Advances in Gene Sequencing Technology Enable Scientists to Respond to the Novel Coronavirus Outbreak in Record Time with Medical Lab Tests, Therapies
Scientist described the speed at which SARS-CoV-2’s full sequence of genetic material was made public as ‘unprecedented’ and medical labs are rushing to validate tests for this new disease
In the United States, headlines scream about the lack of testing for the novel
Coronavirus disease 2019 (COVID-19). News reporters ask daily why it is taking so long for the US healthcare system to begin testing large numbers of patients for SARS-CoV-2, the virus that causes COVID-19. Yet,
pathologists and
clinical laboratory scientists know that new technologies for
gene sequencing and diagnostic testing are helping public health laboratories bring up tests for a previously unknown new disease faster than at any time in the past.
At the center of the effort to develop accurate new assays to detect SARS-CoV-2 and help diagnose cases of the COVID-19 disease are
medical laboratory scientists working in
public health laboratories, in academic medical centers, and in research labs across the United States. Their collective efforts are producing results on a faster timeline than in any previous discovery of a new infectious disease.
For example, during the
severe acute respiratory syndrome (SARS) outbreak in 2003, five months passed between the first recognized case of the disease in China and when a team of Canadian scientists cracked the genetic code of the virus, which was needed to definitively diagnose SARS patients,
ABC News reported.
In contrast, Chinese scientists sequenced this year’s coronavirus (originally named 2019-nCoV) and made it available on Jan. 10, 2020, just weeks after public health officials in Wuhan, China, reported the first case of pneumonia from the unknown virus to the World Health Organization (WHO),
STAT reported.
Increases in sequencing speed enabled biotechnology companies to quickly create synthetic copies of the virus needed for research. Roughly two weeks later, scientists completed sequencing nearly two dozen more samples from different patients diagnosed with COVID-19.
Click here to see image
Molecular biologist Kristian Andersen, PhD (above right, with graduate students who helped sequence the Zika virus), an Associate Professor in the Department of Immunology and Microbiology at Scripps Research in California and Director of Infectious Disease Genomics at Scripps’ Translational Research Institute, worked on the team that sequenced the Ebola genome during the 2014 outbreak. He told STAT that the pace of sequencing of the SARS-CoV-2 coronavirus is “unprecedented.” (Photo copyright:Scripps Research.)
Lower Sequencing Costs Speed COVID-19 Diagnostics Research
Additionally, a significant decline in the cost of
genetic synthesis is playing an equally important role in helping scientists slow the spread of COVID-19. In its coverage of the SARS-CoV-2 outbreak,
The Verge noted that two decades ago “it cost $10 to create a synthetic copy of one single nucleotide, the building block of genetic material. Now, it’s under 10 cents.” Since the coronavirus gene is about 30,000
nucleotides long, that price reduction is significant.
Faster sequencing and cheaper access to synthetic copies is contributing to the development of diagnostic tests for COVID-19, an important step in slowing the disease.
On Feb. 4, 2020, the US Food and Drug Administration (FDA) issued its
first emergency use authorization (EUA) for a diagnostic test for the coronavirus called
2019-nCoV Real-Time RT-PCR Diagnostic Panel. The test was developed by the US Centers for Disease Control and Prevention (CDC).
“This continues to be an evolving situation and the ability to distribute this diagnostic test to qualified medical laboratories is a critical step forward in protecting the public health,” FDA Commissioner
Stephen M. Hahn, MD, said in an
FDA statement.
However, the
Washington Post soon reported that the government-created coronavirus test kits contained a “faulty component,” which as of February 25 had limited testing in the US to only 426 people, not including passengers who returned to the US on evacuation flights. The
Post noted that the nation’s public health laboratories took “the unusual step of appealing to the FDA for permission to develop and use their own [laboratory-developed] tests” for the coronavirus.
“This is an extraordinary request, but this is an extraordinary time,”
Scott Becker,
Chief Executive of the
Association of Public Health Laboratories (APHL), told the
Post.
FREE SPECIAL EDITION WHITE PAPER | Anatomic Pathology at the Tipping Point?
The Economic Case for Adopting Digital Technology and AI Applications Now
Download Your Free White Paper Now
Parallel efforts to develop and validate tests for COVID-19 are happening at the clinical laboratories of academic medical centers and in a number of commercial laboratory companies. As these labs show their tests meet FDA criteria, they become available for use by physicians and other healthcare providers.
Dark Daily’s sister publication,
The Dark Report just published an intelligence briefing about the urgent effort at the clinical laboratory of
Northwell Health to develop both a manual COVID-19 assay and a test that can be run on the automated analyzers already in use in the labs at Northwell Health’s 23 hospitals. (See
TDR, “
Northwell Lab Team Validates COVID-19 Test on Fast Timeline,” March 9, 2020.)
Following the FDA’s March 13 EUA for the Thermo Fisher test, Hahn said, “We have been engaging with test developers and encouraging them to come to the FDA and work with us. Since the beginning of this outbreak, more than 80 test developers have sought our assistance with development and validation of tests they plan to bring through the Emergency Use Authorization process. Additionally,” he continued, “more than 30 laboratories have notified us they are testing or intend to begin testing soon under our new policy for laboratory-developed tests for this emergency. The number of products in the pipeline reflects the significant role diagnostics play in this outbreak and the large number of organizations we are working with to bring tests to market.”
So far, the FDA has issued a total of seven EUAs:
Pharma Company Uses Sequencing Data to Develop Vaccine in Record Time
Even as clinical laboratories work to develop and validate diagnostic tests for COVID-19, drug manufacturers are moving rapidly to develop a COVID-19 vaccine. In February, Massachusetts-based biotechnology company
Moderna Therapeutics (NASDAQ:MRNA) announced it had shipped the first vials of its potential coronavirus vaccine (mRNA-1273) to the
National Institute of Allergy and Infectious Disease (NIAID) for use in a Phase One clinical trial.
“The collaboration across Moderna, with NIAID, and with CEPI [
Coalition for Epidemic Preparedness Innovations] has allowed us to deliver a clinical batch in 42 days from sequence identification,”
Juan Andres, Chief Technical Operations and Quality Officer at Moderna, stated in a
news release.
The
Wall Street Journal (
WSJ) reported that NIAID expects to start a clinical trial of about 20 to 25 healthy volunteers by the end of April, with results available as early as July or August.
“Going into a Phase One trial within three months of getting the sequence is unquestionably the world indoor record,” NIAID Director
Anthony Fauci, MD, told the
WSJ. “Nothing has ever gone that fast.”
DARK DAILY SPECIAL EDITION WHITE PAPER
Critical Factors for Launching a Clinical Decision Support System
in the Hospital Laboratory • Download Your Free Whitepaper
There are no guarantees that Moderna’s coronavirus vaccine will work. Furthermore, it will require further studies and regulatory clearances that could delay widespread distribution until next year.
Nonetheless, Fauci told the
WSJ, “The only way you can completely suppress an emerging infectious disease is with a vaccine. If you want to really get it quickly, you’re using technologies that are not as time-honored as the standard, what I call antiquated, way of doing it.”
In many ways, the news media has overlooked all the important differences in how fast useful diagnostic and therapeutic solutions for COVID-19 are moving from research settings into clinical use, when compared to early episodes of the emergence of a new infectious disease, such as SARS in 2003.
The story the American public has yet to learn is how new genetic sequencing technologies, improved diagnostic methods, and enhanced informatics capabilities are being used by researchers, pathologists, and clinical laboratory professionals to understand this new disease and give healthcare professionals the tools they need to diagnose, treat, and monitor patients with COVID-19.
—Andrea Downing Peck
