NEW YORK – Fry Laboratories, an Arizona-based infectious disease diagnostic testing firm, has developed a next-generation sequencing-based test for SARS-CoV-2, the virus that causes COVID-19, which it plans to commercialize as a kit.
The assay uses a combination of proprietary sample preparation and bioinformatics to do targeted virus genome sequencing and identification. The library preparation method creates amplicons generated by one-step PCR and is contained in a single tube. The method includes indexing and bypasses traditional Illumina sample preparation methods. With automation, the entire workflow requires about seven to eight hours, with five hours on the sequencer. Overall, the concept is like running a targeted quantitative PCR assay, said Jeremy Ellis, CSO at Fry Labs and its sister company BioID Genomics, but uses next-generation sequencing as the analyzer. Specifically, Fry Labs has designed the test to use the same viral genome targets as the qPCR test of the US Centers for Disease Control and Prevention and to run on Illumina's MiSeq platform with a v2 "micro" flow cell.
Fry Labs can get about 1,150 samples into a single MiSeq run, Ellis said, and based on previous assays, this one could be done for $30 per sample or less. Running the assay three times per day would enable it to reach throughput on par with the Roche Cobas system, Ellis suggested.
Company officials said they hope to get US Food and Drug Administration Emergency Use Authorization for a laboratory developed test (LDT) first, then amend the EUA to include kits, which would be sold through BioID Genomics, which was launched late last year to sell a metagenomic sequencing kit.
"We're excited about this because there are many thousands of [MiSeqs] installs, globally," Ellis said. "Being able to bring that untapped technological capability to bear on coronavirus testing is an exciting proposition."
The company is one of several other laboratories that have been trying to harness existing sequencing platforms for high-throughput COVID-19 testing using approaches such as SwabSeq, Dx-Seq, and LAMP-Seq.
Fry Labs, launched in 2007 and based in Scottsdale, Arizona, has been developing NGS-based infectious disease tests since 2013. The firm also offers serology- and microscopy-based diagnostic tests. It has obtained several patents on its rapid infectious disease identification (RIDI) sequencing method. Fry offers two targeted NGS LDTs: a pan-bacterial assay that uses 16S rRNA and a pan-eukaryotic assay that looks at 18S rRNA. These assays run on Thermo Fisher Scientific's IonTorrent platform.
But since early 2019, Fry Labs has been working on a pan-viral assay, based on the core technology developed for its 16S bacterial test, though Ellis declined to disclose how the firm targets viral genomes. In February, Fry Labs had a meeting where it decided to pivot to focus that assay on SARS-CoV-2. Fry Labs has also begun collaborating with researchers at Arizona State University "on tools to enable more efficient, accessible testing for the COVID-19 virus," the firm said in an email. In addition, Los Alamos National Lab is "performing an external validation of our testing protocol and process."
Concurrently, Fry Labs decided to set up BioID Genomics in late 2019 to commercialize its 16S bacterial sequencing tests for the Illumina MiSeq platform. Fry Labs officials did not disclose the exact relationship between the two firms, although they said the companies share management.
Fry Labs decided to use the same genomic targets as the CDC PCR assay for its COVID-19 test because of "regulatory compatibility," Ellis said. "However, we recognize that as the outbreak proceeds, there could be the need to add additional targets," which could be easily added, and the software could be educated to recognize those targets. The initial sample types will include saliva, nasal swabs, and sputum.
The test could be deployed in much the same way qPCR has been used for COVID testing, Ellis suggested. "The benefit of [our] technology is, you would unlock labs with many MiSeqs to perform samples daily," he said. According to Illumina, there are approximately 7,400 MiSeq instruments installed for both research and diagnostic purposes.
Fry Labs officials said they envisioned their test could be used as large corporations institute testing policies for employees returning to work.
The company is now working with consultants to formulate its EUA package. "We're trying to submit as soon as possible," Fry Labs CEO Judith Joseph said. With sufficient funding, she hopes to have the kit available for purchase by the end of the summer.
Several other firms have submitted EUA applications for NGS-based SARS-CoV-2 tests, including Fulgent Genetics and Clear Labs; however, FDA has not yet granted any for such tests.