US for detecting SARS-CoV-2, the coronavirus that causes COVID-19, needs to be scaled up. Many labs are doing three assays per sample during the pandemic, Farmer said – one for the actual virus detection, one as an internal control, and one replicate to ensure the result is valid.
Because SmartChip has thousands of wells, up to 300 samples can be run on one chip, allowing labs to scale up to testing hundreds of patients at a time. Additionally, sample-to-answer time on the platform is less than four hours, enabling multiple runs to be performed daily and adding to the ability to increase testing capacity, he said.
This shorter sample-to-answer time is particularly important for COVID-19 testing, Farmer emphasized. "If you've got an asymptomatic patient that's walking around, not realizing they're infected, you need to know that very quickly," he said. Many of the clinical customers who have shown interest in the SmartChip are positioning it for a turnaround time of 24 hours or less, he added.
Many systems have a standard capacity of 384 wells, which allows for the testing of a little over 100 patients per run, according to BioSyntagma CEO David Richardson. Other instruments that may tout advances like 15-minute run times have limited volumes, he added. "That's great if you're testing like 10 people," he said, "but when you have to test thousands a day or you have to test a whole county … it's about throughput."
Liz Quinn, Takara's director of PCR enzymes and stem cell marketing, also touted the flexibility that SmartChip lends to building custom panels. Because a user can do the liquid dispense patterns in multiple ways, there's flexibility with adding and removing assays, making it easier to interrogate different targets individually.
As the COVID-19 pandemic is expected to stretch for months into the flu season and more diagnostic firms and clinical labs look to combining a SARS-CoV-2 diagnostic test with other respiratory panels or pre-screening patients for the flu before performing the SARS-CoV-2 test, the SmartChip's flexibility will allow for the creation and customization of those bigger panels to test multiple infections, Quinn said.
"Just testing for COVID is going to be somewhat short-lived in the very near future," Richardson added, and many labs will be looking to run multiple panels without sacrificing higher throughputs. Other panels can only fit so many samples and when trying to maximize space, some labs aren't running replicates on multiplex panels, which he called "bad science."
The flexibility of the platform has made it popular in the antibiotic resistance space, with significant instrument placements in Asia where researchers are looking for outbreaks, Quinn said. The platform is also being adapted for epidemiological studies looking at wastewater in water treatment plants for environmental surveillance.
Takara originally targeted gene expression studies for the SmartChip, and that remains a large application for the platform's users, Quinn said, as the company has chemistries optimized for gene expression and single nucleotide polymorphism detection. A review published in 2019 in the journal Molecules found that the SmartChip was the most widely used high-throughput qPCR platform for evaluating antimicrobial resistance genes, and it noted the platform "has better analytical sensitivity as compared to other microfluidic chips" due to the larger reaction volume.
But, Farmer said, the SmartChip's larger wells make the platform well suited for infectious disease diagnostic tests because it allows for the varied viral load in patient samples. Sensitivity is higher due to the 100 nL wells, though he noted that the volumes can't go too low, or the sample will be lost.
Adapting for COVID-19
Takara's COVID-19 panel was developed by adapting the company's current chemistry in its gene expression workflows to perform a one-step rt-qPCR process on the chip. Farmer said the firm used the US Centers for Disease Control and Prevention's primers to adapt the workflow and develop the assay, determining limits of detection, sensitivity, and reproducibility. By using the CDC primers, Quinn said SmartChip's system had similar performance to CDC's test, which was the first to receive EUA from the FDA for SARS-CoV-2. Furthermore, Takara's test showed no cross-reactivity with other coronaviruses. The limit of detection for the SmartChip system was seven copies per microliter.
After Takara created the assay, it shared it with BioSyntagma, a biotech spinoff of Arizona State University based in Scottsdale, Arizona, that applied the test and method in its CLIA-waived setting. Using protocols from the CDC, BioSyntagma validated the test and moved to submit it to the FDA for possible Emergency Use Authorization.
While the test was initially developed for use with nasopharyngeal samples, Richardson said it could work for other sample types, such as saliva. "If the instrument works with one type, it's compatible with really all types," he said. "It's just a matter of submitting a different report to the FDA for each type."
BioSyntagma's partner, Paradigm Laboratories, is submitting the report. Because the data that was generated as part of the EUA submission is included in the report to the FDA, Quinn declined to disclose any specific information about it. She also said that Paradigm hasn't submitted to the FDA for an EUA yet. If an EUA is issued, Paradigm would offer the test as a service.
BioSyntagma and Takara previously worked together to use the SmartChip for oncology indications, but once the pandemic started and the need for high-throughput testing increased, the focus shifted, Richardson said. As testing volumes increased throughout the pandemic, more hospitals and laboratories brought in technicians from outside the clinical lab to run tests, and the SmartChip's easy-to-use platform proved to be a benefit for users who weren't trained in a clinical lab setting.
Several platforms on the market complete with the SmartChip, including Fluidigm's Biomark HD system, which has also been used for COVID-19 testing. According to Richardson, though, cost savings can be achieved with SmartChip consumables, though he acknowledged he hadn't used the Biomark system for several years.
Price is a major consideration for clinical laboratories, so even minor price differences are important. Most labs "are small businesses and margins are everything," Richardson said, adding BioSyntagma has run its tests on the SmartChip, which are more economical per patient.
In an email, a Fluidigm spokesperson responded that the "high throughput, flexibility, and low cost" of the Biomark platform were "evidenced by the system's record as a proven workhorse in the lab for more than a decade." She also noted that there are hundreds of active installations globally and that Fluidigm technology "is the foundation for multiple approaches to SARS-CoV-2 detection." Fluidigm recently filed for EUA for its extraction-free, saliva-based SARS-CoV-2 diagnostic test, which has a capacity of 6,000 tests per day per instrument.
Richardson noted that if all the wells on the SmartChip aren't being used, Takara's test is expensive to run due to the metal disposable cartridge in comparison to other instruments' plastic plates. "But if you fill it up, the margins are way better than they are in other systems, significantly," he said.
Takara's acquisition of WaferGen and the SmartChip in came during a period when Takara was moving toward increased automation and adding automation to current technologies, Farmer said. Takara's main business has been providing reagent tools, PCR enzymes, and other cell biology tools for researchers, but as the next-generation sequencing and PCR spaces move in clinical directions, automation has become crucial to push Takara Bio further into the clinical realm, he said.
Quinn also noted that Takara has been supplying PCR enzymes within the diagnostic space for a decade, so the SmartChip's acquisition allowed the firm to take its enzymes and adapt them for the necessary automation. Now, the US-based subsidiary of Japanese firm Takara Bio has been able to shift its focus to developing new chemistries and applying existing chemistries to those platforms. Farmer added that more users are looking for end-to-end solutions, which Takara is now equipped to provide thanks to the SmartChip.
"It's about complete solutions to the end user rather than providing pieces," Farmer said.