Fusion Genomics: Using Next-Generation Sequencing for Early Virus Detection
In late December, the first high-quality genome map of SARS-CoV-2 became available, and it was this availability that jumpstarted global efforts to effectively diagnose and treat the virus. Now imagine if you could obtain this genome map for any infectious disease for every patient without waiting weeks or months and costing no more than current molecular testing. This will revolutionize infectious diseases diagnostics and treatment. Once this genome-based rapid diagnosis and treatment ability is achieved, we can effectively identify, monitor, and stop future pandemics like COVID-19. This is the mission of Fusion Genomics: to bring the power of DNA sequencing to front line diagnostics of infectious diseases – quickly, reliably, and affordably.
Fusion’s ONETest Dx platform is being tested by leading health authorities around the world for diagnostic testing of infectious diseases, including a collaboration with CQDM  and pharmaceutical giant Merck, to study emergency room patients with influenza-like illnesses at Sunnybrook hospital in Toronto, Ontario. Based on their ONETest platform, Fusion has now developed an assay for all coronaviruses – whether human or zoonotic (from animals) – that can uniquely help government and health officials better understand and plan for a second wave of the virus.
We talk with Mohammad Qadir, President & Chief Scientific Officer at Fusion Genomics, on how he aims to accelerate the availability of their COVID-19 efforts to both contain the current virus and help prevent a future, similar outbreak.
VentureLabs (VL): How does Fusion Genomics’ ONETest platform detect viruses like COVID-19, SARS, or H1N1 influenza before they become widespread outbreaks?
Mohammad Qadir: Our technology, besides addressing hospitalized patients with undiagnosed infections, can also strengthen pre-emergence surveillance. It can help to alert for viruses like COVID-19 in the first place or, at the very least, allow for timely response to mitigate risk for another global crisis.
As we know, the causative virus of the current COVID-19 pandemic came from animals. The viruses that caused the two previous global pandemics – 2003’s SARS outbreak and 2009’s H1N1 swine flu – also came from animals. Current surveillance systems have failed to detect the outbreaks early on at the human-animal interface, leading to delayed responses. This is in part due to a lack of appropriate technologies that can detect broad ranges of human and zoonotic pathogens.
For example, if the CoV-SARS-2 virus mutates again or if there are additional transmissions of the virus to and from any animal sources, current surveillance systems – including the surveillance efforts for genome sequencing CoV-SARS-2 virus using the ARCTIC network’s primer set – will start to fail again, lose sensitivity, and need to be modified. This could take the world back to square one.
Better technologies are urgently needed to prevent not only the possible re-emergence of COVID-19, but also future pandemics.
Over the past four years, Fusion Genomics has developed one of the world’s most advanced infectious diseases diagnostic platforms using next-generation sequencing. ONETest has been used to answer some of the most challenging questions in infectious disease diagnostics and surveillance.
VL: What are the key elements of the ONETest platform?
Mohammad: First is Fusion’s patent-pending pathogen capture technology. It captures the genomes of viruses, bacteria, and other pathogens based on their evolutionary lineages. This allows a single test to capture a wide range of human and zoonotic pathogens and not be constrained by mutations or cross-species transfer. This is followed by our sample-to-sequencer chemistry and our fully-automated cloud-based bioinformatics.
VL: What project is Fusion Genomics working on right now in response to COVID-19?
Mohammad: We have completed the development of a COVID-19 specific surveillance test for all human and major zoonotic corona viruses, including SARs-CoV-2. The test will be undergoing testing with some of our partners in the coming weeks. Public health authorities (if they desire) will be able to deploy it in 8 to 12 weeks.
VL: What are Fusion’s plans to make the use of sequencing-based diagnostics a reality for every patient?
Mohammad: The goal is to enable a diagnosis based on sequencing results within a timeline that aligns well with hospital workflows. To that effect, we are working on OneTest Rapid, the clinical assay that uses an enhanced version of the quantum probes and optimized UniPrep; this can prepare a sample for sequencing in less than four hours.
Learn more about the pioneering work of Fusion Genomics and their ONETest platform at www.fusiongenomics.com
 CQDM is a biopharmaceutical research consortium to fund the development of innovative tools and technologies that will accelerate the discovery and development of safer and more effective drugs.