TGen Looks Beyond COVID-19 as it Advances Pathogen Sequencing
Amidst the darkness of the pandemic, a shining light from the COVID-19 response is the proliferation of better, faster, more accurate — and cost effective — tools for genomic sequencing, improvements needed for a 21st Century public-health and infectious-disease monitoring system that could help prevent or at least lessen the impact of future pandemics. A recent methods study by the Translational Genomics Research Institute (TGen), an affiliate of City of Hope, concludes that the advent of rapid and inexpensive next-generation genomic sequencing technologies have significantly advanced the field of ‘genomic epidemiology,’ which is the study and genetic analysis of the distribution, patterns and causes of disease. Genomic sequencing, the molecular analysis of RNA/DNA, has proven to be an invaluable international resource for tracking COVID-19 variants and outbreaks worldwide.
Since the start of the COVID-19 pandemic in early 2020, TGen has been funded by Arizona foundations and the Arizona Department of Health Services (ADHS), to analyze COVID-19 positive case samples in Arizona by sequencing, or spelling out, the nearly 30,000-letter genetic code of the SARS-CoV-2 virus, which causes the COVID-19 disease.
Using genomic sequencing to track the COVID-19 pandemic in Arizona, TGen launched the Arizona COVID-19 Sequencing Dashboard, which now includes more than 26,000 sequenced genomes of Arizona COVID-19 positive samples, one of the nation’s most robust such efforts. The dashboard lists all the mutations and variants of concern that have circulated in Arizona.
One of the technologies that has advanced TGen’s sequencing of the COVID-19 virus is plexWell, a platform from Massachusetts-based seqWell Inc., which has allowed TGen to accelerate its sequencing by nearly 10-fold. Where TGen at the start of the pandemic could sequence 100’s of virus samples each week, it now can process 1,000’s of samples per week, according to David Engelthaler, Ph.D., director of TGen’s infectious-disease branch, and the study’s senior author.
These advances significantly increased TGen’s sequencing output, according to the TGen study: “This allowed for a high throughput, cost-effective means of processing large numbers of samples with minimal laboratory personnel and infrastructure.”
According to Dan Calvo, seqWell’s President and CEO, “seqWell’s unique and powerful plexWell technology enables scalable multiplexing, greatly simplifying the next-generation sequencing workflow, producing high quality results faster, with fewer steps required. We continue to work on enhancements and new protocols to meet the demands of TGen and other COVID sequencing centers. Our platform enables efficient sequencing of a whole host of pathogens.”
Working with seqWell to implement this technology, TGen has tracked mutations that have led to COVID-19 variants, which make the virus more contagious, or easier to spread, among the vulnerable populations that either have not developed immunity from being infected, or have not been immunized from the disease through readily available and free vaccines.
Recent grants from the U.S. Centers for Disease Control and Prevention (CDC) and the Taiwan Semiconductor Manufacturing Co. have also allowed TGen to further improve its genomic tracking system, which will be made publicly available so it can be shared globally with other research centers.
“We’re looking beyond COVID-19,” Dr. Engelthaler said. “We’re building a pathogen intelligence system that allows scientists to track all types of infectious diseases. These advances in sequencing provide actionable ‘intel’ in real-time, which means cases are identified within hours after an outbreak, not days or weeks.”
TGen’s Megan Folkerts, the study’s lead author, added: “Though the results reported here are specific to the SARS-CoV-2 outbreak, these methods could easily be modified and applied to other genomic epidemiological responses where rapid, high-throughput sequencing is needed.”
The methods study — Sequencing the pandemic: rapid and high-throughput processing and analysis of COVID-19 clinical samples for 21st century public health — was published by F1000Research.
Contributing to this study was the Arizona COVID-19 Genomics Union, a consortium of scientists from TGen and Arizona’s three public universities.
Funding was provided by the Arizona Department of Health Services and the NARBHA Institute.
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