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DNAe Developing POC Sequencing Platform for Coronavirus, Sepsis

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NEW YORK ─ DNAe said Wednesday it has seen encouraging results from early validation of a semiconductor-sequencing technology it is developing to test for infectious diseases, cancers, and other medical conditions at the point of care.

The London-based next generation sequencing firm said a prototype assay running on its LiDia-SEQ platform has successfully detected SARS-CoV-2 sequences in synthesized samples. Though the company will need to next validate the platform's ability to sequence patient samples, the system demonstrated the capability to amplify and sequence nucleic acid fragments associated with SARS-CoV-2 as part of a fully automated process, the firm said.

The demonstration highlights the potential for future use of a self-contained portable instrument for near-patient testing that provides an alternative to current molecular diagnostic technologies and broadens access to testing, Sam Reed, the firm's president, said in an interview.

While many companies are focusing on improving sequencing as a separate step along the path from sample to result, DNAe is integrating process steps with each other and using its semiconductor chip-and-cartridge format to automate them, he said.

Its integrated sequencing platform "encompasses a number of proprietary solutions to enable running them on a cartridge, including the sample extraction method, on-cartridge library preparation, and on-chip clonal amplification, some of which are still in the patent application process," Reed said.

The company is applying different sequencing strategies for different assays and their applications, he noted.

For a bloodstream infection assay under development, for example, it employs amplicon sequencing as part of a combined approach. Some of its primer sets target loci that are conserved, making the tool pan-bacterial and pan-fungal, while other primer sets target organism-specific or antibiotic resistance-specific loci "to make further clinical discriminations that would not be possible by looking purely at conserved regions," Reed said. For other applications, DNAe uses a shotgun sequencing or whole-genome sequencing-based approach.

The point-of-care sequencing platform uses a silicon transistor to detect nucleotides as an electrical signal, the firm said. A single sequencing unit incorporates sample preparation, on-cartridge sequencing, low power electronics, and pH-based methods for simultaneous amplification and detection of nucleic acids. Sequencing occurs on a standard semiconductor chip manufactured using complementary metal oxide semiconductor fabrication, a standard semiconductor processing technique.

Nucleotides incorporated during the step-by-step construction of nucleic acids release hydrogen ions that can be detected as electrical signals, indicating a positive test result. The approach eliminates the need for fluorescent dyes or labels and precision optics in the test system ─ components that make DNA analysis equipment bulky and more expensive, DNAe said.

Preliminary validation of its platform in detecting SARS-CoV-2 represents a business milestone for DNAe which has been developing a point-of-care sequencing technology to compete with current molecular diagnostic technologies for several years.

Overall, the company is seeking to deploy sequencing technology in settings where it has not previously been possible because existing approaches take too much time or are too expensive, Reed said.

Its test to detect bloodstream infections, such as sepsis, operates directly from a blood draw eliminating a time-consuming blood culture and speeding time to result. While the firm's current priorities are its SARS-CoV-2 and bloodstream infection assays, it is also developing assays to detect cancers, viruses associated with influenza, and infections associated with other infectious diseases, Reed said.

Internal validation of the point-of-care system for SARS-CoV-2 comes at a time when health systems and clinicians are under pressure to respond to the COVID-19 pandemic and broaden access to care, Christofer Toumazou, DNAe’s executive chairman and founder, said in an interview.

Its SARS-CoV-2 test uses nasopharyngeal swabs. The device may enable clinicians to detect and isolate infected patients, clear patients from isolation, and decide whether workers, including those treating patients, can return to the job, according to DNAe. The platform could be deployed for rapid screening and triaging of patients in temporary hospitals and in airports when air travel resumes, said Toumazou, a professor at Imperial College London.

Further, DNAe believes its platform could enable rapid genomic sequencing of emerging pathogens, which is important for epidemiological tracking of disease outbreaks. By allowing rapid sequencing of infectious disease pathogens, the platform may provide a basis for quickly developing diagnostic tests based on the genomic sequences of future viruses and strain variations, Reed said.

Bloodstream infections

DNAe recently received Breakthrough Device Designation from the US Food and Drug Administration, enabling it to engage closely with the agency along a path toward regulatory clearance for a direct-from-blood assay it is developing on its platform for bloodstream infections, including sepsis.

For the firm's bloodstream infection assay, one of the primary advantages is the speed at which results are delivered, according to Caroline Popper, cofounder and president of diagnostics consulting firm Popper and Company. The DNAe platform has the potential to detect a broad spectrum of pathogens and resistance genes while also eliminating the time-consuming step associated with obtaining a blood culture, she said.

"It aims to bring sequencing technology close to patients, where it is needed, and answers the important question of whether there is a pathogen associated with disease in the blood and what the pathogen is," said Popper, who is not affiliated with DNAe but has previously done consulting work for the firm and is familiar with its technology.

According to DNAe, its prototype sepsis assay can identify more than 1,000 bacteria markers, 150 fungi or yeast markers, and 35 antimicrobial resistance markers.

The platform's ability to detect a broad range of pathogens directly from blood aligns well with clinical needs associated with infectious diseases and, if commercialized, would give it an advantage over the most advanced molecular diagnostic tests, Popper added.

For infectious disease diagnostics, DNAe's near-term target, a variety of approaches already exist to identify disease pathogens, including molecular methods that employ PCR amplification of pathogens associated with disease.

However, culture-based tests are required before the molecular testing can be performed, impeding clinical decision-making when speed is particularly important, Popper noted.

One exception is a rapid direct-from-blood panels developed by T2 Biosystems. The company's FDA-cleared T2Bacteria Panel for the detection of sepsis-causing pathogens identifies five species of bacteria: Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus.

Its FDA-cleared T2Candida panel detects Candida albicans, Candida tropicalis, Candida parapsilosis, Candida glabrata, and Candida krusei. According to T2 Biosystems, the system can provide results in around four hours while running on its T2 Dx magnetic resonance instrument. The firm said recently that it has licensed a SARS-CoV-2 test to be adapted to its rapid diagnostics platform.

To detect a broad array of pathogens, molecular diagnostic tests generally require use of multiple assays with each targeting a unique organism or set of organisms, Reed said.

By contrast, the DNAe approach has potential to allow a single set of hardware to diagnose a range of causes, whether they are seasonal, pandemic, or rare, he added. "Sequencing of the pathogen also reduces the risk that the performance of the system declines over time due to genetic drift and shift as the pathogens evolve ─ which is a risk associated with RT-PCR or antigen-based tests," Reed said.

Using sequencing, DNAe’s technology has potential to identify pathogens more specifically than is possible using traditional molecular diagnostic testing platforms, Reed said. Further, its sequencing tool can provide detailed strain information that, combined with "highly sensitive sample and library preparation, has the potential to afford a very sensitive test," he said.

DNAe is not providing specific timelines for an anticipated release of its products, but overall it expects to have "deployable systems" ready next year that will enable it to then seek regulatory approvals, Reed said.

In the beginning

As far back as 2015, the firm had announced it was starting development of a point-of-care diagnostic platform that can amplify genotypes by real-time PCR and do targeted semiconductor sequencing all on one chip.

DNAe initially focused on R&D and licensing its technology to others. Thermo Fisher Scientific has a limited, non-exclusive license to some of the firm's intellectual property, and DNAe has been receiving royalties based on the agreement since 2010. Thermo Fisher is using the technology in its Ion Torrent line of sequencers, including the Ion Torrent Genexus Integrated Sequencer, Reed said.

"Ion Torrent made NGS more accessible than it was in the past, first to research groups and then for applications in the higher-end of the diagnostics space," Reed said.

That said, the Ion Torrent sequencers target laboratories with skilled labor as opposed to a point-of-care applications, he noted.

There are no recent publications about DNAe's technology, he said, because the firm has spent the past 18 months focusing on perfecting technical prototypes and having them reviewed by its major funding partners, which include Genting Berhad, a holding company of the Genting Group, an Asian conglomerate, and the US Department of Health and Human Services' Biomedical Advanced Research and Development Authority (BARDA).

In 2018, BARDA approved the second phase of a contract for the development of DNAe's platform for rapid diagnosis of antimicrobial resistant infections and influenza.

The award of $10.98 million, in support of the development of a test prototype, came after the company successfully completed the first phase of a contract that BARDA initiated in 2016. The overall contract is valued at up to $51.9 million.

Developing a sequencer that runs hands-free direct from a whole-blood sample to providing a result in a matter of hours has required reinventing several test processes, Reed said. For many of the steps that are now integrated, "the approach is necessarily novel," he said. "As a result, development of the technology has required a substantial level of R&D, but we were keen to allow the time and dedication needed to get this right."

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