NEW YORK – Molecular food safety testing company Clear Labs has developed an automated nanopore sequencing-based diagnostic COVID-19 assay platform that it plans to launch in the coming weeks.
On Thursday, the company announced an $18 million strategic funding round, part of which will go toward the commercialization of the COVID-19 platform. The round was led by Redmile Group, with participation from existing investors Wing VC, Menlo Ventures, Tyson Ventures, Khosla Ventures, GV, Felicis Ventures, and HBM Genomics, and brings the firm's total funding raised so far to $62 million.
Founded in 2014, the California company, which recently moved from Menlo Park to San Carlos, has been selling an automated sequencing platform, called Clear Safety, to the food industry for Salmonella and Listeria testing, which it has deployed at dozens of food production companies. The system combines library preparation and nanopore sequencing, allows for low-cost testing, and is easy to use, according to Sasan Amini, the firm's cofounder and CEO. Clear Labs had always planned to deploy it for clinical diagnostic testing down the line: "From day one, we already had the vision to go to the clinical space but the COVID-19 pandemic accelerated that timeline," he said.
The first version of the COVID-19 platform, which the company submitted for Emergency Use Authorization to the US Food and Drug Administration last week, starts with RNA that has been extracted from a swab, followed by target amplification and nanopore sequencing. It targets several dozen SARS-CoV-2 amplicons, covering "a good fraction" of the viral genome, he said. Thus, the test provides more than just a yes-or-no answer, adding viral sequence information, but is still very sensitive because of its deep coverage of the amplicons. "This is the first platform that kind of combines a diagnostic test with a secondary genomic sequencing or genomic surveillance functionality," Amini said.
Target amplification, library preparation, and sequencing are all fully automated on the platform, which consists of an OEM liquid handler and an Oxford Nanopore GridIon sequencer that is embedded in the system, as well as reagents and a cloud-based data analysis software that creates a report. "Everything happens in one fully integrated hardware unit," he said. Last year, the company signed a distribution agreement with Oxford Nanopore Technologies for the sequencer and a supply agreement with Integrated DNA Technologies (IDT) for oligonucleotides.
The current design, starting from extracted RNA, allows 192 samples to be completed in eight hours, and the company hopes to increase the throughput and decrease turnaround with the next release. That next version will also expand the assay from SARS-CoV-2 to a panel of other respiratory pathogens, so doctors can test for several diseases with similar symptoms to COVID-19 at once. "As we get closer to the cold season, many of those overlapping diseases are going to surface," he said.
One advantage of the test is its high sensitivity. Based on the data the company generated for its EUA submission, the limit of detection is half a copy of viral RNA per microliter, which Amini said is severalfold better than the gold standard qPCR assay from the US Centers for Disease Control and Prevention. For the next iteration, Clear Labs also plans to tackle the "upstream" part of the assay, starting with the clinical sample, and hopes to "make it happen directly from swabs."
The first systems will ship to early-access customers within a few weeks, Amini said, and more will follow once the EUA is in hand. He did not provide a list price for the system but said that the cost per test would be almost on par with that of a qPCR test.
What is attractive about the platform is its low limit of detection and high specificity, he said, and the fact that it is "even simpler than a PCR machine to operate." In addition, because the assay generates genomic data, it could potentially be used for surveillance, to determine infection clusters, and to look at viral mutations that may have therapeutic significance. "The beauty of all this added surveillance information is, it happens simultaneously with your diagnostic test result" in a single assay, he said.
The assay will be one of the first routine diagnostic applications of nanopore sequencing. Last year, for example, Shield Bio launched a diagnostic nanopore sequencing test to determine antimicrobial susceptibility of gonorrhea infections. Also, startup Day Zero Diagnostics said earlier this month that it is developing a diagnostic antibiotic resistance testing platform that uses nanopore sequencing.
In addition, nanopore sequencing has been used by numerous research groups to track infectious disease outbreaks in the field, starting with the Ebola outbreak in West Africa in 2015.
Clear Labs' system will likely compete with other sequencing-based COVID-19 assays and respiratory panels currently under development, as well as with existing qPCR tests, some of which are also highly automated, and with emerging CRISPR-based and antigen tests. However, "at this time, there is no competition, we're all fighting one problem," Amini said.